A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria

Sealing solid agar in serum bottles for rapid isolation and long-term preservation of chemoautotrophic ammonia-oxidizing bacteria

Ammonia-oxidizing bacteria (AOB) are ubiquitous on the earth and have broad applications in bioremediation. However, the number of their species with standing in nomenclature and deposited in Microbial Culture Collections still remains low. Moreover, only a few novel species have been reported over the last decades. In this study, we sealed agar in serum bottles to develop a kind of solid agar plate with the oxygen concentration in the headspace maintained at low levels. By using these plates, eight AOB isolates including two novel species were obtained. When AOB cells were grown on the sealed solid agar plates, the time to form visible colonies was largely reduced and the maximum diameter of colonies reached 2 mm, which makes the process of AOB isolation rapid and efficient. Based on five AOB isolates, the headspace oxygen concentration had a significant influence on AOB growth either on solid plate or in liquid culture. Especially, when grown under 21 % O2, the number of colonies formed on solid agar plates was very low and sometimes no visible colony formed. Besides the application on AOB isolation, the sealed solid agar plate was also effective for the enumeration and preservation of AOB cells. When preserved under room temperature for more than ten months, the AOB colonies on the plate could still be recovered. This method provides a feasible way to isolate more novel AOB species from the environment and deposit more species in Microbial Culture Collections.

Temperature-resilient superior performances by coupling partial nitritation/anammox and iron-based denitrification with granular formation

Partial nitritation-anammox (PN/A), an energy-neutral process, is widely employed in the treatment of nitrogen-rich wastewater. However, the intrinsic nitrate accumulation limits the total nitrogen (TN) removal, and the practical application of PN/A continues to face a significant challenge at low temperatures (<15 °C). Here, an integrated partial nitritation-anammox and iron-based denitrification (PNAID) system was developed to address the concern. Two up-flow bioreactors were set up and operated for 400 days, with one as the control group and the other as the experiment group with the addition of Fe0. In comparison to the control group, the experiment group with the Fe0 supplement showed better nitrogen removal during the entire course of the experiment at different temperature levels. Specifically, the TN removal efficiency of the control group decreased from 82.9 % to 53.9 % when the temperature decreased from 30 to 12 °C, while in stark contrast, the experiment group consistently achieved 80 % of TN removal in the same condition. Apart from the enhanced nitrogen removal, the experiment group also exhibited better phosphorus removal (10.6 % versus 74.1 %) and organics removal (49.5 % versus 65.1 %). The enhanced and resilient nutrient removal performance of the proposed integrated process under low temperatures appeared to be attributed to the compact structure of granules and the increased microbial metabolism with Fe0 supplement, elucidated by a comprehensive analysis including microbial-specific activity, apparent activation energy, characteristics of granular sludge, and metagenomic sequencing. These results clearly confirmed that Fe0 supplement not only improved nitrogen removal of PN/A process, but also conferred a certain degree of robustness to the system in the face of temperature fluctuations.

Nitrification-denitrification co-metabolism in an algal-bacterial aggregates system for simultaneous pyridine and nitrogen removal

Photosynthetic oxygenation in algal-bacterial symbiotic (ABS) system was mainly concerned to enhance contaminant biodegradation by developing an aerobic environment, while the role of nitrification-denitrification involved is often neglected. In this study, an algal-bacterial aggregates (ABA) system was developed with algae and activated sludge (PBR-1) to achieve simultaneous pyridine and nitrogen removal. In PBR-1, as high as 150 mg·L-1 pyridine could be completely removed at hydraulic residence time of 48 h. Besides, total nitrogen (TN) removal efficiency could be maintained above 80%. Nitrification-denitrification was verified as the crucial process for nitrogen removal, accounting for 79.3% of TN removal at 180 μmol·m-2·s-1. Moreover, simultaneous pyridine and nitrogen removal was enhanced through nitrification-denitrification co-metabolism in the ABA system. Integrated bioprocesses in PBR-1 including photosynthesis, pyridine biodegradation, carbon and nitrogen assimilation, and nitrification-denitrification, were revealed at metabolic and transcriptional levels. Fluorescence in situ hybridization analysis indicated that algae and aerobic species were located in the surface layer, while denitrifiers were situated in the inner layer. Microelectrode analysis confirmed the microenvironment of ABA with dissolved oxygen and pH gradients, which was beneficial for simultaneous pyridine and nitrogen removal. Mechanism of nitrification-denitrification involved in pyridine and nitrogen removal was finally elucidated under the scale of ABA.

Microbial denitrification characteristics of typical decentralized wastewater treatment processes based on 16S rRNA sequencing

Despite the widespread application of decentralized wastewater treatment (WWT) facilities in China, relatively few research has used the multi-media biological filter (MMBF) facilities to investigate the microorganism characteristics. This study utilizes 16S rRNA high-throughput sequencing (HTS) technology to examine the microbial biodiversity of a representative wastewater treatment (WWT) system in an expressway service area. The pathways of nitrogen removal along the treatment route were analyzed in conjunction with water quality monitoring. The distribution and composition of microbial flora in the samples were examined, and the dominant flora were identified using LEfSe analysis. The FAPROTAX methodology was employed to investigate the relative abundance of genes associated with the nitrogen cycle and to discern the presence of functional genes involved in nitrogen metabolism. On average, the method has a high level of efficiency in removing COD, TN, NH3-N, and TP from the effluent. The analysis of the microbial community identified a total of 40 phyla, 111 classes, 143 orders, 263 families, and 419 genera. The phyla that were predominantly observed include Proteobacteria, Acidobacteria, Chloroflexi, Actinobacteria, Nitrospirae, Bacteroidetes. The results show that the system has achieved high performance in nitrogen removal, the abundance of nitrification genes is significantly higher than that of other nitrogen cycle genes such as denitrification, and there are six nitrogen metabolism pathways, primarily nitrification, among which Nitrospirae and Nitrospira are the core differentiated flora that can adapt to low temperature conditions and participate in nitrification, and are the dominant nitrogen removal flora in cold regions. This work aims to comprehensively investigate the diversity and functional properties of the bacterial community in decentralized WWT processes.

Superior nitrogen removal and efficient sludge reduction via partial nitrification-anammox driven by addition of sludge fermentation products for real sewage treatment

Efficient retention and enrichment of anammox bacteria (AnAOB) are essential for the application of municipal wastewater anammox. Herein, an innovative process for highly enriching AnAOB within suspended carrier was developed in a single-stage anaerobic/oxic/anoxic reactor with 5.5 % carrier filling ratio for real sewage. Addition of sludge fermentation products promoted stable maintenance of partial nitrification (nitrite accumulation rate > 90.0 %) and achieved efficient external sludge reduction (27.6-37.9 %). Continuous nitrite supply and carrier addition promoted AnAOB enrichment (2.4 × 1011 gene copies/g dry sludge). Candidatus Brocadia was the predominant bacteria in carriers (18.6 %). The average effluents of total inorganic nitrogen (TIN) and NH4+-N were 1.9 and 0.8 mg/L with removal rates of 97.0 % and 98.7 %. In the anoxic stage, TIN removal rate reached 71.5 %, and the proportion of anammox to nitrogen removal accounted for 82.7 %. This study broadens the application of mainstream sewage anammox and the resource utilization of waste activated sludge.

Selective Enrichment of Nitrososphaera viennensis-Like Ammonia-Oxidizing Archaea over Ammonia-Oxidizing Bacteria from Drinking Water Biofilms

Ammonia-oxidizing archaea (AOA) can oxidize ammonia to nitrite for energy gain. They have been detected in chloraminated drinking water distribution systems (DWDS) along with the more common ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). To date, no members of the AOA have been isolated or enriched from drinking water environments. To begin the investigation of the role of AOA in chloraminated DWDS, we developed a selective approach using biofilm samples from a full-scale operational network as inoculum. A Nitrososphaera viennensis-like AOA taxon was enriched from a mixed community that also included Nitrosomonas-like AOB while gradually scaling up the culture volume. Dimethylthiourea (DMTU) and pyruvate at 100 μM were added to promote the growth of AOA while inhibiting AOB. This resulted in the eventual washout of AOB, while NOB were absent after 2 or 3 rounds of amendment with 24 μM sodium azide. The relative abundance of AOA in the enrichment increased from 0.2% to 39.5% after adding DMTU and pyruvate, and further to 51.6% after filtration through a 0.45-μm pore size membrane, within a period of approximately 6 months. IMPORTANCE Chloramination has been known to increase the risk of nitrification episodes in DWDS due to the presence of ammonia-oxidizing microorganisms. Among them, AOB are more frequently detected than AOA. All publicly available cultures of AOA have been isolated from soil, marine or surface water environments, meaning they are allochthonous to DWDS. Hence, monochloramine exposure studies involving these strains may not accurately reflect their role in DWDS. The described method allows for the rapid enrichment of autochthonous AOA from drinking water nitrifying communities. The high relative abundance of AOA in the resulting enrichment culture reduces any confounding effects of co-existing heterotrophic bacteria when investigating the response of AOA to varied levels of monochloramine in drinking water.

Temporal and functional interrelationships between bacterioplankton communities and the development of a toxigenic Microcystis bloom in a lowland European reservoir

The cyanobacteria-associated microbiome is constantly reshaped by bloom development. However, the synergistic-antagonistic nature of the relationships between Microcystis and its microbiome still remains unclear. Therefore, temporal changes of bacterioplankton communities and their functional potential through different developing stages of a Microcystis toxigenic bloom were investigated, considering bacterioplankton assemblages as particle-attached (PAB) and free-living (FLB) bacteria. 16S rRNA sequencing revealed that PAB were represented by Proteobacteria and Cyanobacteria, while FLB by Proteobacteria and Actinobacteria. Network and ordination analyses indicated that PAB inter-relationships were more complex-numerous connections between taxa with stronger correlations, than FLB-rather influenced by physico-chemical parameters. PAB in pre-summer was diverse with Proteobacteria containing potential taxa involved in nitrogen-transforming processes. In mid-summer, PAB presented a mix-bloom dominated by Snowella, Aphanizomenon, and Microcystis, which were succeeded by toxigenic Microcystis in post-summer. Both periods were associated to potential taxa with parasitic/predatory lifestyles against cyanobacteria. In post-summer, Sutterellaceae were recognized as poor water quality indicators, and their strong association with Microcystis could have represented an increased threat for that period. Microcystis was a major factor significantly reducing PAB diversity and evenness, suggesting that it negatively influenced bacterioplankton assemblages, probably also altering the overall community functional potential.

Continuous plug-flow anammox system for mature landfill leachate treatment: Key zone for anammox pathway

This study established the one-stage partial nitrification coupled anammox and partial denitrification coupled anammox process in an anoxic/oxic continuous plug-flow system and operated for 465 days to treat mature landfill leachate. 97.9 %-98.1 % of inorganic nitrogen was removed when the nitrogen loading rate was maintained at 0.33-0.36 kg N/m³/d, and a high anammox contribution to nitrogen removal (89.8 %-92.4 %) was achieved. The long-term in-situ free ammonia (FA) anoxic treatment contributed to the stable performances of partial nitrification and in-situ fermentation. The employed integrated fixed-film activated sludge technology favored the enrichment of hzsA, hzsB, hdh, amoA, hao, narG, and napA functional genes. The oxic zone, particularly oxic biofilm, was the key zone for anammox pathway, where Candidatus_Kuenenia (from 1.6 % to 8.3 %) with high tolerance to FA and salinity stress outcompeted Candidatus_Brocadia (from 18.3 % to 0.1 %) as the dominant anammox bacteria. This study could provide guidance for anammox-mediated landfill leachate treatment in practical projects.

Removal of Mg2+ inhibition benefited the growth and isolation of ammonia-oxidizing bacteria: An inspiration from bacterial interaction

Ammonia-oxidizing bacteria (AOB) play an important role in the global nitrogen cycle and have broad applications in the nitrogen removal from wastewater. However, the AOB species are sensitive to environmental factors and usually form tight relationships with other microbes, making the AOB isolation and maintenance are difficult and time-consuming. In this study, the relationship that occurred between AOB and their bacterial partners was found to be able to improve the ammonia oxidation; during the co-cultivation, the magnesium ions (Mg²⁺) with removal rate as high as 36.7% was removed from culture medium by the concomitant bacterial species, which was regarded as the main reason for improving ammonia oxidation. During the pure cultivation of AOB isolate, when the concentration of Mg²⁺ reduced to low levels, the ammonia-oxidizing activity was more than 5 times and the amoA gene expression was more than 12 times higher than that grown in the initial culture medium. Based on a newly designed culture medium, the ammonia oxidation of AOB isolate grown in liquid culture was significantly promoted and the visible AOB colonies with much more number and larger diameter were observed to form on agar plates. With the addition of high concentration of calcium carbonate (CaCO₃), AOB colonies could be easily and specifically identified by following the hydrolytic zones that formed around AOB colonies. Another AOB isolates were successively obtained from different samples and within a short time, suggesting the feasibility and effectivity of this culture medium and strategy on the AOB isolation from environments.

Efficient nitrogen removal from mature landfill leachate in a step feed continuous plug-flow system based on one-stage anammox process

A continuous plug-flow multistage anoxic/oxic (A/O) system based on one-stage partial nitrification coupled anammox (PNA) process with integrated fixed-film activated sludge (IFAS) was established and operated over 400 days. A step feed strategy effectively controlled free ammonia concentration and alleviated impacts on ammonia oxidizing bacteria (AOB) and anammox bacteria (AnAOB). During day 301-405, 98.1% of total inorganic nitrogen was removed from mature landfill leachate, whereas chemical oxygen demand (COD) removal efficiency was 52.9%. With the enrichment of AnAOB in oxic biofilm, nitrogen removal via the anammox pathway reached 94.3%-95.0%. During system operation, the dominant anammox genus shifted from Candidatus_Brocadia to Candidatus_Kuenenia. Fluorescent in situ hybridization (FISH) indicated AnAOB encapsulated by AOB colonies were mainly distributed inside of the biofilm, which promoted nitrite utilization by the anammox process. This innovative system and the results are of great value to practical applications.

Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities

Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that—like for AOB—ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production

The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.

Application of aerobic kenaf granules for biological nutrient removal in a full-scale continuous flow activated sludge system

Aerobic granular sludge (AGS) is a biofilm technology that offers more treatment capacity in comparison to activated sludge. The integration of AGS into existing continuous-flow activated sludge systems is of great interest as process intensification can be achieved without the use of plastic-based biofilm carriers. Such integration should allow good separation of granules/flocs and ideally with minor retrofitting, making it an ongoing challenge. This study utilized an all-organic media carrier made of porous kenaf plant stalks with high surface areas to facilitate biofilm attachment and granule development. A 5-stage Bardenpho plant was upgraded with the addition of kenaf media and a rotary drum screen to retain the larger particles from the secondary clarifier underflow whereas flocs were selectively wasted. Startup took 5 months with a sludge volume index (SVI) reduction from >200 to 50 mL g^-1. Most of the kenaf granules fell in the size range of 600-1400 μm and had a clear biofilm layer. The wet biomass density, SVI₃₀, and SVI₃₀/SVI₅ of the kenaf granules were 1035 g L^-1, 30.6 mL g^-1, and 1.0, respectively, which met the standards of aerobic granules. Improved stability of biological phosphorus removal performance enabled a 25% reduction in sodium aluminate usage. Microbial activities of kenaf granules were compared with aerobic granules, showing comparable N and P removal rates and presence of ammonium-oxidizing bacteria and polyphosphate-accumulating organisms in the outer 50-60 μm layer of the granule. This work is the first viable example for integrating fully organic biofilm particles in existing continuous-flow systems.