Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge

Efficient nitrogen removal in a total floc sludge system from domestic wastewater with low C/N: High anammox nitrogen removal contribution driven by endogenous partial denitrification

Since unsustainable partial nitrification prone to unstable nitrogen removal rates, cultivation and enrichment of AnAOB, further improve autotrophic nitrogen removal contribution have been challenges in the mainstream anammox process. This study proposed a new strategy to enrich AnAOB motivated by endogenous partial denitrification (EPD) in total floc sludge system through the AOA process with sustainable nitrification. The results showed that in the presence of NH₄⁺ and NO₃^- at the anoxic stage of N-EPDA, Ca. Brocadia was enriched (0.005%→0.92%) in floc sludge via internal carbon source metabolism of EPD. The C/N and temperature of N-EPDA were also optimized to achieve higher activities of EPD and anammox. The N-EPDA was operated at low C/N ratio (3.1) with anammox nitrogen removal contribution of 78% during the anoxic stage, Eff.TIN of 8.3 mg/L and NRE of 83.5% during phase III, achieved efficient autotrophic nitrogen removal and AnAOB enrichment in the absence of partial nitrification.

How nutrient loading leads to alternative stable states in microbially mediated N-cycle pathways: A new insight into bioavailable nitrogen removal in urban rivers

Excessive nutrients have disrupted pathways of microbial-mediated nitrogen (N) cycle in urban rivers and caused bioavailable N to accumulate in sediments, while remedial actions sometimes fail to recover degraded river ecosystems even when environmental quality has been improved. It is not sufficient to revert the ecosystem to its original healthy state by restoring the pre-degradation environmental conditions, as explained by alternative stable states theory. Understanding the recovery of disrupted N-cycle pathways from the perspective of alternative stable states theory can benefit effective river remediation. Previous studies have found alternative microbiota states in rivers; however, the existence and implications of alternative stable states in microbial-mediated N-cycle pathway remain unclear. Here, high-throughput sequencing and N-related enzyme activities measurement were combined in the field investigation to provide empirical evidence for the bi-stability in microbially mediated N-cycle pathways. According to the behavior of bistable ecosystems, the existence of alternative stable states in microbial-mediated N-cycle pathway have been shown, and nutrient loading, mainly total nitrogen and total phosphorus, were identified as key driver of regime shifts. In addition, potential analysis revealed that reducing nutrient loading shifted the N-cycle pathway to a desirable state characterized by high ammonification and nitrification, probably avoiding the accumulation of ammonia and organic N. It should be noted that the improvement of microbiota status can facilitate the recovery of the desirable pathway state according to the relationship between microbiota states and N-cycle pathway states. Keystone species, including Rhizobiales and Sphingomonadales, were discerned by network analysis, and the increase in their relative abundance may facilitate the improvement of microbiota status. The obtained results suggested that the nutrient reduction should be combined with microbiota management to benefit the bioavailable N removal in urban rivers, therefore providing a new insight into alleviating adverse effects of the nutrient loading on urban rivers.

Research advances of the phosphorus-accumulating organisms of Candidatus Accumulibacter, Dechloromonas and Tetrasphaera: Metabolic mechanisms, applications and influencing factors

Phosphorus-accumulating organisms (PAOs), which harbor metabolic mechanisms for phosphorus removal, are widely applied in wastewater treatment. Recently, novel PAOs and phosphorus removal metabolic pathways have been identified and studied. Specifically, Dechloromonas and Tetrasphaera can remove phosphorus via the denitrifying phosphorus removal and fermentation phosphorus removal pathways, respectively. As the main PAOs in biological phosphorus removal systems, the conventional PAO Candidatus Accumulibacter and the novel PAOs Dechloromonas and Tetrasphaera are thoroughly discussed in this paper, with a specific focus on their phosphorus removal metabolic mechanisms, process applications, community abundance and influencing factors. Dechloromonas can achieve simultaneous nitrogen and phosphorus removal in an anoxic environment through the denitrifying phosphorus removal metabolic pathway, which can further reduce carbon source requirements and aeration energy consumption. The metabolic pathways of Tetrasphaera are diverse, with phosphorus removal occurring in conjunction with macromolecular organics degradation through anaerobic fermentation. A collaborative oxic phosphorus removal pathway between Tetrasphaera and Ca. Accumulibacter, or a collaborative anoxic denitrifying phosphorus removal pathway between Tetrasphaera and Dechloromonas are future development directions for biological phosphorus removal technologies, which can further reduce carbon source and energy consumption while achieving enhanced phosphorus removal.

A global survey reveals a divergent extradiol dioxygenase clade as a widespread complementary contributor to the biodegradation of mono- and polycyclic aromatic hydrocarbons

Extradiol dioxygenation is a key reaction in the microbial aerobic degradation of mono- and polycyclic aromatic hydrocarbon catecholic derivatives. It has been reported that many bacterial enzymes exhibiting such converging functions act on a wide range of catecholic substrates. The present study reports a new subfamily of extradiol dioxygenases (EXDOs) with broad substrate specificity, the HrbC EXDOs. The new clade belongs to the XII cluster within family 2 of the vicinal oxygen chelate superfamily (EXDO-VC2), which is typically characterized by a preference for bicyclic substrates. Coding hrbC orthologs were isolated by activity-based screening of fosmid metagenomic libraries from large DNA fragments derived from heavily PAH-contaminated soils. They occurred as solitary genes within conserved sequences encoding enzymes for amino acid metabolism and were stably maintained in the chromosomes of the Betaproteobacteria lineages harboring them. Analysis of contaminated aquifers revealed coexpression of hrbC as a polycistronic mRNA component. The predicted open reading frames were verified by cloning and heterologous expression, confirming the expected molecular mass and meta-cleavage activity of the recombinant enzymes. Evolutionary analysis of the HrbC protein sequences grouped them into a discrete cluster of 1,2-dihydroxynaphthalene dioxygenases represented by a cultured PAH degrader, Rugosibacter aromaticivorans strain Ca6. The ecological importance and relevance of the new EXDO genes were confirmed by PCR-based mapping in different biogeographical localities contaminated with a variety of mono- and polycyclic aromatic compounds. The cosmopolitan distribution of hrbC in PAH-contaminated aquifers supports our hypothesis about its auxiliary role in the degradation of toxic catecholic intermediates, contributing to the composite EXDO catabolic capacity of the world's microbiomes.

Impacts of bioreactor operating parameters on removal efficiency, biodegradation rate, molecular distribution, and toxicity of commercial naphthenic acids

Effects of naphthenic acids (NAs) concentration (50-200 mg NA L^-1; 35-140 mg TOC L^-1) and loading rate (1.4-1249 mg NA L^-1 h^-1; 1-874 mg TOC L^-1 h^-1) on removal efficiency, removal rate, and molecular distribution of NAs, and effluent toxicity were evaluated for biodegradation of commercial NAs mixture in circulating packed bed bioreactors (CPBBs). Increase of NAs concentration and loading rate (shorter residence times) increased the removal rate, while removal efficiency initially declined and then stabilized. The maximum biodegradation rates for 50, 100, 150, and 200 mg NA L^-1 were 128.0, 321.7, 430.2, and 630.0 mg TOC L^-1 h^-1 at loading rates of 218.5, 455.6, 673.5 and 874.0 mg TOC L^-1 h^-1, respectively, with removal efficiencies of 58.6, 70.6, 63.9 and 72.1%. Analysis of influent and treated effluents with gas chromatography-mass spectrometry showed that molecular weight and cyclicity (C and Z numbers) affected the biodegradation, with low molecular weight acyclic NAs (C = 6-12) were the most amenable to biodegradation and those with intermediate and high molecular weights (C = 13-22) and moderate cyclicity (Z = - 4, - 6) were the most recalcitrant. In the biofilm, Proteobacteria and Actinobacteria were the most abundant phyla, and Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were the dominant classes. Toxicity analyses with Artemia salina and Vibrio fischeri (Microtox) showed that high influent concentrations and loading rates (short residence times) led to higher NAs residual concentration and effluent toxicity. To design and operate large-scale CPBBs, intermediate loading rates and residence times that result in high removal efficiency, reasonable removal rates, and low toxicity are recommended.

"Candidatus Dechloromonas phosphoritropha" and "Ca. D. phosphorivorans", novel polyphosphate accumulating organisms abundant in wastewater treatment systems

Members of the genus Dechloromonas are often abundant in enhanced biological phosphorus removal (EBPR) systems and are recognized putative polyphosphate accumulating organisms (PAOs), but their role in phosphate removal is still unclear. Here, we used 16S rRNA gene sequencing and fluorescence in situ hybridization (FISH) to investigate the abundance and distribution of Dechloromonas spp. in Danish and global wastewater treatment plants. The two most abundant species worldwide revealed in situ dynamics of important intracellular storage polymers, measured by FISH-Raman in activated sludge from four full-scale EBPR plants and from a lab-scale reactor fed with different substrates. Moreover, seven distinct Dechloromonas species were determined from a set of ten high-quality metagenome-assembled genomes (MAGs) from Danish EBPR plants, each encoding the potential for polyphosphate (poly-P), glycogen, and polyhydroxyalkanoates (PHA) accumulation. The two species exhibited an in situ phenotype in complete accordance with the metabolic information retrieved by the MAGs, with dynamic levels of poly-P, glycogen, and PHA during feast-famine anaerobic-aerobic cycling, legitimately placing these microorganisms among the important PAOs. They are potentially involved in denitrification showing niche partitioning within the genus and with other important PAOs. As no isolates are available for the two species, we propose the names Candidatus Dechloromonas phosphoritropha and Candidatus Dechloromonas phosphorivorans.

Electro-assisted autohydrogenotrophic reduction of perchlorate and microbial community in a dual-chamber biofilm-electrode reactor

The electro-assisted autohydrogenotrophic reduction of perchlorate (ClO₄^-) was investigated in a dual-chamber biofilm-electrode reactor (BER), in which the microbial community was inoculated from natural sediments. To avoid the effect of extreme pH and direct electron transfer on perchlorate reduction, a novel cathode configuration was designed. The pH of the cathode compartment was successfully controlled in the range of 7.2-8.4 during whole experiment. The effective biological autohydrogenotrophic reduction of perchlorate was achieved using hydrogen generated in-situ on the electrode surface, and the removal rate of 10 mg L^-1 perchlorate reached 98.16% at HRT of 48 h. The highest perchlorate removal flux reached to 1498.420 mg m^-2·d^-1 with a 0.410 kW·h g-perchlorate^-1 energy consumption. The microbial community evolution in the BER was determined by high-throughput sequencing and the results indicated that the Firmicutes and Bacteroidetes were dominant at phylum level when perchlorate concentration was 10 mg L^-1 or lower. And the Proteobacteria became ascendant at the perchlorate concentration of 20 mg L^-1. The functional populations for perchlorate reduction were successfully enriched including Nitrosomonas (30%), Thermomonas (9%), Comamonas (8%) and Hydrogenophaga (3%). Meanwhile, the proportion of functional population in biofilm linked to perchlorate concentration. With the increase of influent perchlorate concentration, the perchlorate-reducing bacteria (PRB) were enriched successfully and became ascendant.

Antibiotic-induced role interchange between rare and predominant bacteria retained the function of a bacterial community for denitrifying quinoline degradation

AIM

Quinoline is a recalcitrant pollutant in coking wastewater which has been broadly investigated with many isolates possessing aerobic quinoline-degrading ability. However, studies on anaerobic degradation and the corresponding bacteria are very scarce. This study attempted to investigate the role of diverse functional members and the redundancy of quinoline degradation in a lab-scale quinoline denitrifying bioreactor.

METHODS AND RESULTS

Antibiotics were added to the batch culture under denitrifying conditions to disturb the microbial community of the quinoline-degrading bioreactor. According to the results, the nitrate removal rate remained stable, and the quinoline removal rate increased by 9·7% after treatment with streptomycin. However, PCoA analysis of 16S rRNA gene sequencing data of these samples indicated a significant shift in microbial community structures. Specifically, 12 operational taxonomic units (OTUs), including OTU1 (Pseudomonas) and OTU2 (Achromobacter), were significantly enriched. OTU1 replaced OTU8 (Thauera) as the most predominant denitrifying quinoline-degrading member. However, OTU8 and other predominant OTUs (Comamonas and Pseudoxanthomonas), which were hypothesized to contribute essentially to quinoline degradation in the origin bioreactor, became almost undetectable.

CONCLUSION

Functional redundancy due to high biological diversity allowed the role reversal of predominant quinoline-degrading bacteria and other rare bacteria when disturbed by antibiotic stress. Although the abundance of OTU1 was much lower initially, it replaced the essential role of the predominant member OTU8 in the bioreactor community for quinoline degradation once the environmental condition changed.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study indicated that the high biological diversity in a wastewater treatment bacterial community is crucial for maintaining the degrading function of organic pollutants, especially in a changing environment due to external disturbance or stress.

Spatiotemporal Variations in Seston C:N:P Stoichiometry in a Large Eutrophic Floodplain Lake (Lake Taihu): Do the Sources of Seston Explain Stoichiometric Flexibility?

Although sources of seston are much more complicated in lakes compared to oceans, the influences of different sources on the spatiotemporal variations in seston stoichiometry are still underexplored, especially in large eutrophic floodplain lakes. Here, we investigated seston stoichiometric ratios across a typical large eutrophic floodplain lake (Lake Taihu, East China) over one year. In addition, we used the n-alkane proxies to examine the influence of the seston source on seston stoichiometry variation. Throughout the study, the average value of the C:N:P ratio of 143:19:1 across Lake Taihu was close to the canonical lake’s ratios (166:20:1). Similar to other eutrophic lakes, seston C:N ratios varied the least across all environments, but C:P and N:P ratios varied widely and showed a strong decreasing trend in ratios of N:P and C:P from growing season to senescence season. This seasonal change was mainly associated with the decreasing contribution from algal-derived materials in seston pools because the non-algal dominated seston exhibited significantly lower ratios than algal-dominated seston. Furthermore, the spatial heterogeneity of stoichiometric ratios was also related to the seston source. During the senescence season, the terrestrial-dominated seston from agricultural watershed exhibited the lowest ratios in estuary sites compared with other areas. Statistically, the predictive power of environmental variables on stoichiometric ratios was strongly improved by adding n-alkanes proxies. Apart from source indicators, particulate phosphorus (PP) contents also partly explained the spatiotemporal variations in stoichiometric ratios. This study, thus, highlights the utility of multiple-combined n-alkane proxies in addition to simple C:N ratios to get more robust source information, which is essential for interpreting the spatiotemporal variations in seston stoichiometric ratios among eutrophic floodplain lakes and other freshwater ecosystems.

A new framework for approaching precision bioremediation of PAH contaminated soils

Bioremediation is a sustainable treatment strategy which remains challenging to implement especially in heterogeneous environments such as soil and sediment. Herein, we present a novel precision bioremediation framework that integrates amplicon based metagenomic analysis and chemical profiling. We applied this approach to samples obtained at a site contaminated with polycyclic aromatic hydrocarbons (PAHs). Geobacter spp. were identified as biostimulation targets because they were one of the most abundant genera and previously identified to carry relevant degradative genes. Mycobacterium and Sphingomonads spp. were identified as bioaugmentation and genetic bioaugmentation targets, respectively, due to their positive associations with PAHs and their high abundance and species diversity at all sampling locations. Overall, this case study suggests this framework can help identify bacterial targets for precision bioremediation. However, it is imperative that we continue to build our databases as the power of metagenomic based approaches remains limited to microorganisms currently in our databases.

Methane oxidation coupled to perchlorate reduction in a membrane biofilm batch reactor

A specially designed CH₄-based membrane biofilm batch reactor (MBBR) was applied to investigate anaerobic methane oxidation coupled to perchlorate reduction (AnMO-PR). The 0.21 mM ClO₄^- added in the first stage of operation was completely reduced in 28 days, 0.40 mM ClO₄^- was reduced within 23 days in stage 2, and 0.56 mM of ClO₄^- was reduced within 30 days in stage 3. Although some chlorate (ClO₃^-) accumulated, the recovery of Cl^- was over 92%. Illumina sequencing of the 16S rRNA gene documented that the bacterial community was mainly composed by perchlorate-reducing bacteria (PRB), methanotrophic bacteria, and archaea. Real-time quantitative PCR showed the archaeal 16S rRNA and mcrA genes increased as more ClO₄^- was reduced, and the predominant archaea belonged to Methanosarcina mazei, which is related to ANME-3, an archaeon able to perform reverse methanogenesis. Several pieces of evidence support that ClO₄^- reduction by the MBBR biofilm occurred via a synergism between Methanosarcina and PRB: Methanosarcina oxidized methane through reverse methanogesis and provided electron donor for PRB to reduce ClO₄^-. Because methanotrophs were present, we cannot rule out that they also were involved in AnMO-PR if they received O₂ generated by disproportionation of ClO₂^- from the PRB.

Plant compartment and genetic variation drive microbiome composition in switchgrass roots

Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth-promoting bacteria and fungi, however, plant-associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non-native soil. We show that differences in bacterial, archaeal and fungal community composition and diversity are strongly driven by plant compartment and switchgrass genotypes and ecotypes. Plant-associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared with the surrounding soil. Root associated compartments display low-complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot of host-specific bacterial and fungal associations of switchgrass in the field and confirms that host-selected microbiomes persist after transfer to non-native soil.

Assessing the spatial and temporal variability of bacterial communities in two Bardenpho wastewater treatment systems via Illumina MiSeq sequencing

Next generation sequencing provides new insights into the diversity and ecophysiology of bacteria communities throughout wastewater treatment plants (WWTP), as well as the fate of pathogens in wastewater treatment system. In the present study, we investigated the bacterial communities and human-associated Bacteroidales (HF183) marker in two WWTPs in North America that utilize Bardenpho treatment processes. Although, most pathogens were eliminated during wastewater treatment, some pathogenic bacteria were still observed in final effluents. The HF183 genetic marker demonstrated significant reductions between influent and post-Bardenpho treated samples in each WWTP, which coincided with changes in bacteria relative abundances and community compositions. Consistent with previous studies, the major phyla in wastewater samples were predominantly comprised by Proteobacteria (with Gammaproteobacteria and Alphaproteobacteria among the top two classes), Actinobacteria, Bacteroidetes, and Firmicutes. Dominant genera were often members of Proteobacteria and Firmicutes, including several pathogens of public health concern, such as Pseudomonas, Serratia, Streptococcus, Mycobacterium and Arcobacter. Pearson correlations were calculated to observe the seasonal variation of relative abundances of gene sequences at different levels based on the monthly average temperature. These findings profile how changes in bacterial communities can function as a robust method for monitoring wastewater treatment quality and performance for public and environmental health purposes.

Microbial community succession and pollutants removal of a novel carriers enhanced duckweed treatment system for rural wastewater in Dianchi Lake basin

Carriers strengthened duckweed treatment system (CDW), duckweed treatment system (DW) and water hyacinth treatment system (WH) were developed to treat rural wastewater in Dianchi Lake basin. Results showed that adding microbial carrier did not affect the growth and biomass components of duckweed. The following features were discovered in the CDW system. First, the NO₃^--N and TN removal efficiencies were the highest among three systems, reaching 80.02% and 56.42%, respectively. Secondly, Illumina sequencing revealed the highest microbial diversity. Thirdly, a distinct succession of microbial community was observed. Rhodobacter, Bacteria vadinCA02, C39 and Flavobacterium dominated in the start-up stage, and contributed to biofilm formation and pollutants degradation. Acinetobacter, Planctomyces and Methylibium significantly increased in the stable stage, and contributed to nitrogen removal. Finally, highly abundant plant growth-promoting bacteria were found. Comprehensive analysis indicated that the functional bacteria community was closely related to the pollutant removals, plant growth and system operating status.

Microbial nitrate removal efficiency in groundwater polluted from agricultural activities with hybrid cork treatment wetlands

Agricultural practices have raised the level of nutrients reaching aquifers. In Europe, nitrate pollution is considered as one of the main threats for the quality of groundwater in agricultural areas. Treatment wetlands (TWs), also known as Constructed Wetlands, are used for groundwater treatment in areas with an important concentration of nitrogen compounds; total nitrogen removal depends on the type and operation scheme. Cork by-product from the industry has shown clear adsorbent properties to remove organic pollutants. The work is focused on the characterization of microbial communities involved in the nitrate‑nitrogen removal process in groundwater polluted from agricultural activities. The experimental design allowed the comparison of nitrate removal efficiency depending on the filter media material, cork by-product or gravel, used in two hybrid TWs (a vertical flow cell followed by a horizontal subsurface flow cell), installed in areas close to two irrigated agricultural plots at the Lleida plain area (Spain). Both physicochemical and microbial results were consistent and confirm the nitrate removal efficiency using cork as a filter media. A significant (p = 0.0025) higher removal in Bellvís TW using cork compared with the Vilanova de la Barca gravel system was observed, achieving a removal rate from 80 to 99% compared to the 5-46%, respectively. Regarding the community composition of the two different TWs, microorganisms were mainly related to the phylum Proteobacteria, and included members found to be key players in the nitrogen cycle, such as ammonia and nitrite oxidizers, as well as denitrifiers. Also, the group Bacteroidetes turns to be another abundant phylum from our bacterial dataset, whose members are suggested to be strongly involved in denitrification processes. Some groups showed to prevail depending on the type of media (cork or gravel); Firmicutes and Delta and Epsilonproteobacteria had a significant higher abundance in the TW with cork, while Acidobacteria and Planctomyces were prevalent in gravel. Therefore, cork could be an alternative material used by treatment wetlands to minimize the impact in the environment caused by nitrogen pollution in groundwater bodies.

Recycling organic residues in agriculture impacts soil-borne microbial community structure, function and N2O emissions

Recycling residues is a sustainable alternative to improve soil structure and increase the stock of nutrients. However, information about the magnitude and duration of disturbances caused by crop and industrial wastes on soil microbial community structure and function is still scarce. The objective of this study was to investigate how added residues from industry and crops together with nitrogen (N) fertiliser affect the microbial community structure and function, and nitrous oxide (N₂O) emissions. The experimental sugarcane field had the following treatments: (I) control with nitrogen, phosphorus, and potassium (NPK), (II) sugarcane straw with NPK, (III) vinasse (by-product of ethanol industry) with NP, and (IV) vinasse plus sugarcane straw with NP. Soil samples were collected on days 1, 3, 6, 11, 24 and 46 of the experiment for DNA extraction and metagenome sequencing. N₂O emissions were also measured. Treatments with straw and vinasse residues induced changes in soil microbial composition and potential functions. The change in the microbial community was highest in the treatments with straw addition with functions related to decomposition of different ranges of C-compounds overrepresented while in vinasse treatment, the functions related to spore-producing microorganisms were overrepresented. Furthermore, all additional residues increased microorganisms related to the nitrogen metabolism and vinasse with straw had a synergetic effect on the highest N₂O emissions. The results highlight the importance of residues and fertiliser management in sustainable agriculture.

Aerobic granules cultivated with simultaneous feeding/draw mode and low-strength wastewater: Performance and bacterial community analysis

Sequence batch reactors (SBR) with simultaneous feeding/draw mode and low-strength wastewater were used for the cultivation of aerobic granules, and analysis of bacterial community diversity were conducted. Results revealed that the ratio of chemical oxygen demand/total nitrogen removal amount for R1 with real wastewater and R2 with synthetic wastewater decreased from 9.9 to 8.7 and, 29.9 to 21.1, respectively, when volumetric exchange ratio (VER) decreased from 90% (stage I) to 50% (stage II), indicating that organic matter in real and low-strength wastewater was fully utilized with lower VER by denitrifying bacteria. Relative abundances of the genus Dechloromonas, Pseudomonas, Bacillus in R1, which are responsible for denitrifying phosphorus removal, were much higher than that in R2, accounting for the high efficiency of nitrogen and phosphorus removal from real wastewater with low influent C/N ratio of 3.6 on average. These results provide useful information for improving wastewater treatment efficiency in the future.

Bioreactors for oil sands process-affected water (OSPW) treatment: A critical review

Canada has the world's largest oil sands reservoirs. Surface mining and subsequent caustic hot water extraction of bitumen lead to an enormous quantity of tailings (volumetric ratio bitumen:water=9:1). Due to the zero-discharge approach and the persistency of the complex matrix, oil producers are storing oil sands tailings in vast ponds in Northern Alberta. Oil sands tailings are comprised of sand, clay and process-affected water (OSPW). OSPW contains an extremely complex matrix of organic contaminants (e.g., naphthenic acids (NAs), residual bitumen, and polycyclic aromatic hydrocarbons (PAHs)), which has proven to be toxic to a variety of aquatic species. Biodegradation, among a variety of examined methods, is believed to be one of the most cost effective and practical to treat OSPW. A number of studies have been published on the removal of oil sands related contaminants using biodegradation-based practices. This review focuses on the treatment of OSPW using various bioreactors, comparing bioreactor configurations, operating conditions, performance evaluation and microbial community dynamics. Effort is made to identify the governing biotic and abiotic factors in engineered biological systems receiving OSPW. Generally, biofilms and elevated suspended biomass are beneficial to the resilience and degradation performance of a bioreactor. The review therefore suggests that a hybridization of biofilms and membrane technology (to ensure higher suspended microbial biomass) is a more promising option to remove OSPW organic constituents.

Dynamics of microbial community structure and nutrient removal from an innovative side-stream enhanced biological phosphorus removal process

Biological phosphorous (P) and nitrogen (N) removal from municipal wastewater was studied using an innovative anoxic-aerobic-anaerobic side-stream treatment system. The impact of influent water quality including chemical oxygen demand (COD), ammonium and orthophosphate concentrations on the reactor performance was evaluated. The results showed the system was very effective at removing both COD (>88%) and NH₄⁺-N (>96%) despite varying influent concentrations of COD, NH₄⁺-N, and total PO₄^3--P. In contrast, it was found that the removal of P was sensitive to influent NH₄⁺-N and PO₄^3--P concentrations. The maximum PO₄^3--P removal of 79% was achieved with the lowest influent NH₄⁺-N and PO₄^3--P concentration. Quantitative PCR (qPCR) assays showed a high abundance and diversity of phosphate accumulating organisms (PAO), nitrifiers and denitrifiers. The MiSeq microbial community structure analysis showed that the Proteobacteria (especially β-Proteobacteria, and γ-Proteobacteria) were the dominant in all reactors. Further analysis of the bacteria indicated the presence of diverse PAO genera including Candidatus Accumulibacter phosphatis, Tetrasphaera, and Rhodocyclus, and the denitrifying PAO (DPAO) genus Dechloromonas. Interestingly, no glycogen accumulating organisms (GAOs) were detected in any of the reactors, suggesting the advantage of proposed process in term of PAO selection for enhanced P removal compared with conventional main-stream processes.

Unravelling biocomplexity of electroactive biofilms for producing hydrogen from biomass

Leveraging nature's biocomplexity for solving human problems requires better understanding of the syntrophic relationships in engineered microbiomes developed in bioreactor systems. Understanding the interactions between microbial players within the community will be key to enhancing conversion and production rates from biomass streams. Here we investigate a bioelectrochemical system employing an enriched microbial consortium for conversion of a switchgrass-derived bio-oil aqueous phase (BOAP) into hydrogen via microbial electrolysis (MEC). MECs offer the potential to produce hydrogen in an integrated fashion in biorefinery platforms and as a means of energy storage through decentralized production to supply hydrogen to fuelling stations, as the world strives to move towards cleaner fuels and electricity-mediated transportation. A unique approach combining differential substrate and redox conditions revealed efficient but rate-limiting fermentation of the compounds within BOAP by the anode microbial community through a division of labour strategy combined with multiple levels of syntrophy. Despite the fermentation limitation, the adapted abilities of the microbial community resulted in a high hydrogen productivity of 9.35 L per L-day. Using pure acetic acid as the substrate instead of the biomass-derived stream resulted in a three-fold improvement in productivity. This high rate of exoelectrogenesis signifies the potential commercial feasibility of MEC technology for integration in biorefineries.

A comparative study of microbial dynamics and phosphorus removal for a two side-stream wastewater treatment processes

A side-stream process with anoxic/aerobic tanks was designed as a denitrifying enhanced biological phosphorus removal process for wastewater treatment as compared to a modified side-stream process using contact/stabilization tanks.

The effect of malathion on the activity, performance, and microbial ecology of activated sludge

This study evaluated the effect of a VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) surrogate (malathion) on the activity, performance, and ecology of activated sludge bioreactors. In the presence of malathion, the maximum observed respiration rates varied between 43 and 53 μg/O2 min, generally similar to the 49 μg O2/min rates observed in controls. Malathion did not alter the respiration ratio of O2 consumed-to-CO2 produced nor did it impact the shape of the oxygen consumption curves during respirometry. Shorter term (12 h) batch tests showed that both chemical oxygen demand (COD) and ammonia removal were not negatively impacted by the presence of 0.1-3 mg/L malathion. Longer term continuous addition (i.e. 40 days) of 0.1 mg/L of malathion also had no effect on COD and ammonia removal. In contrast to shorter term exposures, longer term continuous addition of 3 mg/L of malathion negatively impacted both COD and nitrogen removal and was associated with shifts in the abundance of species that are common to activated sludge. These results illustrate the impact that chemicals like malathion may have on COD removal, and nitrification, as well as the robustness of activated sludge microbial communities.

Community dynamics of denitrifying bacteria in full-scale wastewater treatment plants

Effective and stable nitrogen removal from wastewater requires abundant and active denitrifying populations. In this study, a one-year investigation of the population dynamics of phylogenetic groups known to harbor nitrate reducers was conducted in three municipal wastewater treatment plants (WWTPs). The bacterial community composition was determined by amplicon sequencing of the 16S rRNA gene, and putative nitrate reducers were identified by sequencing narG and napA genes. Fluorescence in situ hybridization with oligonucleotide probes targeting known nitrate reducers in wastewater revealed that certain bacteria predominated in the WWTPs: Curvibacter-related bacteria, Comamonadaceae, Azoarcus, Thauera, Dechloromonas, and Candidatus Accumulibacter within Rhodocyclaceae. The data showed high diversity in the nitrate-reducing community and a large degree of redundancy, with a relatively stable core group of bacteria in each plant that ensured small yearly variation in nitrate reduction rates.

Microbial communities in riparian soils of a settling pond for mine drainage treatment

Mine drainage leads to serious contamination of soil. To assess the effects of mine drainage on microbial communities in riparian soils, we used an Illumina MiSeq platform to explore the soil microbial composition and diversity along a settling pond used for mine drainage treatment. Non-metric multidimensional scaling analysis showed that the microbial communities differed significantly among the four sampling zones (influent, upstream, downstream and effluent), but not seasonally. Constrained analysis of principal coordinates indicated heavy metals (zinc, lead and copper), total sulphur, pH and available potassium significantly influenced the microbial community compositions. Heavy metals were the key determinants separating the influent zone from the other three zones. Lower diversity indices were observed in the influent zone. However, more potential indicator species, related to sulphur and organic matter metabolism were found there, such as the sulphur-oxidizing genera Acidiferrobacter, Thermithiobacillus, Limnobacter, Thioprofundum and Thiovirga, and the sulphur-reducing genera Desulfotomaculum and Desulfobulbus; the organic matter degrading genera, Porphyrobacter and Paucimonas, were also identified. The results indicated that more microorganisms related to sulphur- and carbon-cycles may exist in soils heavily contaminated by mine drainage.

Multiple paths of electron flow to current in microbial electrolysis cells fed with low and high concentrations of propionate

Microbial electrolysis cells (MECs) provide a viable approach for bioenergy generation from fermentable substrates such as propionate. However, the paths of electron flow during propionate oxidation in the anode of MECs are unknown. Here, the paths of electron flow involved in propionate oxidation in the anode of two-chambered MECs were examined at low (4.5 mM) and high (36 mM) propionate concentrations. Electron mass balances and microbial community analysis revealed that multiple paths of electron flow (via acetate/H2 or acetate/formate) to current could occur simultaneously during propionate oxidation regardless of the concentration tested. Current (57-96 %) was the largest electron sink and methane (0-2.3 %) production was relatively unimportant at both concentrations based on electron balances. At a low propionate concentration, reactors supplemented with 2-bromoethanesulfonate had slightly higher coulombic efficiencies than reactors lacking this methanogenesis inhibitor. However, an opposite trend was observed at high propionate concentration, where reactors supplemented with 2-bromoethanesulfonate had a lower coulombic efficiency and there was a greater percentage of electron loss (23.5 %) to undefined sinks compared to reactors without 2-bromoethanesulfonate (11.2 %). Propionate removal efficiencies were 98 % (low propionate concentration) and 78 % (high propionate concentration). Analysis of 16S rRNA gene pyrosequencing revealed the dominance of sequences most similar to Geobacter sulfurreducens PCA and G. sulfurreducens subsp. ethanolicus. Collectively, these results provide new insights on the paths of electron flow during propionate oxidation in the anode of MECs fed with low and high propionate concentrations.

Nitrification and denitrifying phosphorus removal in an upright continuous flow reactor

Simultaneous nitrification and denitrifying phosphorus removal was achieved in a single-sludge continuous flow bioreactor. The upright bioreactor was aligned with a biomass fermenter (BF) and operated continuously for over 350 days. This study revealed that unknown bacteria of the Saprospiraceae class may have been responsible for the successful nutrient removal in this bioreactor. The successive anoxic-aerobic stages of the bioreactor with upright alignment along with a 60 L BF created a unique ecosystem for the growth of nitrifier, denitrifiers, phosphorus accumulating organisms and denitrifying phosphorus accumulating organisms. Furthermore, total nitrogen to chemical oxygen demand (COD) ratio and total phosphorus to COD ratio of 0.6 and 0.034, respectively, confirmed the comparative advantages of this advanced nutrient removal process relative to both sequencing batch reactors and activated sludge processes. The process yielded 95% nitrogen removal and over 90% phosphorus removal efficiencies.

An 'omics' approach towards the characterisation of laboratory scale anaerobic digesters treating municipal sewage sludge

In this study, laboratory scale digesters were operated to simulate potential shocks to the Anaerobic Digestion (AD) process at a 350 ML/day wastewater treatment plant. The shocks included high (42 °C) and low (32 °C) temperature (either side of mesophilic 37 °C) and a 20% loading of fats, oil and grease (FOG; 20% w:v). These variables were explored at two sludge retention times (12 and 20 days) and two organic loading rates (2.0 and 2.5 kgTS/m(3)day OLR). Metagenomic and metabolomic approaches were then used to characterise the impact of operational shocks in regard to temperature and FOG addition, as determined through monitoring of biogas production, the microbial profile and their metabolism. Results showed that AD performance was not greatly affected by temperature shocks, with the biggest impact being a reduction in biogas production at 42 °C that persisted for 32 ± 1 days. The average biogas production across all digesters at the completion of the experiment was 264.1 ± 76.5 mL/day, with FOG addition observed to significantly promote biogas production (+87.8 mL/day). Metagenomic and metabolomic analyses of the digesters indicated that methanogens and methane oxidising bacteria (MOB) were low in relative abundance, and that the ratio of oxidising bacteria (methane, sulphide and sulphate) with respect to sulphate reducing bacteria (SRB) had a noticeable influence on biogas production. Furthermore, increased biogas production correlated with an increase in short chain fatty acids, a product of the addition of 20% FOG. This work demonstrates the application of metagenomics and metabolomics to characterise the microbiota and their metabolism in AD digesters, providing insight to the resilience of crucial microbial populations when exposed to operational shocks.

Bacterial community responses to a gradient of alkaline mountaintop mine drainage in Central Appalachian streams

Microbial community composition and diversity change along chemical gradients, leading to the expectation that microbial community information might provide new gradient characterizations. Here we examine stream bacteria composition and diversity along a strong chemical gradient in Central Appalachian streams. Coal mining in the region generates alkaline mine drainage (AlkMD), causing dramatic increases in conductivity, alkalinity, sulfate and metals sufficient to degrade stream macrobiota communities throughout the ecoregion. In this study, we examined the relationship between water and biofilm chemistry and biofilm bacteria taxonomic composition in streams where active and reclaimed surface coal mines occupied 0-96% of watershed surface area. We incubated wood veneers in each stream site for 4 months to develop biofilms on similar substrates. We sampled water chemistry at the time of deployment and collection, and after 1 month. Following incubation, we collected biofilms for microbial and chemical characterization. Microbial composition was determined by pyrosequencing 16S rRNA amplicons. Biofilm subsamples were analyzed by inductively coupled plasma mass spectrometry to determine metal concentrations. Our results show that microbial community composition differed significantly between AlkMD-exposed and AlkMD-unexposed sites, and that compositional dissimilarity increased with AlkMD loading. Diversity was not correlated with pH or extent of upstream mining, but instead correlated with biofilm concentrations of Cd, Mn, Zn and Ni. Within mined sites, the extent of upstream mining was negatively correlated with taxonomic richness. Despite major compositional shifts, functional capacity predicted with PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) correlated with mining in only 3 of 43 level-2 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology groups.

Next-generation pyrosequencing analysis of microbial biofilm communities on granular activated carbon in treatment of oil sands process-affected water

The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum Proteobacteria was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of Alpha- and Gammaproteobacteria sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely, Burkholderiales, Pseudomonadales, Bdellovibrionales, and Sphingomonadales, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>10(9) gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O3/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds.

Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients

The significance of salinity in shaping bacterial communities dwelling in estuarine areas has been well documented. However, the influences of other environmental factors such as dissolved oxygen and nutrients in determining distribution patterns of both individual taxa and bacterial communities inhabited local estuarine regions remain elusive. Here, bacterioplankton community structures of surface and bottom waters from eight sites along the Pearl Estuary were characterized with 16S rRNA gene pyrosequencing. The results showed significant differences of bacterioplankton community between freshwater and saltwater sites, and further between surface and bottom waters of saltwater sites. Synechococcus dominated the surface water of saltwater sites while Oceanospirillales, SAR11 and SAR406 were prevalent in the bottom water. Betaproteobacteria was abundant in freshwater sites, with no significant difference between water layers. Occurrence of phylogenetic shifts in taxa affiliated to the same clade was also detected. Dissolved oxygen explained most of the bacterial community variation in the redundancy analysis targeting only freshwater sites, whereas nutrients and salinity explained most of the variation across all samples in the Pearl Estuary. Methylophilales (mainly PE2 clade) was positively correlated to dissolved oxygen, whereas Rhodocyclales (mainly R.12up clade) was negatively correlated. Moreover, high nutrient inputs to the freshwater area of the Pearl Estuary have shifted the bacterial communities toward copiotrophic groups, such as Sphingomonadales. The present study demonstrated that the overall nutrients and freshwater hypoxia play important roles in determining bacterioplankton compositions and provided insights into the potential ecological roles of specific taxa in estuarine environments.

Novel Mass Bio System (MBS) and its potential application in advanced treatment of coal gasification wastewater

A Novel Mass Bio System (MBS), a suspended biologically activated carbon granular carrier cubic particle with 2–5 mm side length and 1.02–1.08 specific gravity was developed for advanced treatment of coal gasification wastewater.

Bacterial communities in batch and continuous-flow wetlands treating the herbicide S-metolachlor

Knowledge of wetland bacterial communities in the context of pesticide contamination and hydrological regime is scarce. We investigated the bacterial composition in constructed wetlands receiving Mercantor Gold(®) contaminated water (960 g L(-1) of the herbicide S-metolachlor, >80% of the S-enantiomer) operated under continuous-flow or batch modes to evaluate the impact of the hydraulic regime. In the continuous-flow wetland, S-metolachlor mass removal was >40%, whereas in the batch wetland, almost complete removal of S-metolachlor (93-97%) was observed. Detection of ethanesulfonic and oxanilic acid degradation products further indicated S-metolachlor biodegradation in the two wetlands. The dominant bacterial populations were characterised by terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing. The bacterial profiles evolved during the first 35 days of the experiment, starting from a composition similar to that of inlet water, with the use of nitrate and to a lesser extent sulphate and manganese as terminal electron acceptors for microbial metabolism. Proteobacteria were the most abundant phylum, with Beta-, Alpha- and Gammaproteobacteria representing 26%, 19% and 17% respectively of total bacterial abundance. Bacterial composition in wetland water changed gradually over time in continuous-flow wetland and more abruptly in the batch wetland. Differences in overall bacterial water structure in the two systems were modest but significant (p=0.008), and S-metolachlor, nitrate, and total inorganic carbon concentrations correlated with changes in the bacterial profiles. Together, the results highlight that bacterial composition profiles and their dynamics may be used as bioindicators of herbicide exposure and hydraulic disturbances in wetland systems.

Advanced analytical mass spectrometric techniques and bioassays to characterize untreated and ozonated oil sands process-affected water

Oil sands process-affected water (OSPW) is a toxic and poorly biodegradable mixture of sand, silt, heavy metals, and organics. In this study, qualitative and quantitative comparisons of naphthenic acids (NAs) were done using ultraperformance liquid chromatography time-of-flight mass spectrometry (UPLC TOF-MS), Fourier transform ion cyclotron resonance (FT-ICR) MS, and ion mobility spectrometry (IMS). The unique combination of these analyses allowed for the determination and correlation of NAs, oxidized NAs, and heteroatom (sulfur or nitrogen) NAs. Despite its lower resolution, UPLC-TOF MS was shown to offer a comparable level of reliability and precision as the high resolution FT-ICR MS. Additionally, the impacts of ozonation (35 mg/L utilized ozone dose) and subsequent NAs degradation on OSPW toxicity were assessed via a collection of organisms and toxicity end points using Vibrio fischeri (nonspecific), specific fish macrophage antimicrobial responses, and fish olfactory responses. Fish macrophages exposed to ozonated OSPW for 1 week showed higher production of reactive oxygen and nitrogen intermediates; however, after 12 weeks the responses were reduced significantly. Fish olfactory tests suggested that OSPW interfered with their perception of odorants. Current results indicate that the quantification of NAs species, using novel analytical methods, can be combined with various toxicity methods to assess the efficiency of OSPW treatment processes.

The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems

It is well known that atmospheric concentrations of carbon dioxide (CO2) (and other greenhouse gases) have increased markedly as a result of human activity since the industrial revolution. It is perhaps less appreciated that natural and managed soils are an important source and sink for atmospheric CO2 and that, primarily as a result of the activities of soil microorganisms, there is a soil-derived respiratory flux of CO2 to the atmosphere that overshadows by tenfold the annual CO2 flux from fossil fuel emissions. Therefore small changes in the soil carbon cycle could have large impacts on atmospheric CO2 concentrations. Here we discuss the role of soil microbes in the global carbon cycle and review the main methods that have been used to identify the microorganisms responsible for the processing of plant photosynthetic carbon inputs to soil. We discuss whether application of these techniques can provide the information required to underpin the management of agro-ecosystems for carbon sequestration and increased agricultural sustainability. We conclude that, although crucial in enabling the identification of plant-derived carbon-utilising microbes, current technologies lack the high-throughput ability to quantitatively apportion carbon use by phylogentic groups and its use efficiency and destination within the microbial metabolome. It is this information that is required to inform rational manipulation of the plant-soil system to favour organisms or physiologies most important for promoting soil carbon storage in agricultural soil.

Assessment of bacterial and structural dynamics in aerobic granular biofilms

Aerobic granular sludge (AGS) is based on self-granulated flocs forming mobile biofilms with a gel-like consistence. Bacterial and structural dynamics from flocs to granules were followed in anaerobic-aerobic sequencing batch reactors (SBR) fed with synthetic wastewater, namely a bubble column (BC-SBR) operated under wash-out conditions for fast granulation, and two stirred-tank enrichments of Accumulibacter (PAO-SBR) and Competibacter (GAO-SBR) operated at steady-state. In the BC-SBR, granules formed within 2 weeks by swelling of Zoogloea colonies around flocs, developing subsequently smooth zoogloeal biofilms. However, Zoogloea predominance (37-79%) led to deteriorated nutrient removal during the first months of reactor operation. Upon maturation, improved nitrification (80-100%), nitrogen removal (43-83%), and high but unstable dephosphatation (75-100%) were obtained. Proliferation of dense clusters of nitrifiers, Accumulibacter, and Competibacter from granule cores outwards resulted in heterogeneous bioaggregates, inside which only low abundance Zoogloea (<5%) were detected in biofilm interstices. The presence of different extracellular glycoconjugates detected by fluorescence lectin-binding analysis showed the complex nature of the intracellular matrix of these granules. In the PAO-SBR, granulation occurred within two months with abundant and active Accumulibacter populations (56 ± 10%) that were selected under full anaerobic uptake of volatile fatty acids and that aggregated as dense clusters within heterogeneous granules. Flocs self-granulated in the GAO-SBR after 480 days during a period of over-aeration caused by biofilm growth on the oxygen sensor. Granules were dominated by heterogeneous clusters of Competibacter (37 ± 11%). Zoogloea were never abundant in biomass of both PAO- and GAO-SBRs. This study showed that Zoogloea, Accumulibacter, and Competibacter affiliates can form granules, and that the granulation mechanisms rely on the dominant population involved.

Investigation of the FeFe-hydrogenase gene diversity combined with phylogenetic microbial community analysis of an anaerobic domestic sewage sludge

Biological hydrogen production through the anaerobic digestion is an environmental friendly alternative for satisfying future hydrogen demands. Microorganisms residing into waste water treatment plants are far from being exhaustively characterized and surveys on hydrogen production through FeFe-hydrogenase in such ecosystems are scarce. This study combined the analysis of 16S rRNA and [FeFe]-hydrogenase (hydA) genes with statistical tools to estimate richness and diversity of the microbial community of a domestic sewage treatment plant at the phylogenetic and functional levels. Archaeal groups were represented by 69 % of sequences assigned to Methanosarcinales and the remaining belonged to Methanomicrobiales. Within the bacterial library, 136 operational taxonomic units (OTUs) were distributed into 9 phyla, being 86 OTUs related to uncultivated bacteria. From these, 25 OTUs represented potential novel taxa within Synergistetes. Proteobacteria was the most predominant (36 % of the OTUs) and diversified phylogenetic group in the bacterial library, most of them assigned to the class Betaproteobacteria. Twenty-two putative hydA sequences were recovered into four distinct clusters and most of them were more closely related to each other than with sequences retrieved from databases, indicating they are hitherto undetected [Fe-Fe]-hydrogenase gene sequences. The richness estimates revealed that the number of sampled sequences was enough for full coverage of the archaeal diversity but not sufficient to cover both bacterial and hydA gene diversities. The results confirmed a great richness and diversity of bacterial and hydA sequences retrieved from the sewage sludge sample, suggesting such environment as a potential reservoir of new hydrogenase genes for biotechnological exploration.

Bacterial Selection during the Formation of Early-Stage Aerobic Granules in Wastewater Treatment Systems Operated Under Wash-Out Dynamics

Aerobic granular sludge is attractive for high-rate biological wastewater treatment. Biomass wash-out conditions stimulate the formation of aerobic granules. Deteriorated performances in biomass settling and nutrient removal during start-up have however often been reported. The effect of wash-out dynamics was investigated on bacterial selection, biomass settling behavior, and metabolic activities during the formation of early-stage granules from activated sludge of two wastewater treatment plants (WWTP) over start-up periods of maximum 60 days. Five bubble-column sequencing batch reactors were operated with feast-famine regimes consisting of rapid pulse or slow anaerobic feeding followed by aerobic starvation. Slow-settling fluffy granules were formed when an insufficient superficial air velocity (SAV; 1.8 cm s(-1)) was applied, when the inoculation sludge was taken from a WWTP removing organic matter only, or when reactors were operated at 30°C. Fast-settling dense granules were obtained with 4.0 cm s(-1) SAV, or when the inoculation sludge was taken from a WWTP removing all nutrients biologically. However, only carbon was aerobically removed during start-up. Fluffy granules and dense granules were displaying distinct predominant phylotypes, namely filamentous Burkholderiales affiliates and Zoogloea relatives, respectively. The latter were predominant in dense granules independently from the feeding regime. A combination of insufficient solid retention time and of leakage of acetate into the aeration phase during intensive biomass wash-out was the cause for the proliferation of Zoogloea spp. in dense granules, and for the deterioration of BNR performances. It is however not certain that Zoogloea-like organisms are essential in granule formation. Optimal operation conditions should be elucidated for maintaining a balance between organisms with granulation propensity and nutrient removing organisms in order to form granules with BNR activities in short start-up periods.

Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics

Application of high-density microarrays to the diagnostic analysis of microbial communities is challenged by the optimization of oligonucleotide probe sensitivity and specificity, as it is generally unfeasible to experimentally test thousands of probes. This study investigated the adjustment of hybridization stringency using formamide with the idea that sensitivity and specificity can be optimized during probe design if the hybridization efficiency of oligonucleotides with target and non-target molecules can be predicted as a function of formamide concentration. Sigmoidal denaturation profiles were obtained using fluorescently labeled and fragmented 16S rRNA gene amplicon of Escherichia coli as the target with increasing concentrations of formamide in the hybridization buffer. A linear free energy model (LFEM) was developed and microarray-specific nearest neighbor rules were derived. The model simulated formamide melting with a denaturant m-value that increased hybridization free energy (ΔG°) by 0.173 kcal/mol per percent of formamide added (v/v). Using the LFEM and specific probe sets, free energy rules were systematically established to predict the stability of single and double mismatches, including bulged and tandem mismatches. The absolute error in predicting the position of experimental denaturation profiles was less than 5% formamide for more than 90 percent of probes, enabling a practical level of accuracy in probe design. The potential of the modeling approach for probe design and optimization is demonstrated using a dataset including the 16S rRNA gene of Rhodobacter sphaeroides as an additional target molecule. The LFEM and thermodynamic databases were incorporated into a computational tool (ProbeMelt) that is freely available at http://DECIPHER.cee.wisc.edu.

Microbial communities involved in enhanced biological phosphorus removal from wastewater--a model system in environmental biotechnology

Enhanced biological phosphorus removal (EBPR) is one of the most advanced and complicated wastewater treatment processes applied today, and it is becoming increasingly popular worldwide as a sustainable way to remove and potentially reuse P. It is carried out by complex microbial communities consisting primarily of uncultured microorganisms. The EBPR process is a well-studied system with clearly defined boundaries which makes it very suitable as a model ecosystem in microbial ecology. Of particular importance are the transformations of C, N, and P, the solid-liquid separation properties and the functional and structural stability. A range of modern molecular methods has been used to study these communities in great detail including single cell microbiology, various -omics methods, flux analyses, and modeling making this one of the best studied microbial ecosystems so far. Recently, an EBPR core microbiome has been described and we present in this article some highlights and show how this complex microbial community can be used as model ecosystem in environmental biotechnology.

Shotgun isotope array for rapid, substrate-specific detection of microorganisms in a microbial community

The shotgun isotope array method has been proposed to be an effective new tool for use in substrate-specific microbe exploration without any prior knowledge of the community composition. Proof of concept was demonstrated by detection of acetate-degrading microorganisms in activated sludge and further verified by independent stable isotope probing (SIP).

Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion

BACKGROUND

The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained.

METHODOLOGY/PRINCIPAL FINDINGS

This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias.

CONCLUSIONS

Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization.

Comparison of partial and full nitrification processes applied for treating high-strength nitrogen wastewaters: microbial ecology through nitrous oxide production

The goal of this study was to compare the microbial ecology, gene expression, biokinetics, and N2O emissions from a lab-scale bioreactor operated sequentially in full-nitrification and partial-nitrification modes. Based on sequencing of 16S rRNA and ammonia monooxygenase subunit A (amoA) genes, ammonia oxidizing bacteria (AOB) populations during full- and partial-nitrification modes were distinct from one another. The concentrations of AOB (XAOB) and their respiration rates during full- and partial-nitrification modes were statistically similar, whereas the concentrations of nitrite oxidizing bacteria (XNOB) and their respiration rates declined significantly after the switch from full- to partial-nitrification. The transition from full-nitrification to partial nitrification resulted in a protracted transient spike of nitrous oxide (N2O) and nitric oxide (NO) emissions, which later stabilized. The trends in N2O and NO emissions correlated well with trends in the expression of nirK and norB genes that code for the production of these gases in AOB. Both the transient and stabilized N2O and NO emissions during partial nitrification were statistically higher than those during steady-state full-nitrification. Based on these results, partial nitrification strategies for biological nitrogen removal, although attractive for their reduced operating costs and energy demand, may need to be optimized against the higher carbon foot-print attributed to their N2O emissions.

Molecular characterization of activated sludge from a seawater-processing wastewater treatment plant

The prokaryotic community composition of activated sludge from a seawater‐processing wastewater treatment plant (Almeria, Spain) was investigated by using the rRNA approach, combining different molecular techniques such as denaturing gradient gel electrophoresis (DGGE), clone libraries and in situ hybridization (FISH and CARD‐FISH). Most of the sequences retrieved in the DGGE and the clone libraries were similar to uncultured members of different phyla. The most abundant sequence recovered from Bacteria in the clone library corresponded to a bacterium from the Deinococcus–Thermus cluster (almost 77% of the clones), and the library included members from other groups such as the Alpha, Gamma and Delta subclasses of Proteobacteria, the Bacteroidetes and Firmicutes. Concerning the archaeal clone library, we basically found sequences related to different orders of methanogenic Archaea, in correspondence with the recovered DGGE bands. Enumeration of DAPI (4′,6‐diamidino‐2‐phenylindole) stained cells from two different activated sludge samples after a mechanical flocculation disruption revealed a mean cell count of 1.6 × 10⁹ ml⁻¹. Around 94% of DAPI counts (mean value from both samples) hybridized with a Bacteria specific probe. Alphaproteobacteria were the dominant bacterial group (36% of DAPI counts), while Beta‐, Delta‐ and Gammaproteobacteria, Bacteroidetes, Actinobacteria and Firmicutes contributed to lower proportions (between 0.5–5.7% of DAPI counts). Archaea accounted only for 6% of DAPI counts. In addition, specific primers for amplification of the amoA (ammonia monooxygenase) gene were used to detect the presence of Beta, Gamma and archaeal nitrifiers, yielding positive amplifications only for Betaproteobacteria. This, together with negative in situ hybridizations with probes for well‐known nitrifiying bacteria, suggests that nitrification is performed by still undetected microorganisms. In summary, the combination of the three approaches provided different and complementary pictures of the real assemblage composition and allowed to get closer to the main microorganisms involved in key processes of seawater‐processing activated sludge.