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

Valorization of pulp and paper industry wastewater using sludge enriched with nitrogen-fixing bacteria

Nitrogen-fixing bacteria (NFB) can reduce nitrogen at ambient pressure and temperature. In this study, we treated effluent from a paper mill in sequencing batch reactors (SBRs) and monitored the abundance and activity of NFB with a view to producing a sludge that could work as a biofertilizer. Four reactors were inoculated with activated sludge enriched with NFB and fed with a high C/N waste (100:0.5) from a paper mill. Though the reactors were able to reduce the organic load of the wastewater by up to 89%, they did not have any nitrogen-fixing activity and showed a decrease in the putative number of NFB (quantified with qPCR). The most abundant species in the reactors treating high C/N paper mill wastewater was identified by Illumina MiSeq 16S rRNA gene amplicon sequencing as Methyloversatilis sp. (relative abundance of 4.4%). Nitrogen fixation was observed when the C/N ratio was increased by adding sucrose. We suspect that real-world biological nitrogen fixation (BNF) will only occur where there is a C/N ratio ≤100:0.07. Consequently, operators should actively avoid adding or allowing nitrogen in the waste streams if they wish to valorize their sludge and reduce running costs. PRACTITIONER POINTS: Efficient biological wastewater treatment of low nitrogen paper mill effluent was achieved without nutrient supplementation. The sludge was still capable of fixing nitrogen although this process was not observed in the wastewater treatment system. This high C/N wastewater treatment technology could be used with effluents from cassava flour, olive oil, wine and dairy industries.

High Resistance of a Sludge Enriched with Nitrogen-Fixing Bacteria to Ammonium Salts and Its Potential as a Biofertilizer

The increasing use of chemical fertilizers causes the loss of natural biological nitrogen fixation in soils, water eutrophication and emits more than 300 Mton CO₂ per year. It also limits the success of external bacterial inoculation in the soil. Nitrogen fixing bacteria can be inhibited by the presence of ammonia as its presence can inhibit biological nitrogen fixation. Two aerobic sludges from wastewater treatment plants (WWTP) were exposed to high ammonium salts concentrations (>450 mg L⁻¹ and >2 dS m⁻¹). Microbial analysis after treatment through 16S pyrosequencing showed the presence of Fluviicola sp. (17.70%), a genus of the Clostridiaceae family (11.17%), and Azospirillum sp. (10.42%), which were present at the beginning with lower abundance. Denaturing gradient gel electrophoresis (DGGE) analysis based on nifH genes did not show changes in the nitrogen-fixing population. Nitrogen-Fixing Bacteria (NFB) were identified and associated with other microorganisms involved in the nitrogen cycle, presumably for survival at extreme conditions. The potential use of aerobic sludges enriched with NFB is proposed as an alternative to chemical fertilizer as this bacteria could supplement nitrogen to the plant showing competitive results with chemical fertilization.

Restoring degraded microbiome function with self-assembled communities

The natural microbial functions of many soils are severely degraded. Current state-of-the-art technology to restore these functions is through the isolation, screening, formulation and application of microbial inoculants and synthetic consortia. These approaches have inconsistent success, in part due to the incompatibility between the biofertilizer, crop, climate, existing soil microbiome and physicochemical characteristics of the soils. Here, we review the current state of the art in biofertilization and identify two key deficiencies in current strategies: the difficulty in designing complex multispecies biofertilizers and the bottleneck in scaling the production of complex multispecies biofertilizers. To address the challenge of producing scalable, multispecies biofertilizers, we propose to merge ecological theory with bioprocess engineering to produce 'self-assembled communities' enriched for particular functional guilds and adapted to a target soil and host plant. Using the nitrogen problem as an anchor, we review relevant ecology (microbial, plant and environmental), as well as reactor design strategies and operational parameters for the production of functionally enriched self-assembled communities. The use of self-assembled communities for biofertilization addresses two major hurdles in microbiome engineering: the importance of enriching microbes indigenous to (and targeted for) a specific environment and the recognized potential benefits of microbial consortia over isolates (e.g. functional redundancy). The proposed community enrichment model could also be instrumental for other microbial functions such as phosphorus solubilization, plant growth promotion or disease suppression.

Microalgal Growth in Paper Industry Effluent: Coupling Biomass Production with Nutrients Removal

Paper and pulp industries produce effluents with high phosphorus concentrations, which need to be treated before their discharge in watercourses. The use of microalgae for this purpose has attracted the attention of researchers because: (i) microalgae can assimilate phosphorus (one of the main nutrients for their growth); and (ii) growing on effluents can significantly reduce the costs and environmental impact of microalgal biomass production. This study evaluated the growth and ability of Chlorella vulgaris to remove the phosphorus from a secondary-treated effluent of a Portuguese paper company. Batch experiments were performed for 11 days using different dilutions of the effluent to evaluate its inhibitory effect on microalgae. Results showed that the non-diluted effluent inhibited microalgal growth, indicating that this bioremediation process is possible after a previous dilution of the effluent. Regarding phosphorus removal, promising results were achieved, especially in the experiments conducted with the most diluted effluent: removal efficiencies obtained in these conditions were (54 ± 1)%. Another interesting finding of this study was microalgal growth in flakes’ form (mainly due to the compounds present in the effluent and to the pH values achieved), which can be an important economic advantage for biomass recovery after the remediation step.

Enrichment of Nitrogen-Fixing Bacteria in a Nitrogen-Deficient Wastewater Treatment System

Anthropogenic nitrogen fixation is essential to sustain a global population of 7.7 billion. However, there has been a long-standing desire to find cheaper and more environmentally friendly alternatives to the Haber-Bosch process. In this study, we developed a new strategy of nitrogen fixation by enriching free-living N₂-fixing bacteria (NFB) in reactors fed with low nitrogen wastewater, analogous to those usually found in certain industrial effluents such as paper mills. Our reactors fixed appreciable quantities of nitrogen with a rate of 11.8 mg N L^-1 day^-1. This rate is comparable to recent "breakthrough" nitrogen-fixing technologies and far higher than observed in low C/N reactors (fed with organic matter and nitrogen). NFB were quantified using quantitative polymerase chain reaction (qPCR) of the nifH (marker gene used to identify biological nitrogen fixation) and 16S rRNA genes. The nifH gene was enriched by a factor of 10 in the nitrogen-fixing reactors (compared to controls) attaining 13% of the bacterial population (1:4.2 copies of nifH to 16S rRNA). The Illumina MiSeq 16S rRNA gene amplicon sequencing of reactors showed that the microbial community was dominated (19%) by Clostridium pasteurianum. We envisage that nitrogen-enriched biomass could potentially be used as a biofertilizer and that the treated wastewater could be released to the environment with very little post-treatment.

Isolation and Identification of Poly β-Hydroxybutyrate Over-Producing Bacteria and Optimization of Production Medium

Background:

Biodegradable polyesters are candidates for the development of environmental friendly plastics. Poly-β-hydroxybutyrate (PHB) is a type of polyester from the hydroxyalkanoates family, synthesized by bacteria as an intracellular material and accumulated as granules in the cytoplasm.

Objectives:

The aim of this study was to isolate Poly β-hydroxybutyrate over producing bacteria and optimize the production medium.

Materials and Methods:

A variety of PHB-accumulating bacterial strains were isolated from Kermanshah oil refinery sludge in Iran. Poly-β-hydroxybutyrate-producing bacterial strains were confirmed by the gas chromatography method. The strain with the highest rate of PHB production was selected. Use of sugar cane molasses, a by-product of the sugar refinery industry, was investigated for the production of PHB. Plackett-Burman statistical method was employed to obtain factors in cell growth and PHB production. Optimization by the Response Surface Method (RSM) was done via two carbon sources, glucose and molasses.

Results:

In the present study, 21 of 63 strains isolated from the refinery oil sludge produced PHB, seven of which were over producers. Poly-β-hydroxybutyrate production was analyzed by Sudan Black B staining, spectrophotometric and gas chromatography (GC) methods. The strain with the highest rate of PHB production was used to optimize the culture medium. Fifteen factors were analyzed in PHB production by the Plackett-Burman method to find the most effective factors. Five important factors were optimized by RSM. Molasses were used as a cheap source of carbon. The maximum PHB obtained from molasses was 6.62 g/L. The phenotypic and 16S rRNA biotyping tests led to the identification of the isolate as Bacillus coagulans.

Conclusions:

The results suggest that B. coagulans is a good candidate for the fermentative production of PHB.

Microalgal biomass and lipid production in mixed municipal, dairy, pulp and paper wastewater together with added flue gases

The aim of the study was to grow microalgae on mixed municipal and industrial wastewater to simultaneously treat the wastewater and produce biomass and lipids. All algal strains grew in all wastewater mixtures; however, Selenastrum minutum had the highest biomass and lipids yields, up to 37% of the dry matter. Nitrogen and phosphorus removal were high and followed a similar trend in all three strains. Ammonium was reduced from 96% to 99%; this reduction was due to algal growth and not to stripping to the atmosphere, as confirmed by the amount of nitrogen in the dry algal biomass. Phosphate was reduced from 91% to 99%. In all strains used the lipid content was negatively correlated to the nitrogen concentration in the algal biomass. Mixtures of pulp and paper wastewater with municipal and dairy wastewater have great potential to grow algae for biomass and lipid production together with effective wastewater treatment.

Support vector regression model of wastewater bioreactor performance using microbial community diversity indices: effect of stress and bioaugmentation

The relationship between microbial community structure and function has been examined in detail in natural and engineered environments, but little work has been done on using microbial community information to predict function. We processed microbial community and operational data from controlled experiments with bench-scale bioreactor systems to predict reactor process performance. Four membrane-operated sequencing batch reactors treating synthetic wastewater were operated in two experiments to test the effects of (i) the toxic compound 3-chloroaniline (3-CA) and (ii) bioaugmentation targeting 3-CA degradation, on the sludge microbial community in the reactors. In the first experiment, two reactors were treated with 3-CA and two reactors were operated as controls without 3-CA input. In the second experiment, all four reactors were additionally bioaugmented with a Pseudomonas putida strain carrying a plasmid with a portion of the pathway for 3-CA degradation. Molecular data were generated from terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the 16S rRNA and amoA genes from the sludge community. The electropherograms resulting from these T-RFs were used to calculate diversity indices - community richness, dynamics and evenness - for the domain Bacteria as well as for ammonia-oxidizing bacteria in each reactor over time. These diversity indices were then used to train and test a support vector regression (SVR) model to predict reactor performance based on input microbial community indices and operational data. Considering the diversity indices over time and across replicate reactors as discrete values, it was found that, although bioaugmentation with a bacterial strain harboring a subset of genes involved in the degradation of 3-CA did not bring about 3-CA degradation, it significantly affected the community as measured through all three diversity indices in both the general bacterial community and the ammonia-oxidizer community (α = 0.5). The impact of bioaugmentation was also seen qualitatively in the variation of community richness and evenness over time in each reactor, with overall community richness falling in the case of bioaugmented reactors subjected to 3-CA and community evenness remaining lower and more stable in the bioaugmented reactors as opposed to the unbioaugmented reactors. Using diversity indices, 3-CA input, bioaugmentation and time as input variables, the SVR model successfully predicted reactor performance in terms of the removal of broad-range contaminants like COD, ammonia and nitrate as well as specific contaminants like 3-CA. This work was the first to demonstrate that (i) bioaugmentation, even when unsuccessful, can produce a change in community structure and (ii) microbial community information can be used to reliably predict process performance. However, T-RFLP may not result in the most accurate representation of the microbial community itself, and a much more powerful prediction tool can potentially be developed using more sophisticated molecular methods.

Pathway of nitrous oxide consumption in isolated Pseudomonas stutzeri strains under anoxic and oxic conditions

The microbial consumption of nitrous oxide (N2O) has gained great interest since it was revealed that this process could mitigate the greenhouse effect of N2O. The consumption of N2O results from its reduction to dinitrogen gas (N2) as part of the denitrification process. However, there is ongoing debate regarding an alternative pathway, namely reduction of N2O to NH4(+), or assimilatory N2O consumption. To date, this pathway is poorly investigated and lacks unambiguous evidence. Enrichment of denitrifying activated sludge using a mineral nitrogen-free medium rendered a mixed culture capable of anoxic and oxic N2O consumption. Dilution plating, isolation and deoxyribonucleic acid fingerprinting identified a collection of Pseudomonas stutzeri strains as dominant N2O consumers in both anaerobic and aerobic enrichments. A detailed isotope tracing experiment with a Pseudomonas stutzeri isolate showed that consumption of N2O via assimilatory reduction to NH4(+) was absent. Conversely, respiratory N2O reduction was directly coupled to N2 fixation.

Development of an analytical microbial consortia method for enhancing performance monitoring at aerobic wastewater treatment plants

An analytical method to produce profiles of bacterial biomass fatty acid methyl esters (FAME) was developed employing rapid agitation followed by static incubation (RASI) using selective media of wastewater microbial communities. The results were compiled to produce a unique library for comparison and performance analysis at a Wastewater Treatment Plant (WWTP). A total of 146 samples from the aerated WWTP, comprising 73 samples of each secondary and tertiary effluent, were included analyzed. For comparison purposes, all samples were evaluated via a similarity index (SI) with secondary effluents producing an SI of 0.88 with 2.7% variation and tertiary samples producing an SI 0.86 with 5.0% variation. The results also highlighted significant differences between the fatty acid profiles of the tertiary and secondary effluents indicating considerable shifts in the bacterial community profile between these treatment phases. The WWTP performance results using this method were highly replicable and reproducible indicating that the protocol has potential as a performance-monitoring tool for aerated WWTPs. The results quickly and accurately reflect shifts in dominant bacterial communities that result when processes operations and performance change.

Integrated perspective for effective bioremediation

Identification of factors which can influence the natural attenuation process with available microbial genetic capacities can support the bioremediation which has been viewed as the safest procedure to combat with anthropogenic compounds in ecosystems. With the advent of molecular techniques, assimilatory capacity of an ecosystem can be defined with changing community dynamics, and if required, the essential genetic potential can be met through bioaugmentation. At the same time, intensification of microbial processes with nutrient balancing, expressing and enhancing the degradative capacities, could reduce the time frame of restoration of the ecosystem. The new concept of ecosystems biology has added greatly to conceptualize the networking of the evolving microbiota of the niche that helps in effective application of bioremediation tools to manage pollutants as additional carbon source.

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.

Biodiversity of active and inactive bacteria in the gut flora of wood-feeding huhu beetle larvae (Prionoplus reticularis)

Huhu grubs (Prionoplus reticularis) are wood-feeding beetle larvae endemic to New Zealand and belonging to the family Cerambycidae. Compared to the wood-feeding lower termites, very little is known about the diversity and activity of microorganisms associated with xylophagous cerambycid larvae. To address this, we used pyrosequencing to evaluate the diversity of metabolically active and inactive bacteria in the huhu larval gut. Our estimate, that the gut harbors at least 1,800 phylotypes, is based on 33,420 sequences amplified from genomic DNA and reverse-transcribed RNA. Analysis of genomic DNA- and RNA-derived data sets revealed that 71% of all phylotypes (representing 95% of all sequences) were metabolically active. Rare phylotypes contributed considerably to the richness of the community and were also largely metabolically active, indicating their participation in digestive processes in the gut. The dominant families in the active community (RNA data set) included Acidobacteriaceae (24.3%), Xanthomonadaceae (16.7%), Acetobacteraceae (15.8%), Burkholderiaceae (8.7%), and Enterobacteriaceae (4.1%). The most abundant phylotype comprised 14% of the active community and affiliated with Dyella ginsengisoli (Gammaproteobacteria), suggesting that a Dyella-related organism is a likely symbiont. This study provides new information on the diversity and activity of gut-associated microorganisms that are essential for the digestion of the nutritionally poor diet consumed by wood-feeding larvae. Many huhu gut phylotypes affiliated with insect symbionts or with bacteria present in acidic environments or associated with fungi.

Bacterial community dynamics in two full-scale wastewater treatment systems with functional stability

AIMS

To characterize the bacterial community dynamics over 1 year in two full-scale wastewater treatment systems operated under constant conditions and exhibiting stable performance.

METHODS AND RESULTS

Functional stability was defined and quantified by the effluent concentration of biological oxygen demand, total nitrogen and ammonia. Community dynamics were investigated using specific PCR followed by terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA gene. The T-RFLP results indicated that during the period of functional stability, the bacterial community structures in two full-scale wastewater treatment systems were not stable, and the average change rates every 15 days of the two systems were 22.6 ± 6.9 and 21.6 ± 7.3%, respectively. The corresponding species with dominant T-RFs were determined by clonal sequencing and T-RFLP. Based on Pareto-Lorenz distribution curves, it was observed that only a small number of micro-organisms were numerically dominant in the two systems.

CONCLUSIONS

The results of this study showed that, throughout the period of the study, the bacterial community structure changed significantly in two full-scale wastewater treatment systems despite the stable function.

SIGNIFICANCE AND IMPACT OF THE STUDY

The findings enrich the theory involving the relation between bacterial community dynamics and functional stability in full-scale wastewater treatment plants.

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.

Dynamics of polyphosphate-accumulating bacteria in wastewater treatment plant microbial communities detected via DAPI (4',6'-diamidino-2-phenylindole) and tetracycline labeling

Wastewater treatment plants with enhanced biological phosphorus removal represent a state-of-the-art technology. Nevertheless, the process of phosphate removal is prone to occasional failure. One reason is the lack of knowledge about the structure and function of the bacterial communities involved. Most of the bacteria are still not cultivable, and their functions during the wastewater treatment process are therefore unknown or subject of speculation. Here, flow cytometry was used to identify bacteria capable of polyphosphate accumulation within highly diverse communities. A novel fluorescent staining technique for the quantitative detection of polyphosphate granules on the cellular level was developed. It uses the bright green fluorescence of the antibiotic tetracycline when it complexes the divalent cations acting as a countercharge in polyphosphate granules. The dynamics of cellular DNA contents and cell sizes as growth indicators were determined in parallel to detect the most active polyphosphate-accumulating individuals/subcommunities and to determine their phylogenetic affiliation upon cell sorting. Phylotypes known as polyphosphate-accumulating organisms, such as a "Candidatus Accumulibacter"-like phylotype, were found, as well as members of the genera Pseudomonas and Tetrasphaera. The new method allows fast and convenient monitoring of the growth and polyphosphate accumulation dynamics of not-yet-cultivated bacteria in wastewater bacterial communities.