Distinct growth stages controlled by the interplay of deterministic and stochastic processes in functional anammox biofilms

Deciphering stratified structure and microbiota assembly of biofilms from a pyrite-based biofilter driven by mixotrophic denitrification

The precise structure and assembly process of pyrite-based biofilms remain poorly understood. The polysaccharides (PN), proteins (PS), and extracellular DNA were enriched in the soluble extracellular polymeric substance (EPS), loosely bound EPS, and tightly bound EPS, respectively, indicating a significant stratified structure of biofilms. The tryptophan facilitated mixotrophic metabolic processes. Both dominant (>1%) and rare species (<0.01 %) harbored core bacteria, including sulfur autotrophic bacteria, sulfate-reducing bacteria, and heterotrophic bacteria. Furthermore, partial least-squares path modeling quantified the contributions of total phosphorus (TP) (λ = 0.32), dissolved organic matter (DOC) (λ = 0.29), and NH4+-N (λ = 0.26) to variations in the microbial community. Nonmetric multidimensional scaling analysis revealed three distinct stages in biofilm development: colonization (0-36 d), succession (36-149 d), and maturation/old (149-215 d). Furthermore, neutral community model indicated that stochastic processes drove the colonization and maturation/old stages, while deterministic processes dominated the succession stage. This study offered valuable insights into the regulation of pyrite-based engineered ecosystems.

Strengthening the enrichment of anaerobic ammonia oxidizing bacteria in biofilms through sludge concentration control

Controlling sludge concentration is an effective means to achieve PN. In this article, the reactor used domestic sewage as raw water and promoted the high enrichment of anammox bacteria by controlling the MLVSS of flocs to 1000-1500 mg/L and increasing the concentration of filler sludge. The measures to reduce the concentration of flocculent sludge increased the proliferation rate of the biofilm and provided sufficient substrate for AnAOB. After 102 days of operation, the abundance of Candidatus Brocadia increased from 0.43% during inoculation to 23.56% in phase VI. The ability of the microbial community to utilize energy metabolism and produce ATP was significantly improved, and the appropriate distribution of anammox bacteria and nitrifying, denitrifying bacteria in the ecological niche led to its high enrichment. In summary, this study proposes a strategy to promote the high enrichment of anammox bacteria in mainstream domestic sewage without adding any chemicals.

Metagenomic evidence of a novel anammox community in a cold aquifer with high nitrogen pollution

The process of anaerobic ammonium oxidation by nitrite (anammox) is a globally essential part of N cycle. To date, 8 Candidatus genera and more than 22 species of anammox bacteria have been discovered in various anthropogenic and natural habitats, including nitrogen-polluted aquifers. In this work, anammox bacteria were detected for the first time in the groundwater ecosystem with high anthropogenic nitrogen pollution (up to 1760 mg NO3--N/L and 280 mg NH4+-N/L) and low year-round temperature (7-8 °C) in the zone of a uranium sludge repository. Further metagenomic analysis resulted in retrieval of metagenome-assembled genomes of 4 distinct anammox bacteria: a new genus named Ca. Frigussubterria, new species in Ca. Kuenenia, and two strains of a new species in Ca. Scalindua. Analysis of the genomes revealed essential genes involved in anammox metabolism. Both strains of Ca. Scalindua chemeplantae had a high copy number of genes encoding the cold shock proteins CspA/B, which can also function as an antifreeze protein (CspB). Ca. Kuenenia glazoviensis and Ca. Frigussubterria udmurtiae were abundant in less N-polluted site, while Ca. Scalindua chemeplantae inhabited both sites. Genes for urea utilization, reduction of insoluble Fe2O3 or MnO2, assimilatory sulfate reduction, reactive oxygen detoxification, nitrate reduction to ammonium, and putatively arsenate respiration were found. These findings enrich knowledge of the functional and phylogenetic diversity of anammox bacteria and improve understanding of the nitrogen cycle in polluted aquifers.

Enhanced AHL-mediated quorum sensing accelerates the start-up of biofilm reactors by elevating the fitness of fast-growing bacteria in sludge and biofilm communities

Quorum sensing (QS)-based manipulations emerge as a promising solution for biofilm reactors to overcome challenges from inefficient biofilm formation and lengthy start-ups. However, the ecological mechanisms underlying how QS regulates microbial behaviors and community assembly remain elusive. Herein, by introducing different levels of N-acyl-homoserine lactones, we manipulated the strength of QS during the start-up of moving bed biofilm reactors and compared the dynamics of bacterial communities. We found that enhanced QS elevated the fitness of fast-growing bacteria with high ribosomal RNA operon (rrn) copy numbers in their genomes in both the sludge and biofilm communities. This led to notably increased extracellular substance production, as evidenced by strong positive correlations between community-level rrn copy numbers and extracellular proteins and polysaccharides (Pearson's r = 0.529-0.830, P < 0.001). Network analyses demonstrated that enhanced QS significantly promoted the ecological interactions among taxa, particularly cooperative interactions. Bacterial taxa with higher network degrees were more strongly correlated with extracellular substances, suggesting their crucial roles as public goods in regulating bacterial interactions and shaping network structures. However, the assembly of more cooperative communities in QS-enhanced reactors came at the cost of decreased network stability and modularity. Null model and dissimilarity-overlap curve analysis revealed that enhanced QS strengthened stochastic processes in community assembly and rendered the universal population dynamics more convergent. Additionally, these shaping effects were consistent for both the sludge and biofilm communities, underpinning the planktonic-to-biofilm transition. This work highlights that QS manipulations efficiently drive community assembly and confer specialized functional traits to communities by recruiting taxa with specific life strategies and regulating interspecific interactions. These ecological insights deepen our understanding of the rules governing microbial societies and provide guidance for managing engineering ecosystems.

Exploring plastic biofilm formation and Escherichia coli colonisation in marine environments

Microorganisms, including potential pathogens, can colonise plastic surfaces in aquatic environments. This study investigates the colonisation of plastic pellets by Escherichia coli (E. coli) as a proxy for faecal pathogens in aquatic environments. Plastic pellets from a polluted beach were placed in seawater aquaria spiked with E. coli. Diverse bacteria, primarily from the Proteobacteria phylum, rapidly colonised the pellets within 24 h, with notable species known for plastic or hydrocarbon degradation. Over 26 days, biofilms formed on the plastic surfaces, reaching bacterial populations of up to 6.8·105 gene copies (gc) of the 16S rRNA mm-2. E. coli, was detected in the pellets for up to 7 days using culture methods, exhibiting varying attachment densities regardless of source or environmental factors. The study highlights plastic biofilms as reservoirs for E. coli, contributing to the survival and persistence of faecal bacteria in aquatic systems. These findings deepen our understanding of the risks associated with plastic pollution in marine settings, offering insights into the behaviour of faecal indicators and their implications for water quality assessments, while providing valuable information on potential pathogen dissemination within plastic-associated microbial communities.

New insights into substrates shaped nutrients removal, species interactions and community assembly mechanisms in tidal flow constructed wetlands treating low carbon-to-nitrogen rural wastewater

A limited understanding of microbial interactions and community assembly mechanisms in constructed wetlands (CWs), particularly with different substrates, has hampered the establishment of ecological connections between micro-level interactions and macro-level wetland performance. In this study, CWs with distinct substrates (zeolite, CW_A; manganese ore, CW_B) were constructed to investigate the nutrient removal efficiency, microbial interactions, metabolic mechanisms, and ecological assembly for treating rural sewage with a low carbon-to-nitrogen ratio. CW_B showed higher removal of ammonia nitrogen and total nitrogen by about 1.75-6.75 % and 3.42-5.18 %, respectively, compared to CW_A. Candidatus_Competibacter (denitrifying glycogen-accumulating bacteria) was the dominant microbial genus in CW_A, whereas unclassified_f_Blastocatellaceae (involved in carbon and nitrogen transformation) dominated in CW_B. The null model revealed that stochastic processes (drift) dominated community assembly in both CWs; however, deterministic selection accounted for a higher proportion in CW_B. Compared to those in CW_A, the interactions between microbes in CW_B were more complex, with more key microbes involved in carbon, nitrogen, and phosphorus conversion; the synergistic cooperation of functional bacteria facilitated simultaneous nitrification-denitrification. Manganese ores favour biofilm formation, increase the activity of the electron transport system, and enhance ammonia oxidation and nitrate reduction. These results elucidated the ecological patterns exhibited by microbes under different substrate conditions thereby contributing to our understanding of how substrates shape distinct microcosms in CW systems. This study provides valuable insights for guiding the future construction and management of CWs.

Microbial community assembly in engineered bioreactors

Microbial community assembly (MCA) processes that shape microbial communities in environments are being used to analyze engineered bioreactors such as activated sludge systems and anaerobic digesters. The goal of studying MCA is to be able to understand and predict the effect of design and operation procedures on bioreactor microbial composition and function. Ultimately, this can lead to bioreactors that are more efficient, resilient, or resistant to perturbations. This review summarizes the ecological theories underpinning MCA, evaluates MCA analysis methods, analyzes how these MCA-based methods are applied to engineered bioreactors, and extracts lessons from case studies. Furthermore, we suggest future directions in MCA research in engineered bioreactor systems. The review aims to provide insights and guidance to the growing number of environmental engineers who wish to design and understand bioreactors through the lens of MCA.

Microbial community structure in a constructed wetland based on a recirculating aquaculture system: Exploring spatio-temporal variations and assembly mechanisms

The diversity, composition and performance of microbial communities within constructed wetlands (CW) were markedly influenced by spatio-temporal variations. A pilot-scale integrated vertical-flow constructed wetland (IVCW) as the biological purification unit within a recirculating aquaculture system (RAS) was established and monitored in this study. The investigation aimed to elucidate the responses of community structure, co-occurrence networks, and assembly mechanisms of the microbial community to spatial and temporal changes. Spatially, all a-diversity indices and microbial networks complexity were significantly higher in the upstream pool of the IVCW than in the downstream pool. Temporally, the richness increased over time, while the evenness showed a decreasing trend. The number of nodes and edges of microbial networks increased over time. Notably, the stable pollutant removal efficiencies were observed during IVCW operations, despite a-diversity and bacterial community networks exhibited significant variations across time. Functional redundancy emerged as a likely mechanism contributing to the stability of microbial ecosystem functions. Null model and neutral model analyses revealed the dominance of deterministic processes shaping microbial communities over time, with deterministic influences being more pronounced at lower a-diversity levels. DO and inorganic nitrogen emerged as the principal environmental factor influencing microbial community dynamics. This study provides a theoretical foundation for the regulation of microbial communities and environmental factors within the context of IVCW.

Anammox process in anaerobic baffled biofilm reactors with columnar packings: Characteristics of flow field and microbial community

The enrichment of anammox bacteria is a key issue in the application of anammox processes. A new type of reactor － anaerobic baffle biofilm reactor (ABBR) developed from anaerobic baffle reactor (ABR) was filled with columnar packings and established for effective enrichment of anammox bacteria. The flow field analysis showed that, compared with ABR, ABBR narrowed the dead zone so as to improve the substrate transferring performances. Two ABBRs with different types of columnar packings (Packings 1 and Packings 2) were constructed to culture anammox biofilms. Packings 1 consisted of the single-form honeycomb carriers while Packings 2 was modular composite packings consisting of non-woven fabric and honeycomb carriers. The effects of different types of columnar packings on microbial community and nitrogen removal were studied. The ABBR filled with Packings 2 had a higher retention rate of biomass than the ABBR filled with Packings 1, making the anammox start-up period be shortened by 21.28%. The enrichment of anammox bacteria were achieved and the dominant anammox bacteria were Candidatus Brocadia in both R1 and R2. However, there were four genera of anammox bacteria in R2 and one genus of anammox bacteria in R1, and the cell density of anammox bacteria in R2 was 95% higher than that in R1. R2 has the advantage of maintaining excellent and stable nitrogen removal performance at high nitrogen loading rate. The results revealed that the packings composed of two types of carriers may have a better enrichment effect on anammox bacteria. This study is of great significance for the rapid enrichment of anammox bacteria and the technical promotion of anammox process.

Distinct microbial characteristics of the robust single-stage coupling system during the conversion from anammox-denitritation to anammox-denitratation patterns

Simultaneous anammox-denitrification is effectively operated in two types, i.e., the anammox-denitritation (SAD pattern) and the anammox-denitratation (PDA pattern). The nitrate derived from inevitable nitrite oxidization likely determines the practical operational pattern of the coupling system, while little information is available regarding the microbial characteristics during the pattern conversion. Here, the single-stage bioreactor coupling anammox with denitrification was operated under conditions with a changed ratio of influent nitrite and nitrate. Results showed that the bioreactor exhibited a robust performance during the conversion from SAD to PDA patterns, corresponding with the total nitrogen removal efficiency ranging from 89.5% to 92.4%. Distinct community structures were observed in two patterns, while functional bacteria including the genera Denitratisoma, Thauera, Candidatus Brocadia, and Ca. Jettenia steadily co-existed. Meanwhile, the high transcription of hydrazine synthase genes demonstrated a stable anammox process, while the up-regulated transcription of nitrite and nitrous oxide reductase genes indicated that the complete denitrification process was enhanced for total nitrogen removal during the PDA pattern. Ecologically, stochastic processes dominantly governed the community assembly in two patterns. The PDA pattern improved the interconnectivity of communities, especially for the cooperative behaviors between dominant denitrifying bacteria and low-abundant species. These findings deepen our understanding of the microbial mechanism underlying the different patterns of the coupling system and potentially expand its engineering application.

Unifying concepts in methanogenic, aerobic, and anammox sludge granulation

The retention of dense and well-functioning microbial biomass is crucial for effective pollutant removal in several biological wastewater treatment technologies. High solids retention is often achieved through aggregation of microbial communities into dense, spherical aggregates known as granules, which were initially discovered in the 1980s. These granules have since been widely applied in upflow anaerobic digesters for waste-to-energy conversions. Furthermore, granular biomass has been applied in aerobic wastewater treatment and anaerobic ammonium oxidation (anammox) technologies. The mechanisms underpinning the formation of methanogenic, aerobic, and anammox granules are the subject of ongoing research. Although each granule type has been extensively studied in isolation, there has been a lack of comparative studies among these granulation processes. It is likely that there are some unifying concepts that are shared by all three sludge types. Identifying these unifying concepts could allow a unified theory of granulation to be formed. Here, we review the granulation mechanisms of methanogenic, aerobic, and anammox granular sludge, highlighting several common concepts, such as the role of extracellular polymeric substances, cations, and operational parameters like upflow velocity and shear force. We have then identified some unique features of each granule type, such as different internal structures, microbial compositions, and quorum sensing systems. Finally, we propose that future research should prioritize aspects of microbial ecology, such as community assembly or interspecies interactions in individual granules during their formation and growth.

Novel insights into carbon nanomaterials enhancing anammox for nitrogen removal: Effects and mechanisms

Carbon nanomaterials (CNMs) possess the properties including large specific surface area, high porosity, and stable chemical structures, presenting significant application advantages in wastewater treatment. Indeed, CNMs are considered to be added to anammox systems to strengthen anammox function, especially to resolve the challenge of anammox technology, i.e., the slow growth rate of anammox bacteria, as well as its high environmental sensitivity. This paper systematically reviews the promotion effects and mechanisms of CNMs on the nitrogen removal performance of anammox system. Among the zero-, one-, and two-dimensional CNMs, two-dimensional CNMs have best promoting effect on the nitrogen removal performance of anammox system due to its excellent conductivity and abundant functional groups. Then, the promotion effects of CNMs on anammox process are summarized from the perspective of anammox activity and bacteria abundance. Furthermore, CNMs not only enhance the anammox process, but also stimulate the coupling of denitrification pathways with anammox, as well as the improvement of system operational stability (alleviating the inhibitions of low temperature and pH fluctuation), thus contributing to the promoted nitrogen removal performance. Essentially, CNMs are capable of facilitating microbial immobilization and electron transfer, which favor to improve the efficiency and stability of anammox process. Finally, this review highlights the gap in knowledge and future work, aiming to provide a deeper understanding of how CNMs can strengthen the anammox system and provide a novel perspective for the engineering of the anammox process.

Effect of anode material and dispersal limitation on the performance and biofilm community in microbial electrolysis cells

In a microbial electrolysis cell (MEC), the oxidization of organic compounds is facilitated by an electrogenic biofilm on the anode surface. The biofilm community composition determines the function of the system. Both deterministic and stochastic factors affect the community, but the relative importance of different factors is poorly understood. Anode material is a deterministic factor as materials with different properties may select for different microorganisms. Ecological drift is a stochastic factor, which is amplified by dispersal limitation between communities. Here, we compared the effects of three anode materials (graphene, carbon cloth, and nickel) with the effect of dispersal limitation on the function and biofilm community assembly. Twelve MECs were operated for 56 days in four hydraulically connected loops and shotgun metagenomic sequencing was used to analyse the microbial community composition on the anode surfaces at the end of the experiment. The anode material was the most important factor affecting the performance of the MECs, explaining 54-80 % of the variance observed in peak current density, total electric charge generation, and start-up lag time, while dispersal limitation explained 10-16 % of the variance. Carbon cloth anodes had the highest current generation and shortest lag time. However, dispersal limitation was the most important factor affecting microbial community structure, explaining 61-98 % of the variance in community diversity, evenness, and the relative abundance of the most abundant taxa, while anode material explained 0-20 % of the variance. The biofilms contained nine Desulfobacterota metagenome-assembled genomes (MAGs), which made up 64-89 % of the communities and were likely responsible for electricity generation in the MECs. Different MAGs dominated in different MECs. Particularly two different genotypes related to Geobacter benzoatilyticus competed for dominance on the anodes and reached relative abundances up to 83 %. The winning genotype was the same in all MECs that were hydraulically connected irrespective of anode material used.

Affinity difference determines the assembly and interaction mode of anammox community reconstructed by siderophores

Anammox community is the core of anammox process. The constancy of the anammox community determines the stability of the anammox process and the ability of withstand environmental impact. Community stability is influenced by the assembly and interaction mode of the community. This study aimed to explore the assembly, interaction mode, and stability of anammox community influenced by two siderophores (enterobactin and putrebactin) specific for Ca. Brocadia and Ca. Kuenenia as produced in our previous research. Siderophores improved the stability of the anammox community, among which vulnerability dropped by 30.02 % and 72.53 % respectively. Enterobactin and putrebactin altered the succession speed and assembly pattern of communities, with a respective increase of 9.77 % and 80.87 % in the deterministic process of anammox community assembly, respectively. Enterobactin and putrebactin reduced the dependence of Ca. Brocadia and Ca. Kuenenia on companion bacteria by 60 items and 27 items respectively. The affinity of different siderophore-Fe with bacterial membrane receptors caused variations in community reconstruction, with Ca. Brocadia and Ca. Kuenenia exhibiting the highest affinity with enterobactin-Fe (-11.4 kcal/mol) and putrebactin-Fe (-9.0 kcal/mol), respectively. This study demonstrated how siderophores can enhance the stability of anammox process by regulating assembly and interaction mode of anammox community, while also revealing the underlying molecular mechanisms.

Linking morphological features to anammox communities in a partial nitritation and anammox (PN/A) biofilm reactor

Partial nitritation/anammox (PN/A) has been recognized as a cost-efficient process for wastewater nitrogen removal. The addition of carriers could help achieve biomass retention and enhance the treatment efficiency by forming the dense biofilm. However, accurately determining the abundance of anammox bacteria (AnAOB) to evaluate the biofilm development still remains challenging in practice without access to specialized facilities and experimental skills. In this study, we explored the feasibility of utilizing the morphological features of anammox biofilm as an indication of the biofilm development progression, and its correlation with microbial communities was also revealed. The time-series biofilms from an integrated fixed-film activated sludge (IFAS) system with stable PN/A performance were sampled representing the different biofilm development stages. The biofilm morphological features including color and texture were respectively quantified by red (R) coordinate and Local binary pattern (LBP) descriptor via image processing. Hierarchy clustering analysis proved that the extracted morphological descriptors could well distinguish the different stages (colonization, succession, and maturation) of biofilm development. The microbial community dynamics of time-series anammox biofilms were investigated using the amplicon sequence variant (ASV) analysis. Candidatus Brocadia, as the typical AnAOB, dominated in the whole communities of 16.3%-20.0%, moreover, the biofilm development was found to be driven by distinct Brocadia species. Linear regression evidenced that the Brocadia abundance could be directly correlated to the value of R and LBP, and the total variation of microbial communities could be significantly explained by the morphological features via redundancy analysis. This study demonstrates a new way to monitor the biofilm development by extracting the visible features of anammox aggregates, which can help facilitate the automated control of anammox-based bioprocess.

Hydrodynamic and anthropogenic disturbances co-shape microbiota rhythmicity and community assembly within intertidal groundwater-surface water continuum

Tidal hydrodynamics drive the groundwater-seawater exchange and shifts in microbiota structure in the coastal zone. However, how the coastal water microbiota structure and assembly patterns respond to periodic tidal fluctuations and anthropogenic disturbance remains unexplored in the intertidal groundwater-surface water (GW-SW) continuum, although it affects biogeochemical cycles and coastal water quality therein. Here, through hourly time-series sampling in the saltmarsh tidal creek, rhythmic patterns of microbiota structure in response to daily and monthly tidal fluctuations in intertidal surface water are disentangled for the first time. The similarity in archaeal community structures between groundwater and ebb-tide surface water (R2=0.06, p = 0.2) demonstrated archaeal transport through groundwater discharge, whereas multi-source transport mechanisms led to unique bacterial biota in ebb-tide water. Homogeneous selection (58.6%-69.3%) dominated microbiota assembly in the natural intertidal GW-SW continuum and the presence of 157 rhythmic ASVs identified at ebb tide and 141 at flood tide could be attributed to the difference in environmental selection between groundwater and seawater. For intertidal groundwater in the tidal creek affected by anthropogenically contaminated riverine inputs, higher microbial diversity and shift in community structure were primarily controlled by increased co-contribution of dispersal limitation and drift (jointly 57.8%) and enhanced microbial interactions. Overall, this study fills the knowledge gaps in the tide-driven water microbial dynamics in coastal transition zone and the response of intertidal groundwater microbiota to anthropogenic pollution of overlying waters. It also highlights the potential of microbiome analysis in enhancing coastal water quality monitoring and identifying anthropogenic pollution sources (e.g., pathogenic Vibrio in aquaculture) through the detection of rhythmic microbial variances associated with intertidal groundwater discharge and seawater intrusion.

Fast start-up of anammox process: Effects of extracellular polymeric substances addition on performance, granule properties, and bacterial community structure

The slow startup is the major obstacle to the application of anaerobic ammonium oxidation (anammox) process in mainstream wastewater treatment. Extracellular polymeric substances (EPS) are one potential resource for stable anammox reactor operation. Response surface analysis was used to optimize the specific anammox activity (SAA) with the addition of EPS; SAA was maximum at a temperature of 35 °C and the EPS concentration of 4 mg/L. By comparing the nitrogen removal of anammox reactors with no EPS (R0), immobilized EPS (EPS-alginate beads) (R1), and liquid EPS (R2), we found that EPS-alginate beads significantly speed up the startup of anammox process and enable the start time to be shortened from 31 to 19 days. As a result of the higher MLVSS content, higher zeta potential, and lower SVI₃₀, anammox granules of R1 exhibited a stronger capacity to aggregate. Moreover, EPS extracted from R1 had higher flocculation efficiencies than EPS derived from R0 and R2. Phylogenetic analysis of 16S rRNA genes revealed that the main anammox species in R1 is Kuenenia taxon. To clarify the relative significance of stochastic vs deterministic processes in the anammox community, neutral model and network analysis are employed. In R1, community assembly became more deterministic and stable than in other cultures. Our results show that EPS might inhibit heterotrophic denitrification and thereby promote anammox activity. This study suggested a quick start-up strategy for the anammox process based on resource recovery, which is helpful for environmentally sustainable and energy-efficient wastewater treatment.

Prokaryotic community interchange between distinct microhabitats causes community pressure on anammox biofilm development

Biofilms are an efficient way to underpin the biological process of wastewater treatment. However, little is known about the driving forces of biofilm formation and development in industrial settings. Long-term observation of anammox biofilms indicated the interplay between different microhabitats (biofilm, aggregate, plankton) was important in sustaining biofilm formation. SourceTracker analysis showed that 88.77 ± 2.26% of initial biofilm originated from the aggregate, however, independent evolution was led by anammox species in the later stage (182d and 245d). Noticeably, the source proportion of aggregate and plankton increased when temperature varied, suggesting an interchange of species between different microhabitats could be helpful to biofilm recovery. The microbial interaction pattern and community variation displayed similar trends, but the unknown source proportion of interaction was very high during the entire incubation (7-245d), thereby the same species may develop different relationships within the distinct microhabitats. The core phyla, Proteobacteria and Bacteroidota, accounted for ∼80% of interactions in all lifestyles, which is consistent with the fact that Bacteroidota played important role in the early stage of biofilm assembly. Although anammox species evolved few links with other OTUs, Candidatus Brocadiaceae still outcompeted the NS9 marine group to dominate the homogeneous selection process in the later stage (56-245d) of biofilm assembly, implying that the functional species may be decoupled from the core species in the microbial network. The conclusions will shed a light on the understanding of biofilm development in large-scale biosystems of wastewater treatment.

Insight into the temporal dynamics of microbial succession and ecology mechanisms in biological activated carbon tanks

Biological activated carbon (BAC) has long been applied in China to guarantee water quality and to achieve drinking water regulations. However, a knowledge gap remains regarding the temporal dynamics of microbial communities, particularly microbe-based assembly and co-occurrence patterns. Accordingly, this study investigated the evolution of BAC microbial communities using a pilot-scale system and examined by multivariate ecological combined with high-throughput Illumina sequencing and statistical methods. The results showed that BAC microbial diversity reached its peak in 2 years and declined thereafter. Microbial communities composition was accompanied by significant temporal evolution in the BAC biofilm. Deterministic processes gained in importance along with time, especially homogeneous selection which contributed 59.09 %-75.63 % to the community assembly in 8-yr, 9-yr, and 10-yr BAC. According to co-occurrence network analysis, microbial networks have more unstable structures over time, as evidenced by higher modularity, heightened connectivity, and fewer keystones. Moreover, the interaction between microbial taxa tended to have a higher proportion of competitive relationships during the operation of the BAC tank, ranging from 13.51 % to 76.35 %. Based on these dynamic ecological processes, microbial community succession in BAC biofilm might undergo four phases: community establishment (Years 0-2); community stability (Years 2-5); community quasi-degradation (Years 5-8); community degradation (Years 8-10). The performance of BAC was greatly influenced by community development, and contaminant removal gradually decreased as community succession proceeded. These results add to our knowledge of microbial ecology and provide the basis for further research into microbial communities' regulation strategies in BAC tanks.

Plant rhizosphere defense system respond differently to emerging polyfluoroalkyl substances F-53B and PFOS stress

Chlorinated polyfluoroalkyl ether sulfonate (F-53B) and perfluorooctanesulfonate (PFOS) are used and emitted as fog inhibitors in the chromium plating industry, and they are widely detected worldwide. To study the effects of F-53B and PFOS on the rhizosphere defense system, they were added at two levels (0.1 and 50 mg L^-1) to the soil where different plants (Lythrum salicaria and Phragmites communis) were grown. In bulk soils, high concentrations of F-53B/PFOS resulted in significant increases in soil pH, NH₄⁺-N, and NO₃^--N (the effect of PFOS on NO₃^--N was not significant). Moreover, the extent of the effects of PFOS and F-53B on the physicochemical properties of bulk soils were different (e.g., PFOS caused an increase of NH₄⁺-N by 8.94%-45.97% compared to 1.63%-25.20% for F-53B). Root exudates and PFASs together influenced the physicochemical properties of rhizosphere soils (e.g., TOC increased significantly in contaminated rhizosphere soils but did not change in non-bulk soils). Under the influence of F-53B/PFOS, the root exudates regulated by plants were changed and weakened the effect of F-53B/PFOS on microbial community of rhizosphere soil. The rhizosphere defense systems of different plants have both similarities and differences in response to different substances and concentrations.

Carrier type affects anammox community assembly, species interactions and nitrogen conversion

The impacts of carrier type on anammox community assembly, species interactions and nitrogen conversion were studied in this work. It was found that in addition to shared species with higher abundance, different carrier types recruited rare species by imposing selection pressure. Results from co-occurrence networks revealed that carrier type strongly influenced interactions between keystone species inhabiting within anammox biofilm through potentially inducing niche differences. Overall, elastic cubic sponges would lead to closer cooperation between different populations, whereas plastic hollow cylinders would trigger fiercer competition. Meanwhile, the results based on metagenomics sequencing showed carrier type significantly affected nitrogen conversion related genes abundances, and higher reads number was detected on the elastic cubic sponges. The information obtained in this work could provide some valuable information for the selection and optimization of carrier type in the anammox process.

Evidence of competition between electrogens shaping electroactive microbial communities in microbial electrolysis cells

In single-chamber microbial electrolysis cells (MECs), organic compounds are oxidized at the anode, liberating electrons that are used for hydrogen evolution at the cathode. Microbial communities on the anode and cathode surfaces and in the bulk liquid determine the function of the MEC. The communities are complex, and their assembly processes are poorly understood. We investigated MEC performance and community composition in nine MECs with a carbon cloth anode and a cathode of carbon nanoparticles, titanium, or stainless steel. Differences in lag time during the startup of replicate MECs suggested that the initial colonization by electrogenic bacteria was stochastic. A network analysis revealed negative correlations between different putatively electrogenic Deltaproteobacteria on the anode. Proximity to the conductive anode surface is important for electrogens, so the competition for space could explain the observed negative correlations. The cathode communities were dominated by hydrogen-utilizing taxa such as Methanobacterium and had a much lower proportion of negative correlations than the anodes. This could be explained by the diffusion of hydrogen throughout the cathode biofilms, reducing the need to compete for space.

Unraveling the ecological mechanisms of bacterial succession in epiphytic biofilms on Vallisneria natans and Hydrilla verticillata during bioremediation of phenanthrene and pyrene polluted wetland

In wetland ecosystem, the microbial succession in epiphytic biofilms of submerged macrophytes remains to be fully elucidated, especially submerged macrophytes used to remediate organic pollutants contaminated sediment. Herein, 16 S rRNA gene sequencing was used to investigate the bacterial dynamics and ecological processes in the biofilms of two typical submerged macrophytes (Vallisneria natans and Hydrilla verticillata) settled in sediment polluted by polycyclic aromatic hydrocarbons (PAHs) at two growth periods. The results presented that the variations of bacterial community in the biofilms were influenced by attached surfaces (explanation ratio: 17.30%), incubation time (32.30%) and environmental factors (39.10%). Bacterial community assembly was mainly driven by dispersal limitation which triggered more positive co-occurrence associations in microbial networks, maintaining ecological stability in the process of bioremediation of PAHs. Additionally, the functional redundancy strength of bacterial community was more affected by attached surface than incubation time. The structural equation model illustrated that community assembly drove β-diversity and explained a part of ecological functions. Environmental factors, community assembly, and β-diversity jointly affected microbial networks. Overall, our study offers new insights into the microbial ecology in biofilms attached on the submerged macrophytes settled in PAH-polluted sediment, providing important information for deeply understanding submerged macrophyte-biofilm complex and promoting sustainable phytoremediation in shallow lacustrine and marshy ecosystems.

Metagenomic insights into the symbiotic relationship in anammox consortia at reduced temperature

Anammox as a promising biological nitrogen removal technology has attracted much attention. However, cold temperature would limit its wide application and little is known about the microbial interactions between anammox bacteria (AnAOB) and heterotrophic bacteria at cold temperature. Here, we observed reduced temperature (25-15 °C) promoted the secretion of EPS and thus stimulated bigger size of granular sludge in a laboratory-scale anammox reactor. We further combined co-occurrence network analysis and genome-centered metagenomics to explore the potential interactions between AnAOB and heterotrophic bacteria. Network analysis suggested 22 out of 25 positively related species were reported as definite heterotrophic bacteria in subnetwork of AnAOB. Genome-centered metagenomics analysis yielded 23 metagenomic assembly genomes (MAGs), and we found that Acidobacteriota-affiliated bacteria could biosynthesize most polysaccharides (PS) precursors and contain the most glycosyltransferases and transporters to facilitate exopolysaccharides biosynthesis, together with partial PS precursors produced by AnAOB. AMX1 as the only anammox genome could synthesize most amino acids and cross feed with some heterotrophs to affect the extracellular protein function. Additionally, Bacteroidota, Planctomycetota, Chloroflexota, and Proteobacteria could contribute folate and molybdopterin cofactor for AMX1 to benefit their activity and growth. Superphylum Patescibacteria could survive by cross-feeding with AnAOB and heterotrophic organisms about organic compounds (Glyceraldehyde-3P and lactate). These cross-feedings maintained the stability of anammox reactor performance and emphasize the importance of heterotrophs in anammox system at reduced temperature.

Enhancing nitrogen removal through directly integrating anammox into mainstream wastewater treatment: Advantageous, issues and future study

Anaerobic ammonium oxidation (anammox) has great potential to be applied to the process of nitrogen removal from mainstream wastewater. However, directly applying complete anammox to the mainstream is typically hindered by low temperatures, a low ammonia concentration, and high organic matter concentrations. Directly integrating anammox into mainstream treatment by enhancing the in-situ enrichment of anammox bacteria in wastewater treatment plants (WWTPs) could effectively improve the nitrogen removal efficiency and reduce the treatment cost. A certain anammox bacteria abundance in full-scale WWTPs provides the feasibility of directly integrating anammox into mainstream treatment and realizing partial mainstream anammox. The technical development status of partial anammox and the mechanisms of achieving partial mainstream anammox by aeration and organic control are summarized. This review provides an enhanced understanding of this novel technical route of partial mainstream anammox treatment for improving the quality, performance, and prospects for this technology to be used in upgrading WWTPs.

Effects of various materials used to promote the direct interspecies electron transfer on anaerobic digestion of low-concentration swine manure

The activation of direct interspecies electron transfer (DIET) by the supplementation of conductive materials is one of the effective and available methods to enhance anaerobic digestion (AD). Microorganisms that colonize the surface of these materials form biofilms, the study of which could provide new insights into the character of the DIET process and its effect on AD. The present study focused on AD performance, microbial community, as well as morphological and topological features of biofilms on various materials used to promote DIET during AD of low-concentration swine manure. The best AD characteristics were observed in stainless steel mesh (SM)/digested cow manure (CM) and polyester felt (PF)/digested sewage sludge (SS) combinations used as material/inoculum, respectively. Thus, potential methane yields in CM-SM and SS-PF were up to 26.4% and 26.2% higher compared to the corresponding controls. Microbial analysis of biofilms revealed the dominance of putatively syntrophic bacteria of the MBA03 group of the Limnochordia class in CM inoculated reactors, and syntrophic proteolytic bacteria of the genus Coprothermobacter and acetogenic Clostridium sensu stricto 1, known for their ability to carry out DIET, in SS inoculated reactors. Biofilms on non-conductive materials contained pili-like structures, which were observed only in SS inoculated reactors. Polyester felt tended to biofoul better than carbon felt, resulting in up to 2.8, 3.2 and 1.8 higher nucleic acid, extracellular polymeric substances, and total biomass content, respectively, depending on the inoculum. These results provide new insights into the different types of DIET that can occur in low-loaded AD systems with attached growth.

Fast formation of anammox granules using a nitrification-denitrification sludge and transformation of microbial community

A lengthy start-up period has been one of the key obstacles limiting the application of the anammox process. In this investigation, a nitrification-denitrification sludge was used to start-up the anammox EGSB process. The transformation process from nitrification-denitrification sludge to anammox granule sludge was explored through the aspects of nitrogen removal performance, granule properties, microbial community structure, and evolution route. A successful start-up of the anammox process was achieved after 94 days of reactor operation. The highest nitrogen removal rate (NRR) obtained was 7.25±0.16 gN/L/d at a nitrogen loading rate (NLR) of 8.0 gN/L/d, and the corresponding nitrogen removal efficiency was a high 90.61±1.99%. The results of the microbial analysis revealed significant changes in anammox bacteria, nitrifying bacteria, and denitrifying bacteria in the sludge. Notably, the anammox bacteria abundance increased from 2.5% to 29.0% during the operation, and Candidatus Kuenenia and Candidatus Brocadia were the dominant genera. Distinct-different successions on Candidatus Brocadia and Candidatus Kuenenia were also observed over the long-term period. In addition, the settling performance, anammox activity and biomass retention capacity of the granules were significantly enhanced during this process, and the corresponding granule evolution route was also proposed. The results in this study indicate the feasibility of using available seed sludge source for the fast-transformation of anammox granules, it is beneficial to the large-scale application of anammox process and the utilization of excess sludge.

Rapid initiation of a single-stage partial nitritation-anammox process treating low-strength ammonia wastewater: Novel insights into biofilm development on porous polyurethane hydrogel carrier

Media-supported biofilm is a powerful strategy for growth and enrichment of slow-growing microorganisms. In this study, a single-stage nitritation-anammox process treating low-strength wastewater was successfully started to investigate the biofilm development on porous polyurethane hydrogel carrier. Suspended biomass migration into the carrier and being entrapment by its internal interconnected micropores dominated the fast initial colonization stage. Both surface-attached growth and embedded growth of microbes occurred during the following accumulation stage. Fluorescence in situ hybridization analysis of mature biofilm indicated that ammonium-oxidizing bacteria located at the outer layers featured a surface-attached growth, while anammox microcolonies housed in the inner layers proliferated as an embedded-like growth. In this way, the growth rate of anammox bacteria (predominated by Candidatus Kuenenia) could be 0.079 d^-1. The anammox potential of the biofilm reactor reached 1.65 ± 0.3 kg/m³/d within two months. This study provides novel insights into nitritation-anammox biofilm formation on the porous polyurethane hydrogel carrier.

Time-lagged interspecies interactions prevail during biofilm development in moving bed biofilm reactor

Clarifying the essential succession dynamics of interspecies interactions during biofilm development is crucial for the regulation and application of biofilm-based processes. In this study, regular and time-series phylogenetic molecular ecological networks (pMENs) were constructed to investigate ordinary and time-lagged interspecies interactions during biofilm development in a moving bed biofilm reactor (MBBR). Positive interactions dominated both regular (89.78%) and time-series (77.04%) ecological networks, suggesting that extensive cooperative behaviors facilitated biofilm development. The pronounced directional interactions (72.52%) in the time-series network further indicated that time-lagged interspecies interactions prevailed in the biofilm development process. Specifically, the proportion of directional negative interactions was higher than that of positive interactions, implying that interspecific competition preferred to be time-lagged. The time-series network revealed that module hubs exhibited extensive time-lagged positive interactions with their neighbors, and most of them exhibited altruistic behaviors. Keystone species possessing more positive interactions were positively correlated with biofilm biomass, NO₃ ^- -N concentrations, and the removal efficiencies of NH₄ ⁺ -N and COD. However, keystone species and peripherals that were negatively targeted by their neighbors showed positive correlations with the concentrations of NO₂ ^- -N, polysaccharides, and proteins in the soluble microbial products. The data highlight that the time-series network can provide directional microbial interactions along with the biofilm development process, which would help to predict the tendency of community shifts and propose efficient strategies for the regulation of biofilm-based processes. This article is protected by copyright. All rights reserved.

Biofilm growth characterization and treatment performance in a single stage partial nitritation/anammox process with a biofilm carrier

Biofilm carriers can avoid microorganism washout while maintaining a high amount of biomass, but are also associated with a long biofilm formation period and biofilm aging. A single stage partial nitritation/anammox process (single stage PN/A) reactor was setup to study the biofilm growth characterization and treatment performance under an NLR of 0.53 to 0.90 gN/L/d over one year. Biofilm growth was divided into three stages: the formation stage, maturation stage and aging stage. The initial biofilm was observed at day 84. A nitrogen removal efficiency of 83.4% was achieved at an NLR of 0.90 gN/L/d during the mature biofilm stage. Starvation, nitrogen gas accumulation and hydroxyapatite formation resulted in biofilm aging. After mechanical stirring treatment, biofilm reactivation was achieved by biofilm re-formation within one month. There is clear potential for phosphorus recovery, as indicated by the 5.24% - 6.29% phosphorus content in the biofilm (similar to the 5%-7% phosphorus content in enhanced biological phosphate removal sludge). The AnAOB genera abundance in the biofilm maintained at a high level of 18.25%-32.31%, while the abundance of AnAOB increased from the initial 4.10% to 13.78% after mechanical stirring treatment in the suspended sludge ensured biofilm reactivation. The results of this study clearly show that mechanical stirring treatment can be used to achieve the biofilm reactivation as the biofilm fills with the hollow cylindrical carrier. This study has potential as a useful reference for the realization of the wide application of the biofilm single stage PN/A process in the future.

Biofilm phenotypes and internal community succession determines distinct growth of anammox bacteria in functional anammox biofilms

In this study, time-series anammox functional biofilms were obtained in a lab-scale simultaneous partial nitritation/anammox process for treating high-strength ammonium. The variations in the biofilm phenotypes, community succession, and anammox bacteria abundance over time were evaluated using optical microscopy, 16S rRNA gene sequencing, and qPCR. The result revealed that biofilm has three distinct stages of the community development trajectory across a 182-day temporal scale. Anammox bacteria growth rates were 0.035 d^-1, 0.0015 d^-1, and 0.011 d^-1, respectively. The diversity and network analysis suggested that the positive priority effect of ammonia oxidizing bacteria was the primary factor for the rapid proliferation of anammox bacteria, and the species replacement triggering priority effect forfeiture and substituted functional recruitment were reasons for the slow proliferation and stable proliferation of anammox bacteria, respectively. Taken together, the higher microbial diversity and stable community composite were key prerequisites for the proliferation of the anammox bacteria.

Varied interspecies interactions between anammox and denitrifying bacteria enhanced nitrogen removal in a single-stage simultaneous anammox and denitrification system

The simultaneous anammox and denitrification (SAD) system has received growing interest for the enhanced nitrogen removal, while the ecological traits of microbial community including spatial distribution characteristics, assembly processes and interspecies interactions have not been fully unraveled. The present study applied metagenomics and ecological analysis methods to gain the ecological traits of microbial communities in the SAD system across different organic substrate loadings. Results showed that organic matter significantly affected the bioreactor performance, and the optimal total nitrogen removal efficiency reached 93.4 ± 0.7% under the COD concentrations of 180 ± 18.2 mg/L. Functional organisms including Candidatus Brocadia (3.9%), Denitratisoma (1.6%), Dokdonella (4.4%) and Thauera (4.6%) obviously enriched under the optimal organic loading conditions. Moreover, microbial communities were significantly governed by deterministic process under high organic concentrations, and the denitrifying organisms displayed important ecological roles in the communities. Although anammox bacteria obviously enriched at the middle of bioreactor, it possessed the highest expression activities at both bottom and middle sites. Denitrifying bacteria that enriched at the bottom sites strongly achieved nitrate reduction and provided nitrite for anammox bacteria, while these organisms trended to compete nitrite with anammox bacteria at the middle site. These findings highlight the importance of microbial ecology in the SAD systems, which may expand our understanding of the synergistic patterns between anammox and denitrifying bacteria.

New Insight Into the Interspecies Shift of Anammox Bacteria Ca. "Brocadia" and Ca. "Jettenia" in Reactors Fed With Formate and Folate

The sensitivity of anaerobic ammonium-oxidizing (anammox) bacteria to environmental fluctuations is a frequent cause of reactor malfunctions. It was hypothesized that the addition of formate and folate would have a stimulating effect on anammox bacteria, which in turn would lead to the stability of the anammox process under conditions of a sharp increase in ammonium load, i.e., it helps overcome a stress factor. The effect of formate and folate was investigated using a setup consisting of three parallel sequencing batch reactors equipped with a carrier. Two runs of the reactors were performed. The composition of the microbial community was studied by the 16S rRNA gene profiling and metagenomic analysis. Among anammox bacteria, Ca. "Brocadia" spp. dominated during the first run. A stimulatory effect of folate on the daily nitrogen removal rate (dN) was identified. The addition of formate led to progress in dissimilatory nitrate reduction and stimulated the growth of Ca. "Jettenia" spp. The spatial separation of two anammox species was observed in the formate reactor: Ca. "Brocadia" occupied the carrier and Ca. "Jettenia"-the walls of the reactors. Biomass storage at low temperature without feeding led to an interspecies shift in anammox bacteria in favor of Ca. "Jettenia." During the second run, a domination of Ca. "Jettenia" spp. was recorded along with a stimulating effect of formate, and there was no effect of folate on dN. A comparative genome analysis revealed the patterns suggesting different strategies used by Ca. "Brocadia" and Ca. "Jettenia" spp. to cope with environmental changes.

Low strength wastewater anammox start-up by stepwise decrement in influent nitrogen: Biofilm formation mechanism and mathematical modelling

The application of mainstream anammox process is hampered by its overlong start-up and instability under disturbance. A lab-scale mainstream anammox moving bed biofilm reactor (MBBR) was successfully started in 120 days with stepwise decrement in influent nitrogen concentration from sidestream to mainstream condition. The initial colonization by Candidatus Jettenia and filamentous fermenter Anaerolineaceae were potentially mediated by hydrophobic interaction and type IV pilus. Ca. Kuenenia with higher substrate affinity outcompeted Ca. Jettenia, and the predominant fermenters shifted to fermentative Ignavibacteriaceae in the mature biofilm. A novel mainstream anammox biofilm development (MABD) model was constructed to describe biofilm growth, population dynamics, and nitrogen removal performance. The simulation results suggested that higher inocula biomass (460-690 mgVSS·L^-1), relative abundance of low-affinity AnAOB in the inocula (e.g., Ca. Jettenia, 1.3-2%), and the early-stage solids retention time (45-68 days) were desired to form thicker biofilm and improve effluent quality during 120-day mainstream anammox MBBR start-up. The mechanistic insights into biofilm formation and predictive power of the newly developed MABD model are of importance to the design and operation of mainstream anammox processes towards more biofilm biomass and higher nitrogen removal efficiency.

Ecological Linkages between a Biofilm Ecosystem and Reactor Performance: The Specificity of Biofilm Development Phases

In biofilm-based engineered ecosystems, the reactor performance was closely linked to interspecies interactions within a biofilm ecosystem, whereas the ecological processes underpinning such linkage were still unenlightened. Herein, the principles of community succession and assembly were integrated to capture the ecological laws of biofilm development by molecular ecological networks and assembly model analysis based on the 16S rRNA sequencing analysis and metagenomics in a well-controlled moving bed biofilm reactor. At the initial colonization phase (days 0-2, driven by initial colonizers), interspecific cooperation (74.18%) facilitated initial biofilm formation, whereas some pioneers, and keystone species disappeared at later phases. At the accumulation phase (days 3-30, rapid biofilm development), interspecific cooperation (81.41 ± 5.07%) contributed to rapid biofilm development and keystone species were mainly involved in quorum sensing or positively correlated with extracellular polymeric substance production. At the maturation phase (days 31-106, a well-adapted quasi-equilibrium state), increased interspecific competition (32.74 ± 4.77%) and higher small-world property facilitated the rapid information transportation and pollutant treatment, and keystone species were positively correlated with the removal of COD and NH₄⁺-N. Homogenizing dispersal diminished the contemporary community dissimilarities, while turnover but rather nestedness governed the temporal variations in the biofilm succession period. This study highlighted the specificity of ecological processes at distinct biofilm development phases, which would advance our understanding on the development-to-function linkages in biofilm-based treatment processes.