Bacterial community composition and function in sewage treatment systems

Sulfur bacteria in wastewater stabilization ponds periodically affected by the 'red-water' phenomenon

Several wastewater stabilization ponds (WSP) in Tunisia suffer periodically from the ‘red-water’ phenomenon due to blooming of purple sulfur bacteria, indicating that sulfur cycle is one of the main element cycles in these ponds. In this study, we investigated the microbial diversity of the El Menzeh WSP and focused in particular on the different functional groups of sulfur bacteria. For this purpose, we used denaturing gradient gel electrophoresis of PCR-amplified fragments of the 16S rRNA gene and of different functional genes involved in microbial sulfur metabolism (dsrB, aprA, and pufM). Analyses of the 16S rRNA revealed a relatively high microbial diversity where Proteobacteria, Chlorobi, Bacteroidetes, and Cyanobacteria constitute the major bacterial groups. The dsrB and aprA gene analysis revealed the presence of deltaproteobacterial sulfate-reducing bacteria (i.e., Desulfobacter and Desulfobulbus), while the analysis of 16S rRNA, aprA, and pufM genes assigned the sulfur-oxidizing bacteria community to the photosynthetic representatives belonging to the Chlorobi (green sulfur bacteria) and the Proteobacteria (purple sulfur and non sulfur bacteria) phyla. These results point on the diversity of the metabolic processes within this wastewater plant and/or the availability of sulfate and diverse electron donors.

OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities

Microorganisms rarely live isolated in their natural environments but rather function in consolidated and socializing communities. Despite the growing availability of high-throughput sequencing and metagenomic data, we still know very little about the metabolic contributions of individual microbial players within an ecological niche and the extent and directionality of interactions among them. This calls for development of efficient modeling frameworks to shed light on less understood aspects of metabolism in microbial communities. Here, we introduce OptCom, a comprehensive flux balance analysis framework for microbial communities, which relies on a multi-level and multi-objective optimization formulation to properly describe trade-offs between individual vs. community level fitness criteria. In contrast to earlier approaches that rely on a single objective function, here, we consider species-level fitness criteria for the inner problems while relying on community-level objective maximization for the outer problem. OptCom is general enough to capture any type of interactions (positive, negative or combinations thereof) and is capable of accommodating any number of microbial species (or guilds) involved. We applied OptCom to quantify the syntrophic association in a well-characterized two-species microbial system, assess the level of sub-optimal growth in phototrophic microbial mats, and elucidate the extent and direction of inter-species metabolite and electron transfer in a model microbial community. We also used OptCom to examine addition of a new member to an existing community. Our study demonstrates the importance of trade-offs between species- and community-level fitness driving forces and lays the foundation for metabolic-driven analysis of various types of interactions in multi-species microbial systems using genome-scale metabolic models.

Bacterial community structure and enzyme activities in a membrane bioreactor (MBR) using pure oxygen as an aeration source

A pilot-scale membrane bioreactor was used to treat urban wastewater using pure oxygen instead of air as a source of aeration, to study its influence on bacterial diversity and levels of enzyme activities (acid and alkaline phosphatases, glucosidase, protease, and esterase) in the sludge. The experimental work was developed in two stages influenced by seasonal temperature. Operational parameters (temperature, pH, BOD5, COD, total and volatile suspended solids) were daily monitored, and enzyme activities measured twice a week. Redundancy analysis (RDA) was used to reveal relationships between the level of enzyme activities and the variation of operational parameters, demonstrating a significant effect of temperature and volatile suspended solids. Bacterial diversity was analyzed by temperature-gradient gel electrophoresis of PCR-amplified partial 16S rRNA genes. Significant differences in community structure were observed between both stages. Sequence analysis revealed that the prevalent Bacteria populations were evolutively close to Alphaproteobacteria (44%), Betaproteobacteria (25%) and Firmicutes (17%).

454 pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants

Activated sludge (AS) contains highly complex microbial communities. In this study, PCR-based 454 pyrosequencing was applied to investigate the bacterial communities of AS samples from 14 sewage treatment plants of Asia (mainland China, Hong Kong, and Singapore), and North America (Canada and the United States). A total of 259 K effective sequences of 16S rRNA gene V4 region were obtained from these AS samples. These sequences revealed huge amount of operational taxonomic units (OTUs) in AS, that is, 1183-3567 OTUs in a sludge sample, at 3% cutoff level and sequencing depth of 16,489 sequences. Clear geographical differences among the AS samples from Asia and North America were revealed by (1) cluster analyses based on abundances of OTUs or the genus/family/order assigned by Ribosomal Database Project (RDP) and (2) the principal coordinate analyses based on OTUs abundances, RDP taxa abundances and UniFrac of OTUs and their distances. In addition to certain unique bacterial populations in each AS sample, some genera were dominant, and core populations shared by multiple samples, including two commonly reported genera of Zoogloea and Dechloromonas, three genera not frequently reported (i.e., Prosthecobacter, Caldilinea and Tricoccus) and three genera not well described so far (i.e., Gp4 and Gp6 in Acidobacteria and Subdivision3 genera incertae sedis of Verrucomicrobia). Pyrosequencing analyses of multiple AS samples in this study also revealed the minority populations that are hard to be explored by traditional molecular methods and showed that a large proportion of sequences could not be assigned to taxonomic affiliations even at the phylum/class levels.

The population dynamics of nitrifiers in ammonium-rich systems

Non-optimal pH, dissolved oxygen concentration, the presence of toxic substances, or the influence of grazers are known to cause disturbances in nitrification. Because activated sludge is a mixture of different organisms, bacteria, and higher organisms, the stability of processes such as carbon removal, nitrification, denitrification, and dephosphatation depends on a range of interactions. These interactions occur both between and within trophic levels. Understanding of the ecology of microorganisms involved in bioprocesses is essential for effective control of startup and operation of a particular process. The aim of the study was to gain further insight into the dynamics of nitrifiers in activated sludge at various sludge ages while treating higher concentrations of ammonium. The results confirmed the importance of Nitrosococcus mobilis and Nitrobacter sp. as the dominant nitrifiers responsible for nitritation and nitratation, respectively, in the presence of unlimited ammonium. The size of the dominant bacteria colony was larger compared to the other species present and reached 25 microm. Problems with nitrification occurred in all high-ammonium loaded reactors. The dynamics of nitrifier population was monitored by oxygen uptake rate (OUR) using a test enabling the OUR measurement separately for ammonium-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). The results reveal the hypersensitivity of nitrifiers to the substrate and products of incomplete nitrification.

Bacterial community characteristics under long-term antibiotic selection pressures

To investigate bacterial community characteristics under long-term antibiotic selection pressures, water samples from the upstream and the downstream sections of two rivers individually receiving the treated penicillin G and oxytetracycline production wastewater, as well as the anaerobic and the aerobic effluent of the penicillin G production wastewater treatment plant, were taken and analyzed. Antibiotic resistance ratios of bacterial communities in water samples were estimated by culture-based analysis. The majority of bacterial colonies (approximately 55%-70%) in both downstream rivers and the aerobic effluent showed resistance to 80 μg/ml of antibiotics tested, while the resistance ratios were less than 10% and 5% respectively for both upstream rivers. Six 16S rRNA gene clone libraries were constructed with 355 sequences and 215 OTUs totally obtained representing 465 clones. The antibiotic stresses seemed not reduce the diversities of bacterial communities in antibiotic containing water samples compared to those in the two reference upstream rivers. Bacterial groups present in the two reference upstream rivers were common residents in freshwater ecosystems, with the dominant groups as the phyla Proteobacteria including Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria, as well as Actinobacteria and Bacteroidetes. The phyla Proteobacteria and Firmicutes were dominant in all antibiotic containing water samples, with the clones belonged to Deltaproteobacteria and Epsilonproteobacteria significantly abundant, as well as Gram-positive low GC bacteria in the classes Clostridia and Bacilli. It thus seemed that Deltaproteobacteria, Epsilonproteobacteria, Clostridia and Bacilli might be specifically associated with antibiotic containing environments.

Dissolved methane oxidation and competition for oxygen in down-flow hanging sponge reactor for post-treatment of anaerobic wastewater treatment

Post-treatment of anaerobic wastewater was undertaken to biologically oxidize dissolved methane, with the aim of preventing methane emission. The performance of dissolved methane oxidation and competition for oxygen among methane, ammonium, organic matter, and sulfide oxidizing bacteria were investigated using a lab-scale closed-type down-flow hanging sponge (DHS) reactor. Under the oxygen abundant condition of a hydraulic retention time of 2h and volumetric air supply rate of 12.95m(3)-airm(-3)day(-1), greater than 90% oxidation of dissolved methane, ammonium, sulfide, and organic matter was achieved. With reduction in the air supply rate, ammonium oxidation first ceased, after which methane oxidation deteriorated. Sulfide oxidation was disrupted in the final step, indicating that COD and sulfide oxidation occurred prior to methane oxidation. A microbial community analysis revealed that peculiar methanotrophic communities dominating the Methylocaldum species were formed in the DHS reactor operation.

Active autotrophic ammonia-oxidizing bacteria in biofilm enrichments from simulated creek ecosystems at two ammonium concentrations respond to temperature manipulation

The first step of nitrification, the oxidation of ammonia to nitrite, is important for reducing eutrophication in freshwater environments when coupled with anammox (anaerobic ammonium oxidation) or denitrification. We analyzed active formerly biofilm-associated aerobic ammonia-oxidizing communities originating from Ammerbach (AS) and Leutra South (LS) stream water (683 ± 550 [mean ± standard deviation] and 16 ± 7 μM NH(4)(+), respectively) that were developed in a flow-channel experiment and incubated under three temperature regimens. By stable-isotope probing using (13)CO(2), we found that members of the Bacteria and not Archaea were the functionally dominant autotrophic ammonia oxidizers at all temperatures under relatively high ammonium loads. The copy numbers of bacterial amoA genes in (13)C-labeled DNA were lower at 30°C than at 13°C in both stream enrichment cultures. However, the community composition of the ammonia-oxidizing bacteria (AOB) in the (13)C-labeled DNA responded differently to temperature manipulation at two ammonium concentrations. In LS enrichments incubated at the in situ temperature (13°C), Nitrosomonas oligotropha-like sequences were retrieved with sequences from Nitrosospira AmoA cluster 4, while the proportion of Nitrosospira sequences increased at higher temperatures. In AS enrichments incubated at 13°C and 20°C, AmoA cluster 4 sequences were dominant; Nitrosomonas nitrosa-like sequences dominated at 30°C. Biofilm-associated AOB communities were affected differentially by temperature at two relatively high ammonium concentrations, implicating them in a potential role in governing contaminated freshwater AOB distributions.

Phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale wastewater treatment plants

The activated sludge process is an essential process for treating domestic and industrial wastewaters in most wastewater treatment plants (WWTPs). This process consists of a mixture of general and special microorganisms in a form of a complex enrichment population. Thus, the exploration of activated sludge microbial communities is crucial to improve the performance of activated sludge process. In this study, we investigated the phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale WWTPs. Four 16S rRNA gene clone libraries were constructed from activated sludge samples. In all samples, Proteobacteria was the most abundant phylogenetic group, followed by Bacteroidetes and Firmicutes. The dominance of Proteobacteria was further demonstrated by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP). Some specific genera, e.g., Nitrosomonas, Thauera, and Dechloromonas, which significantly correlate with the functions and performance of wastewater treatment, were abundant in all samples. A large number of unclassified sequences were found in the library, suggesting that a wide variety of novel species may inhabit complex activated sludge communities. The structures of the bacterial community did not differ significantly among samples. All samples utilized the vast majority of 31 carbon sources of an EcoPlate (Biolog), suggesting that activated sludge microbial communities possess high metabolic potential and equivalent functions required for wastewater treatment.

Stoichiometric and molecular evidence for the enrichment of anaerobic ammonium oxidizing bacteria from wastewater treatment plant sludge samples

Anammox enrichments were readily developed from seven municipal wastewater treatment plants (WWTPs) sludge, but not with methanogenic granular sludge from two agro-industrial WWTPs. Only 50d was required for the first evidence of anammox activity from a return activated sludge obtained from a WWTP operated for nutrient removal. The molar ratios of nitrite and ammonium consumption of approximately 1.32 as well as nitrate and dinitrogen gas product ratios of approximately 0.095 provided evidence of the anammox reaction. The presence of anammox was confirmed by polymerase chain reaction (PCR) using primer sets (PLA46F and AMX820R) specific for anammox bacteria. The 16S rRNA gene fragment of anammox bacteria was detected in seven enrichment cultures (ECs) with demonstrated anammox activity but not in the original inocula from which the ECs were derived and also not in the two methanogenic sludge samples, which indicates the PCR predicted the anammox activity. Two genera, Brocadia and Kuenenia, were successfully identified as the Planctomycetes occurring in the clone libraries of successful anammox enrichments. Brocadia dominated in cultures that were respiked extensively; whereas Kuenenia predominated in cultures that were less aggressively respiked. These findings indicate that respiking management may play an important role on selecting the genus of anammox bacteria. The batch enrichment results clearly illustrate that anammox can be readily enriched from municipal sludge from a wide variety of process operations at WWTPs.

Effect of different salt adaptation strategies on the microbial diversity, activity, and settling of nitrifying sludge in sequencing batch reactors

The effect of salinity on the activity of nitrifying bacteria, floc characteristics, and microbial community structure accessed by fluorescent in situ hybridization and polymerase chain reaction–denaturing gradient gel electrophoresis techniques was investigated. Two sequencing batch reactors (SRB₁ and SBR₂) treating synthetic wastewater were subjected to increasing salt concentrations. In SBR₁, four salt concentrations (5, 10, 15, and 20 g NaCl/L) were tested, while in SBR₂, only two salt concentrations (10 and 20 g NaCl/L) were applied in a more shock-wise manner. The two different salt adaptation strategies caused different changes in microbial community structure, but did not change the nitrification performance, suggesting that regardless of the different nitrifying bacterial community present in the reactor, the nitrification process can be maintained stable within the salt range tested. Specific ammonium oxidation rates were more affected when salt increase was performed more rapidly and dropped 50% and 60% at 20 g NaCl/L for SBR₁ and SBR₂, respectively. A gradual increase in NaCl concentration had a positive effect on the settling properties (i.e., reduction of sludge volume index), although it caused a higher amount of suspended solids in the effluent. Higher organisms (e.g., protozoa, nematodes, and rotifers) as well as filamentous bacteria could not withstand the high salt concentrations.

Extent and variation of phage-borne bacterial 16S rRNA gene sequences in wastewater environments

Phage metagenomes isolated from wastewater over a 12-month period were analyzed. The results suggested that various strains of Proteobacteria, Bacteroidetes, and other phyla are likely to participate in transduction. The patterns of 16S rRNA sequences found in phage metagenomes did not follow changes in the total bacterial community.

Balance of neutral and deterministic components in the dynamics of activated sludge floc assembly

Understanding the processes that generate patterns of community structure is a central focus of ecological research. With that aim, we manipulated the structure of bacterial activated sludge to test the influence of the species richness and composition of bacterial communities on the dynamics of activated sludge floc assembly in lab-scale bioreactors. Bacterial community structure was analyzed using denaturing gradient gel electrophoresis of RT-PCR amplified 16S rRNA. Fingerprinting of four parallel reactors, started with the same source communities added in different proportions, converged to patterns that were more similar than expected by chance, suggesting a deterministic selection in floc development. Evidence for neutral dynamics was suggested by the dependence of the rate of replacement of species (bacterial taxa-time relationships) on the number of available species in the source community. Further indication of stochastic dynamics was obtained by the application of the Sloan neutral model for prokaryotes. The fitting of the observed data to the model predictions revealed that the importance of the stochastic component increased with the size of the reservoir of species richness from which the community is drawn. Taken together, the results illustrate how both neutral and deterministic dynamics operate simultaneously in the assembly of the bacterial floc and show that the balance of the two depends on the richness of the source community.

Biotransformation of a highly chlorinated PCB mixture in an activated sludge collected from a Membrane Biological Reactor (MBR) subjected to anaerobic digestion

The role of anaerobic digestion (AD) on the decontamination and biomethanization of a PCB-spiked sludge obtained from a Membrane Biological Reactor (MBR) pilot plant was investigated throughout a 10-month batch experiment. The study was carried out under mesophilic (35°C) and thermophilic (55°C) conditions and was monitored by means of an integrated chemical, microbiological and molecular biology strategy. Remarkable PCB depletions (higher than 50% of the overall spiked PCBs) and dechlorinations were achieved under methanogenic conditions. The process was not affected by yeast extract addition. Both acetoclastic and hydrogenotrophic methanogens, together with some fermentative eubacteria, were found to persist in all PCB biodegrading microcosms. This finding, together with those obtained from parallel microcosms where specific populations were selectively inhibited, suggested that native methanogens played a key role in the biodegradation and dechlorination of the spiked PCBs. Taken together, the results of this study indicate that AD is a feasible option for the decontamination and the efficient disposal (with the production of a CH(4)-rich biogas) of contaminated MBR sludge, which can be then employed as a fertilizer for agricultural purposes.

Seasonal variations of nitrifying community in trickling filter-solids contact (TF/SC) activated sludge systems

Two full-scale trickling filter/solids contact (TF/SC) basin plants, each successfully performing nitrification, were sampled throughout various seasons over a period of one year. Concentrations of ammonia, nitrate and nitrite were measured at various sampling locations along the treatment train. DNA was also extracted from mixed liquor in the solids contact basins. These DNA samples were subjected to terminal restriction fragment length polymorphism (TRFLP) in order to profile the ammonia oxidizing bacteria and nitrite oxidizing bacteria communities. In both plants, there was a prevalence of Nitrosomonas europaea among the ammonia oxidizing bacteria (AOBs). However, during the summer months, there was increased diversity of Nitrosomonas species. Likewise, Nitrospira spp. was the dominant nitrite oxidizing bacteria (NOBs) in both plants regardless of season. Yet there was an increased presence of Nitrobacter among the NOBs in the summer months. These results add an important understanding of the ecology and dynamics in nitrifying population in full-scale TF/SC wastewater treatment plants.

Identification of sulfur-cycle prokaryotes in a low-sulfate lake (Lake Pavin) using aprA and 16S rRNA gene markers

Geochemical researches at Lake Pavin, a low-sulfate-containing freshwater lake, suggest that the dominant biogeochemical processes are iron and sulfate reduction, and methanogenesis. Although the sulfur cycle is one of the main active element cycles in this lake, little is known about the sulfate-reducer and sulfur-oxidizing bacteria. The aim of this study was to assess the vertical distribution of these microbes and their diversities and to test the hypothesis suggesting that only few SRP populations are involved in dissimilatory sulfate reduction and that Epsilonproteobacteria are the likely key players in the oxidative phase of sulfur cycle by using a PCR aprA gene-based approach in comparison with a 16S rRNA gene-based analysis. The results support this hypothesis. Finally, this preliminary work points strongly the likelihood of novel metabolic processes upon the availability of sulfate and other electron acceptors.

Biodiversity and population dynamics of microorganisms in a full-scale membrane bioreactor for municipal wastewater treatment

The total, ammonia-oxidizing, and denitrifying Bacteria in a full-scale membrane bioreactor (MBR) were evaluated monthly for over one year. Microbial communities were analyzed by denaturing gradient gel electrophoresis (DGGE) and clone library analysis of the 16S rRNA and ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes. The community fingerprints obtained were compared to those from a conventional activated sludge (CAS) process running in parallel treating the same domestic wastewater. Distinct DGGE profiles for all three molecular markers were observed between the two treatment systems, indicating the selection of specific bacterial populations by the contrasting environmental and operational conditions. Comparative 16S rRNA sequencing indicated a diverse bacterial community in the MBR, with phylotypes from the α- and β-Proteobacteria and Bacteroidetes dominating the gene library. The vast majority of sequences retrieved were not closely related to classified organisms or displayed relatively low levels of similarity with any known 16S rRNA gene sequences and thus represent organisms that constitute new taxa. Similarly, the majority of the recovered nosZ sequences were novel and only moderately related to known denitrifiers from the α- and β-Proteobacteria. In contrast, analysis of the amoA gene showed a remarkably simple ammonia-oxidizing community with the detected members almost exclusively affiliated with the Nitrosomonas oligotropha lineage. Major shifts in total bacteria and denitrifying community were detected and these were associated with change in the external carbon added for denitrification enhancement. In spite of this, the MBR was able to maintain a stable process performance during that period. These results significantly expand our knowledge of the biodiversity and population dynamics of microorganisms in MBRs for wastewater treatment.

Anode microbial communities produced by changing from microbial fuel cell to microbial electrolysis cell operation using two different wastewaters

Conditions in microbial fuel cells (MFCs) differ from those in microbial electrolysis cells (MECs) due to the intrusion of oxygen through the cathode and the release of H(2) gas into solution. Based on 16S rRNA gene clone libraries, anode communities in reactors fed acetic acid decreased in species richness and diversity, and increased in numbers of Geobacter sulfurreducens, when reactors were shifted from MFCs to MECs. With a complex source of organic matter (potato wastewater), the proportion of Geobacteraceae remained constant when MFCs were converted into MECs, but the percentage of clones belonging to G. sulfurreducens decreased and the percentage of G. metallireducens clones increased. A dairy manure wastewater-fed MFC produced little power, and had more diverse microbial communities, but did not generate current in an MEC. These results show changes in Geobacter species in response to the MEC environment and that higher species diversity is not correlated with current.

Monitoring of bacterial communities during low temperature thermal treatment of activated sludge combining DNA phylochip and respirometry techniques

Sludge reduction is one of the major challenges in biological wastewater treatment. One approach is to increase the sludge degradation yield together with the biodegradation kinetics. Among the various sludge pretreatment strategies proposed, thermal pretreatment at around 65 °C was described as promising. The enhancement in the biodegradation activity due to the selection of thermophilic hydrolytic bacteria was proposed, but further experiments are needed to demonstrate the specific role of these bacteria. In this study, concentrated activated sludge grown at 20 °C was subjected to thermal treatment at 65 °C for different periods. The originality of the work relied on a polyphasic approach based on the correlation between kinetics (chemical oxygen demand, COD; mixed liquor suspended solids, MLSS), bacterial activity (respirometry) and bacterial community structure (phylochip monitoring) in order to characterize the mechanisms involved in the thermal reduction of sludge. The bacterial activity in the aeration basin decreased to a very low level when recycling sludge was treated at 65 °C from 13 to 60 h, but then, started to increase after 60 h. In parallel to these fluctuations in activity, a drastic shift occurred in the bacterial community structure with the selection of thermophilic bacteria (mainly related to genera Paenibacillus and Bacillus), which are known for their specific hydrolases.

Identifying diazotrophs by incorporation of nitrogen from (15)N(2) into RNA

The diversity and abundance of active diazotrophs was investigated in a New Zealand pulp and paper wastewater by enrichment with (15)N(2). Purified (15)N-RNA was analysed by reverse transcription, molecular cloning and sequence analysis of 16S rRNA to reveal a diverse community of bacteria as indicated by a Shannon Weaver Index value of > 2.8. The major class represented in the enriched culture were the gamma-Proteobacteria at 85% with a secondary group of the phylum Firmicutes present at 8.2%, the remaining sequences were affiliated with the alpha- and beta-Proteobacterial classes (1.4% and 4.3%, respectively). Three dominant genera, Aeromonas, Pseudomonas and Bacillus, were identified by comparison with published sequences and phylogenetic analysis. To confirm that representatives of the taxonomic groups identified from the active enriched nitrogen-fixing community were capable of fixing nitrogen Aeromonas and Pseudomonas species were cultivated and shown to possess nifH genes. In wastewater, fluorescence in situ hybridisation probing revealed that the dominant nitrogen-fixing population identified in this study were present in the population, but at lower levels. The population is, therefore, reliant on a small sub-population of diazotrophs to supply the community's nitrogen needs above that already present in the wastewater.

Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments

Background

Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors.

Results

qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited.

Conclusions

The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.

Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.

Identification of ciliate grazers of autotrophic bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing

It is well understood that protozoa play a major role in controlling bacterial biomass and regulating nutrient cycling in the environment. Little is known, however, about the movement of carbon from specific reduced substrates, through functional groups of bacteria, to particular clades of protozoa. In this study we first identified the active protozoan phylotypes present in activated sludge, via the construction of an rRNA-derived eukaryote clone library. Most of the sequences identified belonged to ciliates of the subclass Peritrichia and amoebae, confirming the dominance of surface-associated protozoa in the activated sludge environment. We then demonstrated that (13)C-labeled protozoan RNA can be retrieved from activated sludge amended with (13)C-labeled protozoa or (13)C-labeled Escherichia coli cells by using an RNA stable isotope probing (RNA-SIP) approach. Finally, we used RNA-SIP to track carbon from bicarbonate and acetate into protozoa under ammonia-oxidizing and denitrifying conditions, respectively. RNA-SIP analysis revealed that the peritrich ciliate Epistylis galea dominated the acquisition of carbon from bacteria with access to CO(2) under ammonia-oxidizing conditions, while there was no evidence of specific grazing on acetate consumers under denitrifying conditions.

Microbial diversity and functional characterization of sediments from reservoirs of different trophic state

Sediment samples from four reservoirs of different trophic state were compared with regard to chemical gradients in the pore water, composition of microbial communities and extracellular enzyme activities. The trophic state was clearly reflected by steep vertical concentration gradients of ammonium and alkalinity in the pore water. A high concentration of these parameters indicated a high microbial in situ activity in the more eutrophic reservoirs. However, the total number of bacteria in sediments seemed hardly to be influenced by the trophic conditions in the water column. Differences in the microbial composition of the sediments became evident by comparative 16S rDNA analysis of extracted DNA and by fluorescence in situ hybridization. Although a high proportion of the cells detectable with the EUB probe could not be identified at the subdomain level, members of the beta-Proteobacteria constituted an important fraction in the sediments of the more eutrophic reservoirs, whereas gamma-subgroup Proteobacteria were most frequently detected in sediment samples from the dystrophic Muldenberg reservoir. The assessment of extracellular enzyme activities (esterases, phosphatases, glucosidases and aminopeptidases, respectively) in sediment samples of the four reservoirs revealed specific patterns of metabolic potentials in accordance with the trophic state and characteristics of the catchment.

Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging

An astonishing diversity of microorganisms thrives on our planet and their activities are fundamental for the functioning of all ecosystems including the human body. Consequently, detailed insights into the functions performed by microorganisms in their natural environment are required to understand human biology and the biology of the world around us and to lay the foundations for targeted manipulation of microbial communities. Isotope-labeling techniques combined with molecular detection tools are frequently used by microbial ecologists to directly link structure and function of microbial communities and to monitor metabolic properties of uncultured microbes at the single-cell level. However, only the recent combination of such techniques with Raman microspectroscopy or secondary ion mass spectrometry enables functional studies of microbes on a single-cell level by using stable isotopes as labels. This review provides an overview of these new techniques and their applications in microbial ecology, which allow us to investigate the ecophysiology of uncultured microbes to an extent that was unimaginable just a few years ago.

Effect of alkaline protease-producing Exiguobacterium sp. YS1 inoculation on the solubilization and bacterial community of waste activated sludge

A new approach to the solubilization of waste activated sludge (WAS) using an alkaline protease-producing bacterial isolate, Exiguobacterium sp. YS1, was investigated under controlled mild alkaline conditions at pH 10. Compared with the noninoculated experiment, the inoculated experiment in an anaerobic bioreactor increased soluble chemical oxygen demand concentration and alkaline protease activity by more than 40%, indicating a synergistic effect could be achieved when both bacterial inoculation and alkaline treatment were combined. Indeed, this combination led to 56.6% COD solubilization after 5days of reaction time. However, the inoculant was not effective in the aerobic bioreactor. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA fragments revealed that the inoculated Exiguobacterium sp. YS1 became the predominant population in the bacterial community during the anaerobic solubilization processes. These results suggest that bioaugmentation of the organism might be useful for enhancing the solubilization of WAS at mild alkaline pH.

Microbial community structure and dynamics in a pilot-scale submerged membrane bioreactor aerobically treating domestic wastewater under real operation conditions

A pilot scale submerged ultra-filtration membrane bioreactor (MBR) was used for the aerobic treatment of domestic wastewater over 9 months of year 2006 (28th March to 21st December). The MBR was installed at a municipal wastewater facility (EMASAGRA, Granada, Spain) and was fed with real wastewater. The experimental work was divided in 4 stages run under different sets of operation conditions. Operation parameters (total and volatile suspended solids, dissolved oxygen concentration) and environmental variables (temperature, pH, COD and BOD(5) of influent water) were daily monitored. In all the experiments conducted, the MBR generated an effluent of optimal quality complying with the requirements of the European Law (91/271/CEE 1991). A cultivation-independent approach (polymerase chain reaction-temperature gradient gel electrophoresis, PCR-TGGE) was used to analyze changes in the structure of the bacterial communities in the sludge. Cluster analysis of TGGE profiles demonstrated significant differences in community structure related to variations of the operation parameters and environmental factors. Canonical correspondence analysis (CCA) suggested that temperature, hydraulic retention time and concentration of volatile suspended solids were the factors mostly influencing community structure. 23 prominent TGGE bands were successfully reamplified and sequenced, allowing gaining insight into the identities of predominantly present bacterial populations in the sludge. Retrieved partial 16S-rRNA gene sequences were mostly related to the alpha-Proteobacteria, beta-Proteobacteria and gamma-Proteobacteria classes. The community established in the MBR in each of the four stages of operation significantly differed in species composition and the sludge generated displayed dissimilar rates of mineralization, but these differences did not influence the performance of the bioreactor (quality of the permeate). These data indicate that the flexibility of the bacterial community in the sludge and its ability to get adapted to environmental changes play an important role for the stable performance of MBRs.

Microbial enumeration of different functional groups and bacterial behavior in acid basic conditions of a biotoxic landfill leachate of Bahía Blanca, Argentina

Leachate is liquid waste from refuse biological decomposition or rainwater percolation in a landfill. This research focused on leachate produced by a landfill in Bahia Blanca, Buenos Aires, Argentina. The research studied the main microbial populations involved in wastewater treatment, analyzed the behavior of bacteria isolated from leachate at different pH values, and appraised leachate biotoxicity. The number of bacteria varied by type, ranging from 1 x 10(4) to 1 x 10(5) CUF/mL aerobic heterotrophic bacteria (AHB); 1 x 10(3) to 1 x 10(5) CUF/mL anaerobic heterotrophic bacteria (ANHB); 1 x 10(5) to 1 x 10(6) CUF/mL sulfite-reducing bacteria (SRB); 1 x 10(3) to 1 x 10(6) NMP/mL nitrate-reducing bacteria (NRB); and 1 x 10(2) to 1 x 10(4) NMP/mL ammonium-oxidizing bacteria (AOB). Several microbial strains developed at pH 5, 7, and 10. These pH values changed to 9 in the culture media after a 48-hour incubation. Leachate was used to water lettuce seeds (Lactuca sativa capitata). Its toxicity was proved by full inhibition of plant development.

Nitrifying community structures and nitrification performance of full-scale municipal and swine wastewater treatment plants

This study evaluated nitrification performance and microbial ecology of nitrifying sludge in two full-scale wastewater treatment plants (WWTPs) including a municipal WWTP treating 20mgNL(-1) of ammonium and a swine WWTP treating 220mgNL(-1) of ammonium. These two plants differed in both wastewater characteristics and operating parameters, such as influent COD, TKN, ammonium, hydraulic retention time, and solids retention time, even though both plants achieve >85% nitrification efficiency. By employing molecular techniques, including terminal restriction fragment length polymorphism, cloning-sequencing and phylogenetic analyses targeting the 16S ribosomal RNA and group specific ammonia-monooxygenase functional gene (amoA), microbial community structures of nitrifying sludge and their significance to nitrification performance were evaluated. The results reveal that for the municipal WWTP Nitrosomonas marina-like AOB (ammonia-oxidizing bacteria) and Nitrospira-like NOB (nitrite-oxidizing bacteria) were the ubiquitously dominant nitrifiers, while Nitrosomonas europaea-, Nitrosomonas oligotropha-, and Nitrosospira-like AOB and Nitrobacter- and Nitrospira-like NOB were the major nitrifying populations found in the swine WWTP. The observed dissimilar nitrifying populations prevailing in these two plants may be related to niche differentiation concerning ammonium concentrations, system operation, and salinity. Moreover, our results suggest that the swine nitrifying sludge, involving relatively diverse AOB and NOB populations that perform the same task but with distinct growth and survival characters, may allow communities to maintain nitrifying capabilities when conditions change such as sudden increases in ammonium concentrations as examined with nitrification kinetic batch tests.

A reformed SBR technology integrated with two-step feeding and low-intensity aeration for swine wastewater treatment

Wastewater from animal farms in China is threatening the quality and security of the local water environment. A traditional sequencing batch reactor (SBR) and a reformed SBR integrated with two-step feeding and low-intensity aeration at laboratory scale were investigated in this study for biological removal of nutrients and organic matter from swine wastewater. A low efficiency and poor stability were found under the traditional SBR, and the reduction of total nitrogen (TN), total phosphorus (TP) and biochemical oxygen demand (BOD5) reached 89.1, 86.0 and 93.9%, respectively. When the wastewater was treated with the reformed SBR under the running cycle of anaerobic/anoxic-anaerobic/anoxic process, the reductions in TN, TP, and BOD5 reached a maximum of 94.0, 99.3 and 99.9%, respectively. The curves of oxidation reduction potential (ORP) and nutrients over time during operation of the reformed SBR could reflect the activity of denitrifying phosphorus-accumulating organisms (DNPAOs).

Removal of ammonium via simultaneous nitrification-denitrification nitrite-shortcut in a single packed-bed batch reactor

A polyurethane packed-bed-biofilm sequential batch reactor was fed with synthetic substrate simulating the composition of UASB reactor effluents. Two distinct ammonia nitrogen concentrations (125 and 250 mg l(-1)) were supplied during two sequential long-term experiments of 160 days each (320 total). Cycles of 24h under intermittent aeration for periods of 1h were applied, and ethanol was added as a carbon source at the beginning of each anoxic period. Nitrite was the main oxidized nitrogen compound which accumulated only during the aerated phases of the batch cycle. A consistent decrease of nitrite concentration started always immediately after the interruption of oxygen supply and addition of the electron donor. Removal to below detection limits of all nitrogen soluble forms was always observed at the end of the 24h cycles for both initial concentrations. Polyurethane packed-bed matrices and ethanol amendments conferred high process stability. Microbial investigation by cloning suggested that nitrification was carried out by Nitrosomonas-like species whereas denitrification was mediated by unclassified species commonly observed in denitrifying environments. The packed-bed batch bioreactor favored the simultaneous colonization of distinct microbial groups within the immobilized microbial biomass. The biofilm was capable of actively oxidizing ammonium and denitrification at high ratios in intermittent intervals within 24h cycles.

Bacterial community composition of a wastewater treatment system reliant on N2 fixation

The temporal stability and change of the dominant phylogenetic groups of the domain bacteria were studied in a model plant-based industrial wastewater treatment system showing high levels of organic carbon removal supported by high levels of N2 fixation. Community profiles were obtained through terminal restriction fragment length polymorphism analysis and cloning of 16S rRNA amplicons followed by sequencing. Bacterial community profiles showed that ten common terminal restriction fragments made up approximately 50% of the measured bacterial community. As much as 42% of the measured bacterial community could be monitored by using quantitative PCR and primers that targeted three dominant operational taxonomic units. Despite changes in wastewater composition and dissolved oxygen levels, the bacterial community composition appeared stable and was dominated by alpha-Proteobacteria and beta-Proteobacteria, with a lesser amount of the highly diverse bacterial phylum Bacteroidetes. A short period of considerable change in the bacterial community composition did not appear to affect treatment performance indicating functional redundancy in this treatment system.