Community dynamics and heterogeneities in mixed bacterial communities subjected to nutrient periodicities

Resistance of aerobic granular sludge microbiomes to periodic loss of biomass

Granular sludge is a biofilm process used for wastewater treatment which is currently being implemented worldwide. It is important to understand how disturbances affect the microbial community and performance of reactors. Here, two acetate-fed replicate reactors were inoculated with acclimatized sludge and the reactor performance, and the granular sludge microbial community succession were studied for 149 days. During this time, the microbial community was challenged by periodically removing half of the reactor biomass, subsequently increasing the food-to-microorganism (F/M) ratio. Diversity analysis together with null models show that overall, the microbial communities were resistant to the disturbances, observing some minor effects on polyphosphate-accumulating and denitrifying microbial communities and their associated reactor functions. Community turnover was driven by drift and random granule loss, and stochasticity was the governing ecological process for community assembly. These results evidence the aerobic granular sludge process as a robust system for wastewater treatment.

Direct evidence for deterministic assembly of bacterial communities in full-scale municipal wastewater treatment facilities

In this study we investigated whether bacterial community composition in full-scale wastewater treatment bioreactors can be better explained by niche- or neutral- based theory (deterministic or stochastic) and whether bioreactor design (continuous-flow vs. fill-and-draw) affected community assembly. Four wastewater treatment facilities (one with quadruplicated continuous-flow bioreactors, two with one continuous-flow bioreactor each, one with triplicated fill-and-draw bioreactors) were investigated. Bioreactor community composition was characterized by sequencing of PCR-amplified 16S rRNA gene fragments. Replicate bioreactors at the same wastewater treatment facility had largely reproducible (i.e., deterministic) bacterial community composition, although bacterial community composition in continuous-flow bioreactors was significantly more reproducible (P < 0.001) than in fill-and-draw bioreactors (Bray-Curtis dissimilarity: μ = 0.48 ± 0.06 vs. 0.58 ± 0.08). Next, we compared our results to previously-used indirect methods for distinguishing between deterministic and stochastic community assembly mechanisms. Synchronicity was observed in the bacterial community composition among bioreactors within the same metropolitan region, consistent with deterministic community assembly. Similarly, a null model-based analysis also indicated that all wastewater bioreactor communities were controlled by deterministic factors and that continuous-flow bioreactors were significantly more deterministic (P < 0.001) than fill-and-draw bioreactors (nearest-taxon index: μ = 3.3 ± 0.6 vs. 2.7 ± 0.8). Our results indicate that bacterial community composition in wastewater treatment bioreactors is better explained by deterministic community assembly theory; simultaneously, our results validate previously-used but indirect methods to quantify whether microbial communities were assembled via deterministic or stochastic mechanisms. IMPORTANCE Understanding the mechanisms of bacterial community assembly is one of the grand challenges of microbial ecology. In environmental systems, this challenge is exacerbated because "replicate" experiments are typically impossible; that is, microbial ecologists cannot fabricate multiple field-scale experiments of identical, natural ecosystems. Our results directly demonstrate that deterministic mechanisms are more prominent than stochastic mechanisms in the assembly of wastewater treatment bioreactor communities. Our results also suggest that wastewater treatment bioreactor design is pertinent, such that the imposition of feast-famine conditions (i.e., fill-and-draw bioreactors) nudge bacterial community assembly more towards stochastic mechanisms compared to the imposition of stringent nutrient limitation (i.e., continuous-flow bioreactors). Our research also validates the previously-used indirect methods (synchronous community dynamics and an application of a null-model) for characterizing the relative importance of deterministic versus stochastic mechanisms of community assembly.

Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors

Aquatic environments are typically not homogenous, but characterized by changing substrate concentration gradients and nutrient patches. This heterogeneity in substrate availability creates a multitude of niches allowing bacteria with different substrate utilization strategies to hypothetically coexist even when competing for the same substrate. To study the impact of heterogeneous distribution of organic substrates on bacterioplankton, bioreactors with freshwater bacterial communities were fed artificial freshwater medium with acetate supplied either continuously or in pulses. After a month-long incubation, bacterial biomass and community-level substrate uptake rates were twice as high in the pulsed treatment compared to the continuously fed reactors even if the same total amount of acetate was supplied to both treatments. The composition of the bacterial communities emerging in the two treatments differed significantly with specific taxa overrepresented in the respective treatments. The higher estimated growth yield in cultures that received pulsed substrate inputs, imply that such conditions enable bacteria to use resources more efficiently for biomass production. This finding agrees with established concepts of basal maintenance energy requirements and high energetic costs to assimilate substrates at low concentration. Our results further imply that degradation of organic matter is influenced by temporal and spatial heterogeneity in substrate availability.

Microbial Communities Are Well Adapted to Disturbances in Energy Input

Although microbial systems are well suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20-day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function were used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appeared inherently well adapted to disturbances in energy input and that changes in community structure in both treatments were more dependent on internal dynamics than on external forcing. The results also showed that the rare biosphere was critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, internal feedbacks were more important than external drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic "unstable" communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems.

Dynamics in microbial communities: unraveling mechanisms to identify principles

Diversity begets higher-order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions and it is this 'system' that is the basis for higher-order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.

Homogeneity and synchronous dynamics of microbial communities in particulate biofilms: from major populations to minor groups

Natural or engineered microbial populations often show variations over time. These variations may be due to environmental fluctuations or intrinsic factors. Thus, studying the dynamics of microbial diversity for different communities living in a spatially homogeneous landscape is of interest. As a model ecosystem, nitrifying biofilm communities were grown in a two litre inverse turbulent bed reactor (ITBR) containing an estimated 200 million small particles (about 150 μm in diameter). Each particulate biofilm is considered as a distinct community growing in the neighborhood of other similar particles, in a homogeneous and well-controlled environmental context. A molecular approach was adopted to test how microbial community structures might evolve: either in synchrony, converging or diverging. The shape of biofilm was observed by microscopy for each particle. The biomass content was evaluated by quantitative PCR and showed similar values for each particle. The microbial community structure was evaluated by Capillary Electrophoresis-Single Strand Conformation Polymorphism (CE-SSCP) fingerprinting and showed extraordinary homogeneity between particles, even though transitory community structures were observed when reactor operating conditions were modified. This homogeneity was observed for the Bacteria primer set but, more interestingly, was also observed when minor non-nitrifying bacteria making up the biofilm, representing about 5% and 10% of total cells, were targeted.

Performance of a submerged membrane bioreactor for the aerobic treatment of abattoir wastewater

The performance of a submerged membrane bioreactor (SMBR) has been investigated for abattoir wastewater (AW) treatment. The chemical oxygen demand (COD) of permeate has not exceeded 25 mg L(-1) providing an average COD removal of 98%. Microbiological analysis showed that the SMBR has allowed a complete removal of fecal coliforms, Listeria and Salmonella. A significant reduction in the excess biomass production was also observed. In fact, the yield of biomass production (Yobs) ranged between 0 and 0.106 g suspended solids/g COD removed. The study of the dynamic of bacterial communities using the single strand conformation polymorphism (SSCP) method showed a significant change in the population structure and revealed a correlation between the sludge production yield and the bacterial communities.

Microbial biofilms on facial prostheses

The composition of microbial biofilms on silicone rubber facial prostheses was investigated and compared with the microbial flora on healthy and prosthesis-covered skin. Scanning electron microscopy showed the presence of mixed bacterial and yeast biofilms on and deterioration of the surface of the prostheses. Microbial culturing confirmed the presence of yeasts and bacteria. Microbial colonization was significantly increased on prosthesis-covered skin compared to healthy skin. Candida spp. were exclusively isolated from prosthesis-covered skin and from prostheses. Biofilms from prostheses showed the least diverse band-profile in denaturing gradient gel electrophoresis (DGGE) whereas prosthesis-covered skin showed the most diverse band-profile. Bacterial diversity exceeded yeast diversity in all samples. It is concluded that occlusion of the skin by prostheses creates a favorable niche for opportunistic pathogens such as Candida spp. and Staphylococcus aureus. Biofilms on healthy skin, skin underneath the prosthesis and on the prosthesis had a comparable composition, but the numbers present differed according to the microorganism.

Effect of oxic/anoxic switches on bacterial communities and PAH biodegradation in an oil-contaminated sludge

PURPOSE

We studied the effect of alternations of aeration on both the autochthonous bacterial communities from an oily sludge to the endogenous polycyclic aromatic hydrocarbons (PAH) biodegradation compared to a permanent oxic condition.

METHODS

Genomic and transcriptional analyses associated with chemical measurements were used to assess the dynamics of bacteria coupled to PAH removal during an incubation of 26 days.

RESULTS AND CONCLUSIONS

The autochthonous bacterial communities of an oil sludge showed a strong potential to adapt and degrade PAH when they were subjected to alternating anoxic/oxic conditions, as well as under an oxic condition. In addition, changes in the bacterial communities were related to the different phases of hydrocarbon degradation, and the removal efficiency of PAH was similar in both switching and permanent oxic conditions. This methodology could be useful for an alternative solution of oil sludge treatment with a low-cost processing, as its efficiency is similar to that of a permanent oxic incubation which is more expensive in oxygen supply.

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.

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

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

Maintenance of phenol hydroxylase genotypes at high diversity in bioreactors exposed to step increases in phenol loading

To better understand how the composition of bacterial communities changes in response to different environmental conditions, we examined the influence of increasing phenol load on the distribution of the protein-coding functional gene of the largest subunit of phenol hydroxylase (LmPH) and of the 16S rRNA gene in lab-scale activated sludge reactors. LmPH diversity was assessed initially from a total of 124 clone sequences retrieved from two reactors exposed to a low (0.25 g L(-1)) and a high (2.5 g L(-1)) phenol concentration. The quantitative changes in the concentration of the eight detected genotypes accompanied changes in the phenol degradation rates, indicating a community structure-function relationship. Nonmetric dimensional analysis showed that LmPH genotypes and the denaturing gradient gel electrophoresis banding patterns clustered together by phenol concentration, rather than by reactor identity. Seven isolates, representing cultivated strains of each of the observed LmPH genotypes, exhibited a rather narrow range of physiological diversity, in terms of the growth rate and the kinetic parameters of the phenol-degrading activity. We suggest that lab-scale reactors support many ecological niches, which allow the maintenance of a high diversity of ecotypes through varying concentrations of phenol, but the ability of particular strains to become dominant members of the community under the different environmental conditions cannot be predicted easily solely from their phenol-degrading properties.

Nonrandom assembly of bacterial populations in activated sludge flocs

The aim of this work was to investigate the dynamics of assembly of bacterial populations in activated sludge flocs. We approached this question by following the development of active bacterial populations during floc development in four replicated lab-scale activated sludge reactors, in which solid retention time (SRT) was set at 4 days. The null hypothesis was that the similarities in community composition could be accounted for by the probability that the same organisms occur in more than one replicated reactor. Microscopic imaging showed that the size of flocs in reactors with biomass retention increased during the first few days until a steady-state size was reached. The diversity and community structure of the sludge in all reactors were analyzed during a period of up to ten SRT, using denaturing gradient gel electrophoresis (DGGE) of reverse-transcription polymerase chain reaction-amplified 16S rRNA. High rates of change in DGGE profiles from consecutive sampling points suggested a high level of dynamics in all reactors. This conclusion was confirmed by the application of the Raup and Crick probability-based similarity index (S(RC)) for the comparison of rRNA-based fingerprinting patterns, which indicated that bacterial communities within reactors were not significantly similar after three SRT (0.05 < S(RC) < 0.95) and became significantly dissimilar after five SRT (S(RC) < 0.05). More importantly, significant similarity between replicate reactors was observed at all times analyzed (S(RC) > 0.95). The fact that the patterns between replicates were more reproducible than expected by chance under highly dynamic conditions allowed us to reject the null hypothesis that activated sludge floc communities assemble randomly from the available source pool of bacteria. We suggest that communities progressively recruit from the available pool of bacterial species, each with particular ecological requirements that determine their time of emergence into the community.

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.

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.

A constructed alkaline consortium and its dynamics in treating alkaline black liquor with very high pollution load

Background

Paper pulp wastewater resulting from alkaline extraction of wheat straw, known as black liquor, is very difficult to be treated and causes serious environmental problems due to its high pH value and chemical oxygen demand (COD) pollution load. Lignin, semicellulose and cellulose are the main contributors to the high COD values in black liquor. Very few microorganisms can survive in such harsh environments of the alkaline wheat straw black liquor. A naturally developed microbial community was found accidentally in a black liquor storing pool in a paper pulp mill of China. The community was effective in pH decreasing, color and COD removing from the high alkaline and high COD black liquor.

Findings

Thirty-eight strains of bacteria were isolated from the black liquor storing pool, and were grouped as eleven operational taxonomy units (OTUs) using random amplified polymorphic DNA-PCR profiles (RAPD). Eleven representative strains of each OTU, which were identified as genera of Halomonas and Bacillus, were used to construct a consortium to treat black liquor with a high pH value of 11.0 and very high COD pollution load of 142,600 mg l⁻¹. After treatment by the constructed consortium, about 35.4% of color and 39,000 mg l⁻¹ (27.3%) COD_cr were removed and the pH decreased to 7.8. 16S rRNA gene polymerase chain reaction denaturant gradient gel electrophoresis (PCR-DGGE) and gas chromatography/mass spectrometry (GC/MS) analysis suggested a two-stage treatment mechanism to elucidate the interspecies collaboration: Halomonas isolates were important in the first stage to produce organic acids that contributed to the pH decline, while Bacillus isolates were involved in the degradation of lignin derivatives in the second stage under lower pH conditions.

Conclusions/Significance

Tolerance to the high alkaline environment and good controllability of the simple consortium suggested that the constructed consortium has good potential for black liquor treatment. Facilitating the treatment process by the constructed consortium would provide a promising opportunity to reduce the pollution, as well as to save forest resources and add value to a waste product.

The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics

Multiple forces structure natural microbial communities, but the relative roles and interactions of these drivers are poorly understood. Gradients of physical and chemical parameters can be especially influential. In traditional ecological theory, variability in environmental conditions across space and time represents habitat heterogeneity, which may shape communities. Here we used aquatic microbial communities as a model to investigate the relationship between habitat heterogeneity and community composition and dynamics. We defined spatial habitat heterogeneity as vertical temperature and dissolved oxygen (DO) gradients in the water column, and temporal habitat heterogeneity as variation throughout the open-water season in these environmental parameters. Seasonal lake mixing events contribute to temporal habitat heterogeneity by destroying and re-creating these gradients. Because of this, we selected three lakes along a range of annual mixing frequency (polymictic, dimictic, meromictic) for our study. We found that bacterial community composition (BCC) was distinct between the epilimnion and hypolimnion within stratified lakes, and also more variable within the epilimnia through time. We found stark differences in patterns of epilimnion and hypolimnion dynamics over time and across lakes, suggesting that specific drivers have distinct relative importance for each community.

Impact of non-ionic surfactant on the long-term development of lab-scale-activated sludge bacterial communities

The development of bacterial communities in replicate lab-scale-activated sludge reactors degrading a non-ionic surfactant was evaluated by statistical analysis of denaturing gradient gel electrophoresis (DGGE) fingerprints. Four sequential batch reactors were fed with synthetic sewage, two of which received, in addition, 0.01% of nonylphenol ethoxylates (NPE). The dynamic character of bacterial community structure was confirmed by the differences in species composition among replicate reactors. Measurement of similarities between reactors was obtained by pairwise similarity analysis using the Bray Curtis coefficient. The group of NPE-amended reactors exhibited the highest similarity values (Sjk=0.53+/-0.03), indicating that the bacterial community structure of NPE-amended reactors was better replicated than control reactors (Sjk=0.36+/-0.04). Replicate NPE-amended reactors taken at different times of operation clustered together, whereas analogous relations within the control reactor cluster were not observed. The DGGE pattern of isolates grown in conditioned media prepared with media taken at the end of the aeration cycle grouped separately from other conditioned and synthetic media regardless of the carbon source amendment, suggesting that NPE degradation residuals could have a role in the shaping of the community structure.