Shifts in the microbial community, nitrifiers and denitrifiers in the biofilm in a full-scale rotating biological contactor

Insight into biofilm formation of wastewater treatment processes: Nitrogen removal performance and biological mechanisms

Biofilm formation affects biological nitrogen (N) removal, and a sequencing batch biofilm reactor (SBBR) was set up to evaluate the changes in N removal and microbial characteristics during biofilm formation. The results indicated that the average effluent concentration of chemical oxygen demand (COD), ammonia nitrogen (NH4+-N) and total nitrogen (TN) in the SBBR were 27.48, 1.41, and 13.52 mg L-1, respectively after biofilm formation. Furthermore, this process increased microbial richness, but reduced microbial diversity. Patescibacteria, Proteobacteria, and Bacteroides were the dominant phyla that did not change after biofilm formation. After biofilm formation, Firmicutes was eliminated while Spirochaetes involved in the interspecies relationship. Biofilm increased the nitrification and denitrification relating coding genes abundance (hao, narG, narZ, nxrA, narH, narY, nxrB, napA, napB, norB, norC and nosZ), and enhanced the processes of N respiration and denitrification, carbohydrate metabolism, amino acid metabolism and membrane transport. Meanwhile, correlation analysis between genera and transcriptome reflected that Zooglea, Micropruina, Aeromonas and Tessaracoccus played essential roles in biofilm formation and N removal. The key enzyme abundance of EC:1.7.99.1, EC:1.7.2.4, and EC:1.1.1.42 of N and tricarboxylic acid (TCA) cycle increased after biofilm formation. This study can reveal the effect of biofilm formation on biological N removal and provide a theoretical foundation for the application of biofilm process.

Enhanced treatment of low C/N ratio rural sewage by a modified multi-stage tidal flow constructed wetland at low temperature: Quantitative contributions of key functional genera

Rural sewage treatment was traditionally faced contradiction between low-treatment rates and the need for low-cost development. To address this challenge, we explored the coupling of effluent circulation and step-feeding strategies in a multi-stage tidal flow constructed wetland (TFCW) to achieve stable nitrogen (N) removal performance under conditions of low carbon-to-nitrogen (C/N) ratios and low temperatures. The modified multi-stage TFCW demonstrated the ability to significantly reduce the concentrations of effluent NH4+-N and NO3--N by 33.9 % and 54.8 % respectively, resulting in values of 7.47 mg/L and 3.93 mg/L. Additionally, it achieved an average TN removal efficiency of 69.2 %. The improved N removal performance of rural sewage by the modified multi-stage TFCW at low temperatures was primarily attributed to autotrophic nitrification, heterotrophic nitrification, and autotrophic denitrification. Among the identified functional genera, Nitrosomonas and Nitrosospira played key roles as autotrophic nitrification bacteria (ANB), contributing to 28.2 % of NH4+-N removal. The key heterotrophic nitrification bacteria (HNB) Acidovorax and Rudaea were mainly responsible for 71.3 % of NH4+-N removal via the two-step ammonia assimilation through the organic nitrogen pathway. Furthermore, Rhodanobacter and Acinetobacter emerged as key autotrophic denitrification bacteria (ADNB), accounting for 79.9 % of NO3--N conversion and removal. In summary, this study provides valuable theoretical insights and supports ongoing efforts in biological regulation to address the challenges associated with rural sewage treatment.

Role of Biofilms in Waste Water Treatment

Biofilm cells have a different physiology than planktonic cells, which has been the focus of most research. Biofilms are complex biostructures that form on any surface that comes into contact with water on a regular basis. They are dynamic, structurally complex systems having characteristics of multicellular animals and multiple ecosystems. The three themes covered in this review are biofilm ecology, biofilm reactor technology and design, and biofilm modeling. Membrane-supported biofilm reactors, moving bed biofilm reactors, granular sludge, and integrated fixed-film activated sludge processes are all examples of biofilm reactors used for water treatment. Biofilm control and/or beneficial application in membrane processes are improving. Biofilm models have become critical tools for biofilm foundational research as well as biofilm reactor architecture and design. At the same time, the differences between biofilm modeling and biofilm reactor modeling methods are acknowledged.

An anoxic-aerobic system combined with integrated vertical-flow constructed wetland to highly enhance simultaneous organics and nutrients removal in rural China

The biggest problem in the treatment of rural domestic sewage is that the existing treatment projects require the big investment and the high operation and maintenance costs. To overcome this problem, cost-effective, low-consuming, resource-recovering and easy-maintenance technologies are urgently demanded. To this end, a novel anoxic-aerobic system combined with integrated vertical-flow constructed wetland (IVFCW) with source separation was proposed for treating rural sewage in this study. The anoxic-aerobic system contained the anoxic filter (ANF), two-stage waterwheel driving rotating biological contactors (ts-WDRBCs). Key parameters of ts-WDRBCs were identified to be 0.6 m drop height and 4 r/min rotational speed found on oxygenated clean water experiments. Then, the optimal operating parameters were determined to be 200% reflux ratio and 3 h hydraulic retention time of ts-WDRBCs. During the 80-day operation, 91.58 ± 1.86% COD, 96.17 ± 0.92% NH₄⁺-N, 82.71 ± 3.92% TN and 92.28 ± 2.78% TP were removed under the optimal operating parameters. Compared with other treatment technologies, this combined bio-ecological system could achieve the higher simultaneous organics and nutrients removal. The effluent NO₃^--N/NH₄⁺-N concentration ratio of ts-WDRBCs was 2.15 ± 0.54, which was proved to be beneficial for plants growth. The microbial communities coexisted in each section ensured the desired removal performance of combined bio-ecological system. Summarily, high performance together with low investment costs and cheap operation costs are characteristics that make this system a promising and competitive alternative for rural sewage treatment.

Significant production of nitric oxide by aerobic nitrite reduction at acidic pH

The acidic (i.e., pH ∼5) activated sludge process is attracting attention because it enables stable nitrite accumulation and enhances sludge reduction and stabilization, compared to the conventional process at neutral pH. Here, this study examined the production and potential pathways of nitric oxide (NO) and nitrous oxide (N₂O) during acidic sludge digestion. With continuous operation of a laboratory-scale aerobic digester at high dissolved oxygen concentration (DO>4 mg O₂ L^-1) and low pH (4.7±0.6), a significant amount of total nitrogen (TN) loss (i.e., 18.6±1.5% of TN in feed sludge) was detected. Notably, ∼40% of the removed TN was emitted as NO, with ∼8% as N₂O. A series of batch assays were then designed to explain the observed TN loss under aerobic conditions. All assays were conducted with a low concentration of volatile solids (VS), i.e., VS<4.5 g L^-1. This VS concentration is commensurate with the values commonly found in the aeration tanks of full-scale wastewater treatment systems, and thus no significant nitrogen loss should be expected when DO is controlled above 4 mg O₂ L^-1. However, nitrite disappeared at a significant rate (with the chemical decomposition of nitrite excluded), leading to NO production in the batch assays at pH 5. The nitrite reduction could be associated with endogenous microbial activities, e.g., nitrite detoxification. The significant NO production illustrates the importance of aerobic nitrite reduction during acidic aerobic sludge digestion, suggesting this process cannot be neglected in developing acidic activated sludge technology.

Temporal Succession of Bacterial Community Structure, Co-occurrence Patterns, and Community Assembly Process in Epiphytic Biofilms of Submerged Plants in a Plateau Lake

In shallow macrophytic lakes, epiphytic biofilms are formed on the surface of submerged plant stems and leaves because of algae and bacterial accumulation. Epiphytic biofilms significantly impact the health of the host vegetation and the biogeochemical cycling of lake elements. However, community diversity, species interactions, and community assembly mechanisms in epiphytic bacterial communities (EBCs) of plants during different growth periods are not well understood. We investigated the successional dynamics, co-occurrence patterns, and community assembly processes of epiphytic biofilm bacterial communities of submerged plants, Najas marina and Potamogeton lucens, from July to November 2020. The results showed a significant seasonal variation in EBC diversity and richness. Community diversity and richness increased from July to November, and the temperature was the most important driving factor for predicting seasonal changes in EBC community structure. Co-occurrence network analysis revealed that the average degree and graph density of the network increased from July to November, indicating that the complexity of the EBC network increased. The bacterial community co-occurrence network was limited by temperature, pH, and transparency. The phylogeny-based null model analysis showed that deterministic processes dominated the microbial community assembly in different periods, increasing their contribution. In addition, we found that as the dominance of deterministic processes increased, the microbial co-occurrence links increased, and the potential interrelationships between species became stronger. Thus, the findings provide insights into the seasonal variability of EBC assemblage and co-occurrence patterns in lacustrine ecosystems.

Niche differentiation and symbiotic association among ammonia/nitrite oxidizers in a full-scale rotating biological contactor

Although the distribution of ammonia/nitrite oxidizers had been profiled in different habitats, current understanding is still limited regarding their niche differentiation in the integrated biofilm reactors, the symbiotic associations of ammonia/nitrite oxidizers, as well as the parasitic interaction between viruses and those functional organisms involved in the nitrogen cycle. Here, the integrated metagenomics and metatranscriptomics are applied to profile the ammonia/nitrite oxidizers communities and transcriptional activities changes along the flowpath of a concatenated full-scale rotating biological contactor (RBC) (frontend Stage-A and backend Stage-B). 19 metagenome-assembled genomes (MAGs) of ammonia/nitrite oxidizers were recovered by using a hybrid assembly approach, including four ammonia-oxidizing bacteria (AOB), two ammonia-oxidizing archaea (AOA), two complete ammonia oxidation bacteria (comammox), eight nitrite-oxidizing bacteria (NOB), and three anaerobic ammonium oxidation bacteria (anammox). Diverse AOB and anammox dominated Stage-A and collectively contributed to nitrogen conversion. With the decline of ammonia concentration along the flowpath, comammox and AOA appeared and increased in relative abundance in Stage-B, accounting for 8.8% of the entire community at the end of this reactor, and their dominating role in nitrogen turnover was indicated by the high transcription activity of their corresponding function genes. Moreover, the variation in the abundance of viruses infecting ammonia and nitrite oxidizers suggests that viruses likely act as a biotic factor mediating ammonia/nitrite oxidizer populations. This study demonstrates that complex factors shaped niche differentiation and symbiotic associations of ammonia/nitrite oxidizers in the RBC and highlights the importance of RBCs as model systems for the investigation of biotic and abiotic factors affecting the composition of microbiomes.

Identification of key water parameters and microbiological compositions triggering intensive N2O emissions during landfill leachate treatment process

Landfill leachate treatment processes tend to emit more N₂O compared to domestic wastewater treatment. This discrepancy may be ascribed to leachate water characteristics such as high refractory COD, ammonium (NH₄⁺) content, and salinity. In this work, the leachate influent was varied to examine the N₂O emission scenarios. NH₄⁺-N, COD, and Cl^- concentrations ranged between 1000-2500, 1000-10,000, and 500-3000 mg L^-1, respectively. Simultaneously, we attempted to combine statistical analysis with high-throughput sequencing to understand the microbial mechanism with regards to N₂O emission. Results show that the strong N₂O emissions occur in the nitrifying tank due to the intensive aeration. The system receiving the lowest COD shows the maximum N₂O emission factor of 42.7% of the removed nitrogen. Both redundancy analysis and a structural equation model verify that insufficient degradable organics are the key water parameter triggering intensive N₂O emission within the designed influent limits. Furthermore, two essential but non-abundant functional bacteria, Flavobacterium (acting as a denitrifier) and Nitrosomonas (acting as a nitrifier), are identified as the core functional species that dramatically influence N₂O emissions. An increase in influent COD promotes the proliferation of Flavobacterium and inhibits Nitrosomonas, which in turn reduce N₂O release. Meanwhile, two keystone species of Castellaniella and Saprospiraceae unclassified are recognized. They may supply a suitable niche and integrity of the microbial community for N-cycle functional bacteria. These findings reveal the essential role of non-abundant species in microbial community, and expand the current understanding of microbial interactions underlying N₂O dynamics in leachate treatment systems.

Nutrients Removal from Aquaculture Wastewater by Biofilter/Antibiotic-Resistant Bacteria Systems

The presence of nutrients in aquaculture water bodies causes serious problems for aquatic ecosystems, requiring the development of technical solutions to reduce their amounts. This work identifies some bacterial strains that are able to reduce nutrient quantities and studies the effect of antibiotics on bacterial growth, on the ability to form biofilms on different solid supports, and on the ability to reduce nutrients in aquaculture wastewater. Bacterial biofilm adhesion on different substrates depends on the surface properties of the substrate, on the bacterial types that form the biofilm, but also on biofilm–substrate interactions. The obtained results revealed the high capacity of biofilm-forming bacterial strains of Pseudomonas aeruginosa and Chromobacterium violaceum to eliminate up to 87% of nitrate and nitrite ions and up to 62% of phosphate ions in the presence of concentrations of 0.1–0.4 µg/mL of oxytetracycline antibiotic from aquaculture wastewater.

The structure and assembly mechanisms of plastisphere microbial community in natural marine environment

The microbial colonization profiles on microplastics (MPs) in marine environments have recently sparked global interest. However, many studies have characterized plastisphere microbiomes without considering the ecological processes that underly microbiome assembly. Here, we carried out a three-timepoint exposure experiment at 1-, 4-, and 8-week and investigated the colonization dynamics for polyethylene, polypropylene, polystyrene, polyvinyl chloride, and acrylonitrile-butadiene-styrene MP pellets in natural coastal water. Using high-throughput sequencing of 16S rRNA, we found diversity and evenness were higher (p < 0.05) in the plastisphere communities than those in seawater, and microorganisms colonizing were co-influenced by environmental factors, polymer types, and exposure duration. Functional potential and co-occurrence network analysis revealed that MP exposure enriched the xenobiotic biodegradation potential and reduced the complexity of the MP microbial network. Simultaneously, null-model analyses indicated that stochastic processes contributed a bigger role than deterministic processes in shaping plastisphere microbial community structure with dispersal limitations contributing to a greater extent to microbial succession trajectories. These results implied the plastic surface had a more important role as a raft onto which microbes attach rather than selectively recruiting plastic-specific microbial colonizers. Our work strengthened the understanding of the ecological mechanisms by which microbial community patterns are controlled during colonization by plastic-associated microbes.

Performance and mechanism of a novel woodchip embedded biofilm electrochemical reactor (WBER) for nitrate-contaminated wastewater treatment

In this study, a woodchip biofilm electrode reactor (WBER) with woodchips embedded anode and cathode was developed, and its denitrification mechanism was analyzed by investigating the denitrification performance, organic matter change, redox environment and microbial community. The results show that the WBER with a carbon rod as anode (C-WBER) had a higher denitrification efficiency (2.58 mg NO- 3-N/(L·h)) and lower energy consumption (0.012 kWh/g NO- 3-N) at 350 mA/m². By reducing the hydroxyl radical and dissolved oxygen concentrations, anode embedding technology effectively decreased the inhibition on microorganisms. Lignin decomposition, nitrification and aerobic denitrification were carried out in anode. Additionally, hydrogen autotrophic denitrification and heterotrophic denitrification were occurred in cathode. The WBER effectively removed nitrate and reduced the cost, providing a theoretical basis and direction for further develop BERs.

Treatment of mustard tuber wastewater (MTWW) using a pilot-scale packed cage rotating biological contactor system: process modeling and optimization

The water quality range for wastewater treatment projects in the food processing industry changes constantly. To fully understand the threshold for pollutant removal with the lowest possible energy consumption, the relationship between pollutant removal and wastewater treatment conditions was established using response surface methodology (RSM). The optimum conditions for total COD, TN, and NH₃-N removal from saline mustard tuber wastewater (MTWW) with a packed cage rotating biological contactor (RBC) system were investigated by experiments based on a Box-Behnken design (BBD). The independent variables were organic load (ORL), rotational disk velocity (RDV), and immersion rate (IR). Parameters of COD, TN, and NH₃-N removal efficiency were selected as responses. The optimal conditions for the best COD, TN, and NH₃-N removal efficiency with the lowest energy consumption were found to be at an ORL of 26.71 kg/day, a RDV of 1.62 rpm (7.62 m/s), and an IR of 46%. After the optimization, the energy cost was evaluated by coupling energy performance indicators with organic pollution efficiencies to be the highest class of performance. This research demonstrates that the suggested models have a good predicting and fitting ability in interrelations between the pollutant removal and process parameters of the packed cage RBC system treating saline MTWW.

Efficacy of heated tourmaline in reducing biomass clogging within woodchip bioreactors

Woodchip bioreactors can effectively remove waterborne nitrates from subsurface agricultural drainage and prevent the eutrophication of receiving water, but rapid biofilm growth can severely reduce water flux and denitrification efficiency of this practice within a few years. Tourmaline minerals with thermal excitation could generate reactive oxygen species which would inhibit bacterial growth. In this study, laboratory scale woodchip bioreactors were set up to test the anti-clogging and denitrification efficiency of heated woodchips with tourmaline, heated woodchips without tourmaline, and unheated woodchips. The results showed that the heated tourmaline treatment could reduce the clogging and optimize the nitrate removal rate (47.6 g N/m³/day) under all three hydrologic retention times tested (1, 4, and 8 h). Dissolved oxygen and pH values fluctuated with the removal rate and temperature change, while temperature was identified as the key factor impacting the tourmaline treatment. The heated tourmaline treatment had the lowest biofilm growth (lowest DNA concentration), while the 16S rRNA and a higher abundance of nirS-, nirK-, and nosZ-encoding denitrifying bacteria (based on qPCR) confirmed the higher denitrification efficiency of the heated tourmaline treatment.

Triclosan in contact with activated sludge and its impact on phosphate removal and microbial community

Triclosan (TCS) is applied in a wide range of pharmaceutical and personal care products to prevent or reduce bacterial growth. In this study, the effects of TCS on phosphate removal and bacterial community shifts of activated sludge, especially on functional bacteria variation, were investigated. Compared with the control group (R-control), the treatment group (R-TCS) with 100 μg/L TCS inhibited the microbial growth. In addition, the phosphorus removal efficiency of PO₄^3--P and total phosphorus removal rates declined by 15.99% and 7.81%, respectively. Proteobacteria gradually dominated the microorganisms. The growths of Proteobacteria and Bacteroidetes were inhibited when 150 μg/L of TCS was added. Moreover, the differences in the microbial community structures of the R-control and R-TCS groups gradually expanded, no obvious difference was observed in the final stage, and the interrelationships of microbes in the latter weakened. The long-term addition of TCS impairs the growth of polyphosphate-accumulating organisms (PAOs).

Effects of co-loading of polyethylene microplastics and ciprofloxacin on the antibiotic degradation efficiency and microbial community structure in soil

Microplastics (MPs) have become a global environmental concern while soil plastic pollution has been largely overlooked. In view of the severe antibiotic contamination in arable soils owing to land application of sewage sludge and animal manure, the invasion of MPs along with antibiotics may pose an unpredictable threat to soil microbial communities and ecological health. In this work, polyethylene MPs and ciprofloxacin (CIP) were applied to a soil microcosm to investigate the CIP degradation behavior and their combined effects on soil microbial communities. Compared with that of the individual amendment of CIP, the co-amendment of CIP and MPs reduced the CIP degradation efficiency during the 35 d cultivation period. In addition, the high-throughput sequencing results illustrated that the combined loading of MPs and CIP in soil significantly decreased the microbial diversity compared with that of individual contamination. As for the community structure, the microbial compositions at the phylum level were consistent among all treatments, and the most dominant phyla were Proteobacteria, Actinobacteria, and Chloroflexi. At the genus level, only one genus, namely Arthrobacter, was remarkably changed in the CIP-amended soil compared with that in the blank control, but four genera were significantly altered in the MPs-CIP co-amended soil. Serratia and Achromobacter were abundant in the combined polluted soil, which might have been involved in accelerated depletion of soil total nitrogen based on redundancy analysis. These findings may contribute to the understanding of bacterial responses to the combined pollution of MPs and antibiotics in soil ecosystems.

Deciphering the succession dynamics of dominant and rare genera in biofilm development process

Deciphering the succession dynamics of dominant and rare taxa is crucial to understand the stability and ecosystem functions of biofilm communities. However, the essential laws of the succession dynamics based on dominant and rare taxa were still unenlightened. Herein, we investigated the succession dynamics of dominant and rare genera in multi-species biofilms developed in flow cells fed with 10 and 40 mg-TOC/L LB broth. The relative abundance of dominant genera (Enterobacteria and Acinetobacter) decreased remarkably (from 94.63% to 73.22%) in 10 mg-TOC/L LB broth, whereas they kept relatively steady (93.75 ± 4.23%) along with the cultivation time in 40 mg-TOC/L LB broth. Fluorescence in situ hybridization showed that rare genera tended to form clusters at both concentrations, while weaker dispersal of dominant genera caused patchier biofilm structures in 10 mg-TOC/L LB broth compared to that in 40 mg-TOC/L LB broth. Null model analyses further demonstrated that the stochastic ecological drift was more pronounced in the community assembly of biofilms in 10 mg-TOC/L LB broth (73.33%) than those in 40 mg-TOC/L LB broth (60.95%), weakening the competitive superiority of dominant taxa in the patchier biofilms. In addition, the co-occurrence network reflected that the positive interactions among rare genera contributed to exclude dominant genera in 10 mg-TOC/L LB broth, whereas negative interactions only occurred between the dominant Enterobacter and Acinetobacter or rare Comamonas in 40 mg-TOC/L LB broth. This study highlighted the distinctive succession dynamics of dominant and rare genera in biofilms at different substrate concentrations, which would advance our understanding of the biofilm communities in biofilm-related process.

Achieving single-stage autotrophic nitrogen removal by composite membrane aerated biofilm with gel under two microbial entrapping patterns: experimental and modeling aspects

Single-stage autotrophic nitrogen removal offers advantages of low energy and carbon consumptions. Based on previous work about a novel composite membrane aerated biofilm (CMAB), two microbial entrapping patterns (mixed and stratified patterns) were evaluated for their applicability to artificially regulate the spatial distribution of distinct microbial aggregates for single-stage autotrophic nitrogen removal. Experimental results showed that the stratified pattern caused little accumulation of NO₂^- and NO₃^-, which leads to a superior nitrogen removal performance compared with the mixed pattern. Candidatus Kuenenia was found to be the major anammox bacterium in the gel film of the mixed pattern and the outer film of the stratified pattern. In contrast, Nitrosomonas, as a representative genus of ammonia-oxidizing bacteria, was substantially enriched in the inner film of the stratified pattern and the gel film of the mixed pattern. Finally, modeling results further confirmed the advantages of the stratified pattern with respect to the formation of rational microbial and nutrient profiles in gel films. The ratio of partial nitrification and anammox film thicknesses should remain below 3:2 to obtain a high fraction of anammox bacteria and to avoid NO₂^- accumulation. Increasing O₂ surface loading does not affect microbial profiles, but can greatly promote the TN removal performance only in the stratified pattern. Overall, the stratified pattern should be employed to achieve optimal microbial profiles and nitrogen removal efficiency.

Intermittent rotation as an innovative strategy for achieving nitritation in rotating biological contactors

The nitritation step is essential when the anammox process is focused, and alternative technologies to achieve partial nitritation-anammox are required. Rotating Biological Contactors (RBCs) are a promising and cost-effective technology, allowing the development of aerobic and anoxic zones in the biofilm, coupled to low energy consumption. This study evaluated nitritation in a RBC with two discs rotation strategies: continuous and intermittent. Continuous rotation resulted in high dissolved oxygen (DO) concentrations and was not favorable for achieving stable nitritation. However, intermittent rotation, coupled with a nitrogen load of 1000 g N·m^-3·d^-1 and a HRT of 12 h, decreased DO by 77.8% and resulted in nitritation efficiencies of 45.3%. FISH analyses suggested that simultaneous partial nitritation/anammox (PN/A) could also be favored. These results indicated that intermittent rotation may be a core strategy for producing an anammox-suitable effluent or even to promote PN/A in RBCs, upgrading their applicability for wastewater treatment.

Simultaneous nitrogen and carbon removal in a packed A/O reactor: effect of C/N ratio on microbial community structure

In this research, a novel packed anoxic/oxic moving bed biofilm reactor (MBBR) was established to achieve high-organic matter removal rates, despite the carbon/nitrogen (C/N) ratio of 2.7-5.1 in the influent. Simultaneous nitrification-denitrification (SND) was investigated under a long sludge retention time of 104 days. The system exhibited excellent performance in pollutant removal, with chemical oxygen demand and total nitrogen (TN) enhanced to 93.6-97.4% and 34.4-60%, respectively. Under low C/N conditions, the nitrogen removal process of A/O MBBR system was mainly achieved by anaerobic denitrification. The increase of C/N ratio enhanced SND rate of the aerobic section, where dissolved oxygen was maintained at the range of 4-6 mg/L, and resulted in higher TN removal efficiency. The microbial composition and structures were analyzed utilizing the MiSeq Illumina sequencing technique. High-throughput pyrosequencing results indicated that the dominant microorganisms were Proteobacteria and Bacteroidetes at the phylum level, which contributes to the removal of organics matters. In the aerobic section, abundances of Nitrospirae (1.12-29.33%), Burkholderiales (2.15-21.38%), and Sphingobacteriales (2.92-11.67%) rose with increasing C/N ratio in the influent, this proved that SND did occur in the aerobic zone. As the C/N ratio of influent increased, the SND phenomenon in the aerobic zone of the system is the main mechanism for greatly improving the removal rate of TN in the aerobic section. The C/N ratio in the aerobic zone is not required to be high to exhibit good TN removal performance. When C/NH₄⁺ and C/TN in the aerobic zone were higher than 2.29 and 1.77, respectively, TN removal efficiency was higher than 60%, which means that carbon sources added to the reactor could be saved. This study would be vital for a better understanding of microbial structures within a packed A/O MBBR and the development of cost-efficient strategies for the treatment of low C/N wastewater.

Multi-omics analysis reveals niche and fitness differences in typical denitrification microbial aggregations

Suspended floc and fixed biofilm are two commonly applied strategies for heterotrophic denitrification in wastewater treatment. These two strategies use different carbon sources and reside within different ecological niches for microbial aggregation, which were hypothesized to show distinct microbial structures and metabolic fitness. We surveyed three floc reactors and three biofilm reactors for denitrification and determined if there were distinct microbial aggregations. Multiple molecular omics approaches were used to determine the microbial community composition, co-occurrence network and metabolic pathways. Proteobacteria was the dominating and most active phylum among all samples. Carbon source played an important role in shaping the microbial community composition while the distribution of functional protein was largely influenced by salinity. We found that the topological network features had different ecological patterns and that the microorganisms in the biofilm reactors had more nodes but less interactions than those in floc reactors. The large niche differences in the biofilm reactors explained the observed high microbial diversity, functional redundancy and resulting high system stability. We also observed a lower proportion of denitrifiers and higher resistance to oxygen and salinity perturbation in the biofilm reactors than the floc reactors. Our findings support our hypothesis that niche differences caused a distinct microbial structure and increased microbial ecology distribution, which has the potential to improve system efficiency and stability.

Enhanced nitrogen removal in an aerobic granular sequencing batch reactor under low DO concentration: Role of extracellular polymeric substances and microbial community structure

In this study, the role of extracellular polymeric substances (EPSs) in nitrogen removal and the microbial community structure of aerobic granular sludge (AGS) were analyzed under different dissolved oxygen (DO) conditions (6-7, 4-5, and 2-3 mg·L^-1). The EPSs transported and retained nitrogen in the denitrification process, and the total inorganic nitrogen (TIN) in the EPSs decreased from 6.09 to 5.54 mg·g^-1 MLSS when the DO concentration decreased from 6-7 to 2-3 mg·L^-1. The microbial community showed different core denitrifying bacterial populations involved in nitrogen removal in the AGS system under different DO conditions, with more species when they were higher relative abundances of denitrifying bacteria participating in the nitrogen removal process in AGS under low DO conditions, including Hydrogenophilaceae, Thauera, Enterobacter, Xanthomonadaceae_unclassified, Comalmonadaceae_unclassified, Nitrosomonas and Paracoccus. This study provides a more comprehensive understanding of the DO effect on the TIN removal mechanism by AGS.

Material inter-recycling for advanced nitrogen and residual COD removal from bio-treated coking wastewater through autotrophic denitrification

For wastewaters containing high strength sulfide and nitrogen (e.g. coking wastewater), sulfide might be precipitated and recovered using ferrous salt. This study systematically investigated the feasibility of recovered and precipitated FeS (comparing to commercial FeS minerals) to support autotrophic denitrification for advance nitrogen removal from bio-treated coking wastewater in fluidized bed reactors. The reactor with precipitated FeS could achieve simultaneous removal of NO₃^--N and inert COD with high efficiencies of around 96.3% and 30.5%, at NO₃^--N and COD loading rates of 4.18 mg·L^-1·h^-1 and 8.06 mg·L^-1·h^-1, respectively. Whereas, the performance of commercial FeS reduced gradually and irreversibly after two days, which became completely ineffective after 40 days. Thiobacillus and Rhodanobacter dominated the biomass, which played a key role in the FeS-based denitrification process. This material inter-recycling concept benefits an advance and more sustainable treatment of wastewaters with high strength sulfide and nitrogen.

Influence of FeONPs amendment on nitrogen conservation and microbial community succession during composting of agricultural waste: Relative contributions of ammonia-oxidizing bacteria and archaea to nitrogen conservation

Composting amended with iron oxide nanoparticles (FeONPs, α-Fe₂O₃ and Fe₃O₄ NPs) were conducted to study the impacts of FeONPs on nitrogen conservation and microbial community. It was found that amendment of FeONPs, especially α-Fe₂O₃ NPs, reduced total nitrogen (TN) loss, and reserved more NH₄⁺-N and mineral N. Pearson correlation analysis revealed that decrease of ammonia-oxidizing bacteria (AOB) in FeONPs treatments played more important role than ammonia-oxidizing archaea (AOA) in reserving more NH₄⁺-N and mineral N, and reducing TN loss. Bacterial community composition at phylum level did not shift with addition of FeONPs. Firmicutes, Actinobacteria, and Proteobacteria were the three most dominant phyla in all treatments. Overall, this study provides a method to reduce TN loss and improve mineral N reservation during composting, and gives a deep insight into the role of AOB and AOA in nitrogen transformation.

Dependency of DNA extraction efficiency on cell concentration confounds molecular quantification of microorganisms in groundwater

Quantification of microbes in water systems is essential to industrial practices ranging from drinking water and wastewater treatment to groundwater remediation. While quantification using DNA-based molecular methods is precise, the accuracy is dependent on DNA extraction efficiencies. We show that the DNA yield is strongly impacted by the cell concentration in groundwater samples (r = -0.92, P < 0.0001). This has major implications for industrial applications using quantitative polymerase chain reaction (qPCR) to determine cell concentrations in water, including bioremediation. We propose a simple normalization method using a DNA recovery ratio, calculated with the total cell count and DNA yield. Application of this method to enumeration of bacteria and archaea in groundwater samples targeting phylogenetic markers (16S rRNA) demonstrated an increased goodness of fit after normalization (7.04 vs 0.94 difference in Akaike's information criteria). Furthermore, normalization was applied to qPCR quantification of functional genes and combined with DNA sequencing of archaeal and bacterial 16S rRNA genes to monitor changes in abundance of methanogenic archaea and sulphate-reducing bacteria in groundwater. The integration of qPCR and DNA sequencing with appropriate normalization enables high-throughput quantification of microbial groups using increasingly affordable and accessible techniques. This research has implications for microbial ecology and engineering research as well as industrial practice.

Enrichments/Derichments of Root-Associated Bacteria Related to Plant Growth and Nutrition Caused by the Growth of an EPSPS-Transgenic Maize Line in the Field

During the past decades, the effects of the transgenic crops on soil microbial communities have aroused widespread interest of scientists, which was mainly related to the health and growth of plants. In this study, the maize root-associated bacterial communities of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) transgenic glyphosate-tolerant (GT) maize line CC-2 (CC2) and its recipient variety Zhengdan958 (Z958) were compared at the tasseling and flowering stages by high-throughput sequencing of V3-V4 hypervariable regions of 16S rRNA gene (16S rDNA) amplicons via Illumina MiSeq. In addition, real-time quantitative PCR (qPCR) was also performed to analyze the nifH gene abundance between CC2 and Z958. Our results showed no significant difference in alpha/beta diversity of root-associated bacterial communities at the tasseling or flowering stage between CC2 and Z958 under field growth conditions. The relative abundances of the genera Bradyrhizobium and Bacillus including species B. cereus and B. muralis were significantly lower in the roots of CC2 than that of Z985 under field conditions. Both these species are regarded as plant growth promoting bacteria (PGPB), as they belong to both nitrogen-fixing and phosphate-solubilizing bacterial genera. The comparison of the relative abundance of nitrogen-fixing/phosphate-solubilizing bacteria at the class, order or family levels indicated that only one class Bacilli, one order Bacillales and one family Bacillaceae were found to be significantly lower in the roots of CC2 than that of Z985. These bacteria were also enriched in the roots and rhizospheric soil than in the surrounding soil at both two stages. Furthermore, the class Betaproteobacteria, the order Burkholderiales, the family Comamonadaceae, and the genus Acidovorax were significantly higher in the roots of CC2 than that of Z985 at the tasseling stage, meanwhile the order Burkholderiales and the family Comamonadaceae were also enriched in the roots than in the rhizospheric soil at both stages. Additionally, the nifH gene abundance at the tasseling stage in the rhizosphere soil also showed significant difference. The relative abundance of nifH gene was higher in the root samples and lower in the surrounding soil, which implicated that the roots of maize tend to be enriched in nitrogen-fixing bacteria.

Effective removal of nitrate by denitrification re-enforced with a two-stage anoxic/oxic (A/O) process from a digested piggery wastewater with a low C/N ratio

The combined process of a long-term biogas digester and double anoxic/oxic tanks is very commonly used in piggery wastewater treatment in South China, but the effluent does not meet the discharge standard of total nitrogen (TN) and chemical oxygen demand (COD_Cr) due to a low C/N ratio and insufficient organic carbon in digested piggery wastewater. Thus, a typical two-stage anoxic/oxic (A1/O1/A2/O2) process, which is widely used to treat digested piggery wastewater in the engineering application, was selected for study on a laboratory scale. Finally, the average removal efficiency of ammonia nitrogen in the two-stage AO process was 98.7%; at the same time, the content of nitrate increased to 180-190 mg/L. To further eliminate nitrogen, an anaerobic tank (S1), which was equipped the sludge that was acclimated in our laboratory by a high nitrogen loading slurry, was employed to treat the effluent from the two-stage AO process and contributed more than 70% removal efficiency. Further analysis showed that ammonia-oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) in the O1 and O2 tanks together contributed to the conversion of ammonia nitrogen to nitrate, but the process of heterotrophic denitrification was inhibited in the A1 and A2 tanks because of insufficient carbon sources. In addition, most of the nitrate concentration was reduced under conditions with insufficient carbon sources, while Thauera-dominated the bacterial population in the sludge sample of the S1 tank.

Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions

The bacterial community of an anaerobic granular sludge associated with uranium depletion was investigated following its exposure to uranium under different initial pH conditions (pH 4.5, 5.5, and 6.5). The highest uranium removal efficiency (98.1%) was obtained for the sample with an initial pH of 6.5, which also supported the highest bacterial community richness and diversity. Venn diagrams visualized the decrease in the number of genera present in both the inoculum and the uranium-exposed biomass as the initial pH decreased from 6.5 to 4.5. Compared with the inoculum, a significant increase in the abundances of the phyla Chloroflexi and Proteobacteria was observed following uranium exposure. At initial pH conditions of 6.5 to 4.5, the proportions of the taxa Anaerolineaceae, Chryseobacterium, Acinetobacter, Pseudomonas, and Sulfurovum increased significantly, likely contributing to the observed uranium removal. Uranium exposure induced a greater level of dynamic diversification of bacterial abundances than did the initial pH difference.

Nitrogen cycling during wastewater treatment

Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.

rDNA- and rRNA-derived communities present divergent assemblage patterns and functional traits throughout full-scale landfill leachate treatment process trains

Understanding the influences of microbial interactions and niche heterogeneities on microbial communities and functional traits is critical for determining its engineering and ecological significance. However, little is known about microbial community assemblage and functional gene expression throughout full-scale landfill leachate treatment plants. Here, we applied a combination of 16S rRNA and rDNA amplicon sequencing, shotgun metagenomic, and qPCR approaches to unveil the ecological associations between distinct communities, functional gene expression and nitrogen cycling processes. By comparing the rDNA and rRNA-derived communities, the rRNA/rDNA ratios suggested that 57.2% of rare taxa were active, and their abundance decreased as increasing of potential activities. In particular, rDNA- and rRNA-based communities exhibited divergent assemblage patterns, and stronger intra-associations among core taxa in the rRNA-based communities than in rDNA-based communities. Furthermore, results regarding both bacterial assemblage and functional traits indicated that the habitat filtering and niche differentiation (treatment units) exerted selection on microbial communities based on functional traits, particular for key ecological functions related to nitrogen cycling. Collectively, our findings provide insights into structure-function associations at the local level and shed light on ecological rules guiding rDNA- and rRNA-based community assembly in landfill leachate treatment systems.

Linking microbial respiratory activity with phospholipid fatty acid of biofilm from full-scale bioreactors

Deficiency of researches on biotic community-driven biofilm activity makes biofilm regulation lack of quantitative response for decades. Based on three full-scale aerobic bioreactors in wastewater treatment plants, this study for the first time linked microbial respiratory activity with phospholipid fatty acid (PLFA) of biofilm developed on fixed and suspended carriers. Results showed that C16:00, C18:00, C16:1, ω7c, C18:1, ω7c, C12:00 and C18:1ω9c were top six biomarkers of PLFA among different sources of samples and Gram-negative bacteria (G-) was more abundant than Gram-positive bacteria (G+) with average G-/G+ of 2.98. It's interesting to find defective revealing of PLFA-based biofilm activity by specific oxygen uptake rate (SOUR). Further modeling indicated that C16:00 achieved the optimal quantitative response to STOUR with the best model of composite, growth, or exponential curve (R² = 0.416, p = 0.005). This research was promising to provide important reference for biofilm regulation and accurate control of biofilm-based process.

Day/night temperature differences (DNTD) trigger changes in nutrient removal and functional bacteria in membrane bioreactors

Temperature is a well-known environmental stress that influences both microbial metabolism and community structure in the biological wastewater treatment systems. In this study, responses of biological performance and sludge microbiota to the long-term day/night temperature differences (DNTD) were investigated in membrane bioreactors (MBRs). The results showed that the functional bacteria could sustained their ecological functions at low DNTD (20/30 °C), resulting in relatively stable performance with respect to nutrient removal. However, when the activated sludge was subjected to a high DNTD (17/33 °C), the effluent concentrations of COD, TN and TP were significantly higher in MBR-B than that in MBR-A. In addition, more severe membrane fouling occurred under the perturbation of high DNTD as revealed by the transmembrane pressure (TMP) profile, which was mainly attributed to the accumulation of extracellular polymeric substances (EPS). The results of 16S rRNA gene sequencing showed that DNTD showed negligible effect on the bacterial community structures. Nonetheless, the functional bacteria responded differently to DNTD, which were in accordance with the bioreactor performances. Specifically, Nitrospina (NOB) and Tetrasphaera (PAOs) appeared to be sensitive to both low and high DNTD. In contrast, a low DNTD showed marginal effects on the denitrifiers, while a high DNTD significantly decreased their abundances. More strikingly, filamentous bulking bacteria were found to be well-adapted to DNTD, indicating their tolerance to the daily temperature fluctuation. This study will advance our knowledge regarding the response of microbial ecology of activated sludge to daily temperature variations in full-scale MBRs.

Achieving mainstream nitrogen removal through simultaneous partial nitrification, anammox and denitrification process in an integrated fixed film activated sludge reactor

The anaerobic ammonium oxidation (anammox) is becoming a critical technology for energy neutral in mainstream wastewater treatment. However, the presence of chemical oxygen demanding in influent would result in a poor nitrogen removal efficiency during the deammonification process. In this study, the simultaneous partial nitrification, anammox and denitrification process (SNAD) for mainstream nitrogen removal was investigated in an integrated fixed film activated sludge (IFAS) reactor. SNAD-IFAS process achieved a total nitrogen (TN) removal efficiency of 72 ± 2% and an average COD removal efficiency was 88%. The optimum COD/N ratio for mainstream wastewater treatment was 1.2 ± 0.2. Illumina sequencing analysis and activity tests showed that anammox and denitrifying bacteria were the dominant nitrogen removal microorganism in the biofilm and the high COD/N ratios (≥2.0) leaded to the proliferation of heterotrophic bacteria (Hydrogenophaga) and nitrite-oxidizing bacteria (Nitrospira) in the suspended sludge. Network analysis confirmed that anammox bacteria (Candidatus Kuenenia) could survive in organic matter environment due to that anammox bacteria displayed significant co-occurrence through positive correlations with some heterotrophic bacteria (Limnobacter) which could protect anammox bacteria from hostile environments. Overall, the results of this study provided more comprehensive information regarding the community composition and assemblies in SNAD-IFAS process for mainstream nitrogen removal.

Bacteria That Make a Meal of Sulfonamide Antibiotics: Blind Spots and Emerging Opportunities

The release of sulfonamide antibiotics into the environment is alarming because the existence of these antibiotics in the environment may promote resistance in clinically relevant microorganisms, which is a potential threat to the effectiveness of antibiotic therapies. Controllable biodegradation processes are of particular significance for the inexpensive yet effective restoration of sulfonamide-contaminated environments. Cultivation-based techniques have already made great strides in successfully isolating bacteria with promising sulfonamide degradation abilities, but the implementation of these isolates in bioremediation has been limited by unknown microbial diversity, vast population responsiveness, and the impact of perturbations from open and complex environments. Advances in DNA sequencing technologies and metagenomic analyses are being used to complement the information derived from cultivation-based procedures. In this Review, we provide an overview of the growing understanding of isolated sulfonamide degraders and identify shortcomings of the prevalent literature in this field. In addition, we propose a technical paradigm that integrates experimental testing with metagenomic analysis to pave the way for improved understanding and exploitation of these ecologically important isolates. Overall, this Review aims to outline how metagenomic studies of isolated sulfonamide degraders are being applied for the advancement of bioremediation strategies for sulfonamide contamination.

Deciphering the core fouling-causing microbiota in a membrane bioreactor: Low abundance but important roles

Currently, membrane biofouling in membrane bioreactors (MBRs) is normally attributed to the occurrence of abundant bacterial species on membranes, whereas the roles of low-abundance bacteria have not been paid sufficient attention. In this study, the linear discriminant analysis (LDA) effect size (LEfSe) algorithm was used to identify active biomarkers, determining 67 different phylotypes among Bulk sludge, low-fouling Bio-cake (10 kPa), high-fouling Bio-cake (25 kPa) and Membrane pore in a membrane bioreactor with NaOCl backwash. Interestingly, a large proportion of the active biomarkers in bio-cake samples, such as Methylophilaceae, Burkholderiaceae, Paucibacter and Pseudoxanthomonas, did not fall within the abundant taxa (i.e., <0.05% relative abundance), indicating the preferential growth of these low-abundance bacteria on the membrane surface. Furthermore, the characterization of microbial interactions using a random matrix theory (RMT)-based network approach obtained a network consisting of 120 nodes and 228 edges. Specifically, network analysis showed the presence of an intense competition among bacterial species in the fouling-related communities, suggesting that negative interactions have an important effect on determining the microbial community structure. More importantly, the LEfSe algorithm and network analysis showed that most of the core species of the bio-cake, such as Burkholderiaceae, Bacillus and Rhodothermaceae, merely amounted to a very low relative abundance (<1%), suggesting their unrecognized and over-proportional ecological role in triggering the initial biofilm formation and subsequent biofilm maturation during MBR operation. Overall, this work should improve our understanding of the bacterial community structure on the fouled membranes in MBRs.

Soil Bacterial Community Structure and Co-occurrence Pattern during Vegetation Restoration in Karst Rocky Desertification Area

Vegetation restoration has been widely used in karst rocky desertification (KRD) areas of southwestern China, but the response of microbial community to revegetation has not been well characterized. We investigated the diversity, structure, and co-occurrence patterns of bacterial communities in soils of five vegetation types (grassland, shrubbery, secondary forest, pure plantation and mixed plantation) in KRD area using high-throughput sequencing of the 16S rRNA gene. Bray-Curtis dissimilarity analysis revealed that 15 bacterial community samples were clustered into five groups that corresponded very well to the five vegetation types. Shannon diversity was positively correlated with pH and Ca2+ content but negatively correlated with organic carbon, total nitrogen, and soil moisture. Redundancy analysis indicated that soil pH, Ca2+ content, organic carbon, total nitrogen, and soil moisture jointly influenced bacterial community structure. Co-occurrence network analysis revealed non-random assembly patterns of bacterial composition in the soils. Bryobacter, GR-WP33-30, and Rhizomicrobium were identified as keystone genera in co-occurrence network. These results indicate that diverse soil physicochemical properties and potential interactions among taxa during vegetation restoration may jointly affect the bacterial community structure in KRD regions.

Myriophyllum aquaticum Constructed Wetland Effectively Removes Nitrogen in Swine Wastewater

Removal of nitrogen (N) is a critical aspect in the functioning of constructed wetlands (CWs), and the N treatment in CWs depends largely on the presence and activity of macrophytes and microorganisms. However, the effects of plants on microorganisms responsible for N removal are poorly understood. In this study, a three-stage surface flow CW was constructed in a pilot-scale within monospecies stands of Myriophyllum aquaticum to treat swine wastewater. Steady-state conditions were achieved throughout the 600-day operating period, and a high (98.3%) average ammonia removal efficiency under a N loading rate of 9 kg ha^-1 d^-1 was observed. To determine whether this high efficiency was associated with the performance of active microbes, the abundance, structure, and interactions of microbial community were compared in the unvegetated and vegetated samples. Real-time quantitative polymerase chain reactions showed the abundances of nitrifying genes (archaeal and bacterial amoA) and denitrifying genes (nirS, nirK, and nosZ) were increased significantly by M. aquaticum in the sediments, and the strongest effects were observed for the archaeal amoA (218-fold) and nirS genes (4620-fold). High-throughput sequencing of microbial 16S rRNA gene amplicons showed that M. aquaticum greatly changed the microbial community, and ammonium oxidizers (Nitrosospira and Nitrososphaera), nitrite-oxidizing bacteria (Nitrospira), and abundant denitrifiers including Rhodoplanes, Bradyrhizobium, and Hyphomicrobium, were enriched significantly in the sediments. The results of a canonical correspondence analysis and Mantle tests indicated that M. aquaticum may shift the sediment microbial community by changing the sediment chemical properties. The enriched nitrifiers and denitrifiers were distributed widely in the vegetated sediments, showing positive ecological associations among themselves and other bacteria based on phylogenetic molecular ecological networks.

Spatiotemporal heterogeneity of core functional bacteria and their synergetic and competitive interactions in denitrifying sulfur conversion-assisted enhanced biological phosphorus removal

Denitrifying sulfur conversion-assisted enhanced biological phosphorus removal (DS-EBPR) has recently been developed for simultaneously removing nitrogen and phosphorus from saline sewage with minimal sludge production. This novel process could potentially enable sustainable wastewater treatment. Yet, the core functional bacteria and their roles are unknown. Here, we used high-throughput 16S rRNA gene sequencing coupled with principal coordinates analysis and ANOVA with Tukey's test to unravel the spatiotemporal heterogeneity of functional bacteria and their synergetic and competitive interactions. We did not find any obvious spatial heterogeneity within the bacterial population in different size-fractionated sludge samples, but the main functional bacteria varied significantly with operation time. Thauera was enriched (9.26~13.63%) as become the core functional genus in the DS-EBPR reactors and links denitrifying phosphorus removal to sulfide oxidation. The other two functional genera were sulfate-reducing Desulfobacter (4.31~12.85%) and nitrate-reducing and sulfide-oxidizing Thiobacillus (4.79~9.92%). These bacteria cooperated in the DS-EBPR process: Desulfobacter reduced sulfate to sulfide for utilization by Thiobacillus, while Thauera and Thiobacillus competed for nitrate and sulfide as well as Thauera and Desulfobacter competed for acetate. This study is the first to unravel the interactions among core functional bacteria in DS-EBPR, thus improving our understanding of how this removal process works.

Ecological Network Inference From Long-Term Presence-Absence Data

Ecological communities are characterized by complex networks of trophic and nontrophic interactions, which shape the dy-namics of the community. Machine learning and correlational methods are increasingly popular for inferring networks from co-occurrence and time series data, particularly in microbial systems. In this study, we test the suitability of these methods for inferring ecological interactions by constructing networks using Dynamic Bayesian Networks, Lasso regression, and Pear-son’s correlation coefficient, then comparing the model networks to empirical trophic and nontrophic webs in two ecological systems. We find that although each model significantly replicates the structure of at least one empirical network, no model significantly predicts network structure in both systems, and no model is clearly superior to the others. We also find that networks inferred for the Tatoosh intertidal match the nontrophic network much more closely than the trophic one, possibly due to the challenges of identifying trophic interactions from presence-absence data. Our findings suggest that although these methods hold some promise for ecological network inference, presence-absence data does not provide enough signal for models to consistently identify interactions, and networks inferred from these data should be interpreted with caution.

Response of wastewater biofilm to CuO nanoparticle exposure in terms of extracellular polymeric substances and microbial community structure

The growing production and application of CuO nanoparticles increase the chance that these particles will be released into wastewater treatment plants (WWTPs) and interact with microorganisms. However, the toxicity response mechanism of biofilm to NP exposure may be different from that of activated sludge due to the denser and stronger microbial aggregate structure of biofilm. Thus, in this study, the response to CuO NPs of wastewater biofilm collected from a rotating biological contactor was investigated. Short-term exposure (24h) to CuO NPs led to a great loss in cell viability, and SEM-EDS images revealed that the nano-CuO aggregates were not transformed to Cu-S species in the biofilm samples. In response, more extracellular polymeric substance (EPS) (especially loosely bound-EPS) was produced in wastewater biofilm exposed to CuO NPs, with a higher content of protein compared to polysaccharides. The shifts of fluorescence intensity and peak locations in 3D-EEM fluorescence spectra indicated chemical changes of the EPS components. FT-IR analysis revealed that exposure to nano-CuO had more distinct effects on the functional groups of proteins and polysaccharides in LB-EPS. Illumina sequencing of 16S rRNA gene amplicons revealed that CuO NPs enhanced bacterial diversity. The bacterial community structure significantly shifted, with a significantly increased abundance of Comamonas, a slight increase in Zoogloea, and a notable decrease in Flavobacterium. The shifts of these dominant genera may be associated with altered EPS production, which might result in microbial community function fluctuations. In conclusion, exposure to high concentrations of CuO NPs has the potential to shape wastewater biofilm bacterial community structure.

Structure, Variation, and Co-occurrence of Soil Microbial Communities in Abandoned Sites of a Rare Earth Elements Mine

Mining activity for rare earth elements (REEs) has caused serious environmental pollution, particularly for soil ecosystems. However, the effects of REEs on soil microbiota are still poorly understood. In this study, soils were collected from abandoned sites of a REEs mine, and the structure, diversity, and co-occurrence patterns of soil microbiota were evaluated by Illumina high-throughput sequencing targeting 16S rRNA genes. Although microbiota developed significantly along with the natural restoration, the microbial structure on the site abandoned for 10 years still significantly differed from that on the unmined site. Potential plant growth promoting bacteria (PGPB) were identified by comparing 16S sequences against a self-constructed PGPB database via BLAST, and it was found that siderophore-producing and phosphorus-solubilizing bacteria were more abundant in the studied soils than in reference soils. Canonical correspondence analysis indicated that species richness of plant community was the prime factor affecting microbial structure, followed by limiting nutrients (total carbon and total nitrogen) and REEs content. Further co-occurring network analysis revealed nonrandom assembly patterns of microbiota in the studied soils. These results increase our understanding of microbial variation and assembly pattern during natural restoration in REE contaminated soils.

Effects of DO levels on surface force, cell membrane properties and microbial community dynamics of activated sludge

In this paper, we employ atomic force microscopy (AFM), fluorescence recovery after photobleaching (FRAP) technique, phospholipid fatty acids (PLFA) and MiSeq analysis to study the effects of traditional dissolved oxygen (DO) levels (0.71-1.32mg/L, 2.13-3.02mg/L and 4.31-5.16mg/L) on surface force, cell membrane properties and microbial community dynamics of activated sludge. Results showed that low DO level enhanced the surface force and roughness of activated sludge; the medium DO level decreased cell membrane fluidity by reducing the synthesis of branched fatty acids in the cell membrane; high DO level resulted in the highest protein content in the effluent by EEM scanning. Abundance of Micropruina, Zoogloea and Nakamurella increased and Paracoccus and Rudaea decreased with the increase of DO levels. RDA analysis suggested that saturated fatty acids (SFA), anteiso-fatty acids (AFA) and iso-fatty acids (IFA) were closely related to effluent quality as well as some genera.

Nitrification at different salinities: Biofilm community composition and physiological plasticity

This paper describes an experimental study of microbial communities of three moving bed biofilm reactors (MBBR) inoculated with nitrifying cultures originated from environments with different salinity; freshwater, brackish (20‰) and seawater. All reactors were run until they operated at a conversion efficiency of >96%. The microbial communities were profiled using 454-pyrosequencing of 16S rRNA gene amplicons. Statistical analysis was used to investigate the differences in microbial community structure and distribution of the nitrifying populations with different salinity environments. Nonmetric multidimensional scaling analysis (NMDS) and the PERMANOVA test based on Bray-Curtis similarities revealed significantly different community structure in the three reactors. The brackish reactor showed lower diversity index than fresh and seawater reactors. Venn diagram showed that 60 and 78% of the total operational taxonomic units (OTUs) in the ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) guild, respectively, were unique OTUs for a given reactor. Similarity Percentages (SIMPER) analysis showed that two-thirds of the total difference in community structure between the reactors was explained by 10 OTUs, indicating that only a small number of OTUs play a numerically dominant role in the nitrification process. Acute toxicity of salt stress on ammonium and nitrite oxidizing activities showed distinctly different patterns, reaching 97% inhibition of the freshwater reactor for ammonium oxidation rate. In the brackish culture, inhibition was only observed at maximal level of salinity, 32‰. In the fully adapted seawater culture, higher activities were observed at 32‰ than at any of the lower salinities.

Bacterial communities in full-scale wastewater treatment systems

Bacterial metabolism determines the effectiveness of biological treatment of wastewater. Therefore, it is important to define the relations between the species structure and the performance of full-scale installations. Although there is much laboratory data on microbial consortia, our understanding of dependencies between the microbial structure and operational parameters of full-scale wastewater treatment plants (WWTP) is limited. This mini-review presents the types of microbial consortia in WWTP. Information is given on extracellular polymeric substances production as factor that is key for formation of spatial structures of microorganisms. Additionally, we discuss data on microbial groups including nitrifiers, denitrifiers, Anammox bacteria, and phosphate- and glycogen-accumulating bacteria in full-scale aerobic systems that was obtained with the use of molecular techniques, including high-throughput sequencing, to shed light on dependencies between the microbial ecology of biomass and the overall efficiency and functional stability of wastewater treatment systems. Sludge bulking in WWTPs is addressed, as well as the microbial composition of consortia involved in antibiotic and micropollutant removal.

Predicting microbial interactions through computational approaches

Microorganisms play a vital role in various ecosystems and characterizing interactions between them is an essential step towards understanding the organization and function of microbial communities. Computational prediction has recently become a widely used approach to investigate microbial interactions. We provide a thorough review of emerging computational methods organized by the type of data they employ. We highlight three major challenges in inferring interactions using metagenomic survey data and discuss the underlying assumptions and mathematics of interaction inference algorithms. In addition, we review interaction prediction methods relying on metabolic pathways, which are increasingly used to reveal mechanisms of interactions. Furthermore, we also emphasize the importance of mining the scientific literature for microbial interactions - a largely overlooked data source for experimentally validated interactions.

Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology

Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation.