Deciphering bacterial social traits via diffusible signal factor (DSF) -mediated public goods in an anammox community

Deciphering the code of temperature rise on aerobic granular sludge stability: A DSF-c-di-GMP mediated regulatory mechanism

Diffusible signal factor (DSF)-c-di-GMP-mediated strategies have been proposed as an effective regulatory approach for signal molecules in aerobic granular sludge (AGS). The increase in temperature from low to normal levels had a significant impact on AGS stability. In this study, two reactors were established to investigate the effects of different temperature rise modes (abrupt or gradual) on AGS stability. Following the temperature rise, the DSF concentration in Reactor 1 (R1, abrupt) rose nearly fourfold by day 125, while LB-EPS levels decreased by 70%. In contrast, in Reactor 2 (R2, gradual), the DSF concentration increased by only twofold, and TB-EPS levels decreased by 25%. Flavobacterium (R1: 3.64%→0.41%, R2: 3.70%→1.97%) and Thauera (R1: 28.62%→4.01%, R2: 27.56%→13.10%), which are associated with EPS and signal molecule production, exhibited significantly different trends in response to the different temperature rise modes. Batch experiments exhibited that the exogenous addition of DSF and the DSF inhibitor, salicylic acid (SA), can regulate EPS content by altering the concentration of signaling molecules, particularly the LB-EPS, thereby reducing the risk of sludge collapse. These findings offer novel insights into the role of DSF in bacterial communication during AGS formation under temperature rise, providing a basis for regulating AGS formation and stability.

A comprehensive review of antibiotics stress on anammox systems: Mechanisms, applications, and challenges

Anaerobic ammonia oxidation (anammox), an energy-efficient technology for treating ammonium-rich wastewater, faces the challenge of antibiotic stress in sewage. This paper systematically evaluated the impact of antibiotics on anammox by considering both inhibitory effects and recovery duration. This review focused on cellular responses, including extracellular polymeric substances (EPS), quorum sensing (QS), and enzymes. Then, the physiological properties of cells and the interactions between nitrogen and carbon metabolism under antibiotic stress were discussed, particularly within the anammoxosome. The microbial community evolution and the development and transfer of antibiotic resistance genes (ARGs) were further analyzed to reveal the resistance mechanisms of anammox. To address the limitations imposed by antibiotics, the development of bio-augmentation and combined processes based on molecular biology techniques, such as bio-electrochemical systems (BES), has been suggested. This review offered new insights into the mechanisms of antibiotic inhibition during the anammox process and aimed to advance their engineering applications.

Quorum quenching inhibits the formation and electroactivity of electrogenic biofilm by weakening intracellular c-di-GMP and extracellular AHL-mediated signal communication

Electrogenic biofilm formation has been shown to be induced by intracellular c-di-GMP signaling and extracellular quorum sensing, but their interactions have been rarely explored. This study explored the effects of quorum quenching (induced by adding acylase) on electrogenic biofilm development and its underlying mechanisms. Quorum quenching impaired the electricity generation and electroactivity of electrogenic biofilms as indicated by dye decolorization rate. It significantly decreased the proportion of typical exoelectrogen Geobacter from 62.0% to 36.5% after 90 days of operation, and enriched some other functional genera (e.g., Dysgonomonas and Sphaerochaeta) to ensure normal physiological function. Moreover, metagenomic analysis revealed that the addition of acylase weakened the potential of chemical communication, as indicated by the decrease in the abundance of genes encoding the production of AHL and c-di-GMP, and the increase in the abundance of aiiA and pvdQ genes (encoding quorum quenching) and cdgC gene (responsible for c-di-GMP breakdown). Functional contribution analysis indicated that Geobacter was a major contributor to hdtS gene (encoding AHL synthesis). These findings demonstrated that quorum quenching adversely impaired not only quorum sensing but also intracellular c-di-GMP signaling, ultimately inhibiting the development of biofilm. This work lays the foundation for regulating electrogenic biofilm development and improving the performance of microbial electrochemical system using signal communication strategy.

Metagenomic insight into the diffusion signal factor mediated social traits of anammox consortia after starvation

Biomass starvation is common in biological wastewater treatment. As a social trait of microbial community, how quorum sensing (QS) regulated bacterial trade-off through interactions after starvation remains unclear. This study deciphered the mechanism of anaerobic ammonium oxidation (anammox) consortia in response to starvation, including reducing extracellular electron transfer (EET), adenosine 5'-triphosphate (ATP) content and amino acid metabolism. Metagenomic analysis has shown that the addition of the diffusion signal factor (DSF) resulted in a high abundance of antioxidant genes, which contributed to achieving redox balance in anammox bacteria. There was an enrichment of Geobacter and Methanosarcina, which were QS-responsive direct interspecific electron transfer participants. Furthermore, DSF stimulated the nitrogen and carbon metabolism of Ca. Kuenenia_stuttgartiensis, promoting syntrophy of metabolic intermediates within microbial community. This study highlighted the effect of DSF on the microbial interaction patterns and deciphered the QS-based social traits of anammox consortia after starvation, facilitating the stable operation of the anammox process.

Tracing the electron transfer behavior driven by hydrophyte-derived carbon materials empowered autotrophic denitrification in iron-based constructed wetlands: Efficacy and enhancement mechanism

Iron-based constructed wetlands (ICWs) displayed great potential in deep nitrogen elimination for low-polluted wastewater. However, the unsatisfactory denitrification performance caused by the limited solubility and sluggish activity of iron substrates needs to be improved in an eco-effective manner. To fill this gap, the bioavailability of iron substrates (iron scraps) affected by wetland biomass-derived carbon materials with potential conductivity were explored. Results indicated that the cumulative removal of TN in biochar-added ICW (BC-ICW) and activated carbon-added ICW (AC-ICW) increased by 29.04 % and 22.96 %, respectively. The carbon matrix of AC played the geo-conductor role to facilitate the rapid release of iron ions, as indicated by the higher TN removal efficiency of AC-ICW (45.36 ± 1.45 %) at the early stage, while the reduced conductivity of AC negatively impacted the nitrogen removal. BC-ICW exhibited intensified denitrification potential, with higher TN removal capacity (52.08 ± 3.04 %) and effluent Fe2+ concentration. Electroactive bacteria (EB) (Geobacter, Desulfovibrio, Shewanella, etc.) associated with extracellular electron transfer were enriched in BC-ICW, as well as the expanded niches breadth and improved microbial community diversity. The electron-shuttling effect of BC was mainly attributed to its oxygenated functional groups (quinone/phenolic moieties), which supported the electron transfer from EB to extracellular iron oxides, as evidenced by the increased Fe(III)(hydro)oxides bioavailability. Besides, biochar concurrently up-regulated the gene expression of electron transport chains/mediators and denitrification reductases, suggesting that BC boosted the active iron cycle and iron-mediated autotrophic denitrification in ICWs by accelerating intracellular and extracellular electron transfer. This work explored the electron transfer behavior of biomass-derived carbon materials coupled with ICWs to enhance denitrification, providing insights into the sustainable application of biomass derived carbon-assisted ICWs in tertiary treatment.

Acyl-Homoserine Lactone Enhances the Resistance of Anammox Consortia under Heavy Metal Stress: Quorum Sensing Regulatory Mechanism

Anaerobic ammonium oxidation (anammox) represents an energy-efficient process for the removal of biological nitrogen from ammonium-rich wastewater. However, the susceptibility of anammox bacteria to coexisting heavy metals considerably restricts their use in engineering practices. Here, we report that acyl-homoserine lactone (AHL), a signaling molecule that mediates quorum sensing (QS), significantly enhances the nitrogen removal rate by 24% under Cu2+ stress. A suite of macro-/microanalytical and bioinformatic analyses was exploited to unravel the underlying mechanisms of AHL-induced Cu2+ resistance. Macro-/microanalytical evidence indicated that AHL regulations on the production, spatial distribution, and functional groups of extracellular polymeric substances were not significant, ruling out extracellular partitioning and complexation as a principal mechanism. Meanwhile, molecular biological evidence showed that AHL upregulated the transcriptional levels of resistance genes (sod, kat, cysQ, and czcC responsible for antioxidation defense, Cu2+ sequestration, and transport) to appreciable extents, indicating intracellular resistance as the primary mechanism. This study yielded a mechanistic understanding of the regulatory roles of AHL in extracellular and intracellular resistance of anammox consortia, providing a fundamental basis for utilizing QS regulation for efficient nitrogen removal in wastewaters with heavy metal stress.

Bacterial communication intelligently regulates their interactions in anammox consortia under decreasing temperatures

Bacterial communication could affect their interactions, but whether this regulation has "intelligence" is still unknown. Here, we operated an anammox reactor under temperature gradient from 35 °C to 15 °C. As results, expression abundance of bacterial communication genes increased by 12 % significantly after temperature declined. Division of labor among distinct signal molecules was evidenced by complementary roles of acyl-homoserine lactones (AHLs) and diffusible signal factor (DSF) in affecting bacterial interactions and niche differentiation respectively. DSF based inter-and intra-communication helped bacteria match their investments and rewards during cross-feedings. When temperature was below 25 °C, transcription regulator Clp governed by DSF inclined to promote folate and molybdenum cofactor biosynthesis, which coincidentally benefited one anammox species more than another. Meanwhile, for the anammox species with lower benefits, Clp also inclined to decrease biosynthesis of costly tryptophan and vitamin B1 rewarding others. Interestingly, bacterial communication inclined to influence the bacteria with many cooperators in the community or with high capacity to export cofactors for cross-feedings when temperature decreased. As results, these bacteria were enriched which could lead to closer interactions in whole community to adapt to low temperatures. The discovered intelligence of bacterial communication opened another window for understanding bacterial sociobiology.

Multidimensional Insights into Organics Stress on Anammox systems: From a "Molecule-Cell-Ecology" Perspective

Anaerobic ammonium oxidation (anammox) is efficient and cost-effective for treating high-strength ammonia wastewater, but the organics in wastewater will affect its stability. To address this challenge, it is crucial to gain a deep understanding of the inhibitory effects and mechanisms of organics stress on anammox bacteria. The review provided a comprehensive classification of organics and evaluated their specific effects on the anammox system according to their respective characteristics. Based on the micro to macro perspective, the "molecule-cell-ecology" inhibitory mechanism of organics on anammox bacteria was proposed. The molecular observation systematically summarized the binding process and action sites of organics with anammox bacteria. At the cellular observation, the mechanisms of organics effects on extracellular polymeric substances, membranes, and anammoxosome of anammox bacteria were also expounded. At the ecological observation, the dynamic changes in coexisting populations and their role in organics transformation were further discussed. Further revelations on response mechanisms and inhibition mitigation strategies were proposed to broaden the applicability of anammox systems for organic wastewater. This review offered a multidimensional understanding of the organics inhibitory mechanism of anammox bacteria and provided a theoretical foundation for anammox systems.

Arginine enhances activity of anammox consortia and process stability with increased nitrogen loading

Cross-feeding based on amino acids metabolism is an important strategy by which anammox bacteria and the co-existing heterotrophs facilitate their own growth and survival. Arginine is one of the necessary amino acids required for bacterial protein biosynthesis but whether adding arginine could benefit growth of anammox bacteria remains unknown. In this study, arginine was supplemented at dose of 5 mg·L-1 to promote the nitrogen removal performance of anammox bioreactors under varied loading rates. The results showed that nitrogen removal efficiency increased by 10.2 % under higher loading rates. Arginine addition substantially simulated the secretion of extracellular proteins and polysaccharides within anammox consortia as a strategy against unfavorable conditions. Canditatus Kuenenia dominated the anammox consortia and their 16S rRNA abundance and anammox-related functional genes were significantly increased by up to 0.42 times and 5.81 times, respectively. The findings of this study provided a feasible strategy to improve the performance of anammox reactors with arginine supplementation.

Role of diffusible signal factor in regulating aerobic granular sludge formation under temperature shocks

Signal-molecule-mediated strategies are proposed for aerobic granular sludge (AGS), but the regulatory mechanisms behind AGS formation are largely unexplored. In this study, two sequence batch reactors (SBRs) were operated to investigate the regulation of diffusible signal factor (DSF) in AGS formation. DSF secretion in Reactor 2 (R2: 10 °C→25 °C) decreased by 15 % compared to Reactor 1 (R1: 25 °C→10 °C), correlating with a 26 % increase in extracellular polymeric substance (EPS) concentration, resulting in a 63 % acceleration of the granulation process. After temperature shocks in R2, DSF concentration increased by 70 %, while EPS concentration decreased by 47 %. Batch tests confirmed that DSF inhibited EPS secretion. Combined 16S rRNA analysis and machine learning identified key bacteria responsible for secreting EPS and signal molecule. The decrease in the abundances of these bacteria reduced EPS production. These findings on DSF regulation of EPS secretion provide an in-depth understanding of enhanced AGS granulation.

Research on intensive nitrogen removal of municipal sewage by mainstream anaerobic ammonia oxidation process

The anaerobic ammonia oxidation (anammox) process is a pivotal nitrogen removal technique, playing a significant role in the field of wastewater treatment. The paper commences by delineating the merits of the anammox process in comparison to conventional nitrification-denitrification techniques. Subsequently, it delves into the characteristics of different sludge morphologies process of the behavior of anammox bacteria and their reactions to environmental factors. Revising the issues associated with managing urban sewage in mainstream areas., it discusses the issues faced by the anammox process under reduced nitrogen loads, such as restricted activity due to decreased the levels of ammonia nitrogen and nitrite concentrations, as well as the impact of environmental factors like low temperature, organic matter, and sulfur ions. Following this, a comprehensive review of various types of coupled anammox processes is provided, highlighting the advantages and characteristics of partial nitrification (PN), partial denitrification (PD), methane-dependent nitrite/nitrate reduction (DAMO), sulfur-driven autotrophic denitrification (SAD), iron ammonia oxidation (feammox) and algae photoautotrophy coupling techniques, emphasizing their significance in system stability and resource utilization efficiency. Future research directions include exploring the applicability of the anammox process under various temperature conditions and addressing NO3--N issues in effluent. The findings from these studies will offer valuable insights for further enhancing the optimization of the anammox process in mainstream urban wastewater treatment.

Monitoring the Biochemical Activity of Single Anammox Granules with Microbarometers

Granule-based anaerobic ammonium oxidation (Anammox) is a promising biotechnology for wastewater treatments with extraordinary performance in nitrogen removal. However, traditional analytical methods often delivered an average activity of a bulk sample consisting of millions and even billions of Anammox granules with distinct sizes and components. Here, we developed a novel technique to monitor the biochemical activity of individual Anammox granules in real-time by recording the production rate of nitrogen gas with a microbarometer in a sealed chamber containing only one granule. It was found that the specific activity of a single Anammox granule not only varied by tens of folds among different individuals with similar sizes (activity heterogeneity) but also revealed significant breath-like dynamics over time (temporal fluctuation). Statistical analysis on tens of individuals further revealed two subpopulations with distinct color and specific activity, which were subsequently attributed to the different expression levels of heme c content and hydrazine dehydrogenase activity. This study not only provides a general methodology for various kinds of gas-producing microbial processes but also establishes a bottom-up strategy for exploring the structural-activity relationship at a single sludge granule level, with implications for developing a better Anammox process.

Evolution of quorum sensing process and their regulatory role on biochemical metabolism during the organic loading rate increase in dry anaerobic digestion

The organic loading rate (OLR) is a critical parameter affecting the stability of dry anaerobic digestion (AD) of kitchen waste (KW), and significantly impacting the variations in physicochemical parameters and microbial communities. However, the evolution of quorum sensing (QS) and their role on anaerobic biochemical metabolism during the increase in OLR in dry AD remain unknown. Therefore, this study systematically elucidated the matter through multi-omics analysis based on a pilot-scale dry AD of KW. The results demonstrated that fluctuations in the OLR significantly influenced the microbial QS in dry AD. When the OLR ≤4.0 g·VS/L·d, the system operated stably, and methane production increased. The enrichment of Proteobacteria was crucial for sustaining high levels of functional genes associated with various types of QS, including acyl-homoserine lactones (AI-1), autoinducer-2 (AI-2), autoinducer-3 (AI-3), and gamma-aminobutyric acid (GABA). This enabled cooperative communication among microbes under low OLR. Furthermore, most genes associated with these QS processes positively affected hydrolysis, acidogenesis, and methanogenesis. When the OLR increased to 6.0 g·VS/L·d, the fatty acids and hydrogen partial pressure increased significantly. The autoinducing peptides (AIP)-type became the predominant QS and was positively correlated with fatty acids abundance. Syntrophaceticus and Syntrophomonas may promote syntrophic oxidation of acetate at high OLR through AIP-type QS. These findings provided new insights into the QS processes of microbes during dry AD of KW and a theoretical foundation for optimizing biochemical metabolic processes in dry AD through QS.

Mechanisms of anammox granular sludge reactor effluent as biostimulant: Shaping microenvironment for anammox metabolism

Effluent from anammox granular sludge (AnGS) bioreactor contains microbes and microbial products. This study explored mechanisms of utilizing AnGS-effluent as biostimulant for anammox process enhancement. Compared with no AnGS-effluent supplemented control reactor, 5.0 and 1.3 times higher ammonium nitrogen and total inorganic nitrogen removal rates, respectively were obtained with continuous AnGS-effluent supplementation after 98 days' operation. Anammox bacteria from Candidatus Brocadia accounted for 0.1 % (DNA level) and 1.3 %-1.5 % (RNA level) in control reactor, and 2.9 % (DNA level) and 54.5 %-55.4 % (RNA level) in the AnGS-effluent-fed reactor. Influent microbial immigration evaluation showed that bacterial immigration via AnGS-effluent supplementation was not the main contributor to active anammox community development. Amino acids biosynthesis, B-vitamins and coenzymes metabolism related pathways were facilitated by AnGS-effluent supplementation. AnGS-effluent supplementation aided anammox metabolic activity by shaping microenvironment and microbial interactions. This study provides insights into enhancing anammox bacterial metabolism with AnGS-effluent microbial products as biostimulant.

Unveiling long-term combined effect of salinity and Lead(II) on anammox activity and microbial community dynamics in saline wastewater treatment

The study assessed the effect of salinity and lead (Pb(II)) on the anammox sludge for nitrogen removal from saline wastewater. Results showed decreased nitrogen removal and specific anammox activity (SAA) with elevated salinity and Pb(II). SAA reduced from 541.3 ± 4.3 mg N g-1 VSS d-1 at 0.5 mg/L Pb(II) to 436.0 ± 0.2 mg N g-1 VSS d-1 at 30 g/L NaCl, further to 303.6 ± 7.1 mg N g-1 VSS d-1 under 30 g/L NaCl + 0.5 mg/L Pb(II). Notably, the combined inhibition at salinity (15-20 g/L NaCl) and Pb(II) (0.3-0.4 mg/L) exhibited synergistic effect, while higher salinity and Pb(II) aligned with independent inhibition models. Combined inhibition decreased protein/polysaccharides ratio, indicating more severe negative effect on anammox aggregation capacity. Metagenomics confirmed decreased Candidatus Kuenenia, and enhanced denitrification under elevated salinity and Pb(II) conditions. This study offers insights into anammox operation for treating saline wastewater with heavy metals.

Communication leads to bacterial heterogeneous adaptation to changing conditions in partial nitrification reactor

Recently, it is reported that bacterial communication coordinates the whole consortia to jointly resist the adverse environments. Here, we found the bacterial communication inevitably distinguished bacterial adaptation among different species in partial nitrification reactor under decreasing temperatures. We operated a partial nitrification reactor under temperature gradient from 30 °C to 5 °C and found the promotion of bacterial communication on adaptation of ammonia-oxidizing bacteria (AOB) was greater than that of nitrite-oxidizing bacteria (NOB). Signal pathways with single-component sensing protein in AOB can regulate more genes involved in bacterial adaptation than that with two-component sensing protein in NOB. The negative effects of bacterial communication, which were seriously ignored, have been highlighted, and Clp regulator downstream diffusible signal factor (DSF) based signal pathways worked as transcription activators and inhibitors of adaptation genes in AOB and NOB respectively. Bacterial communication can induce differential adaptation through influencing bacterial interactions. AOB inclined to cooperate with DSF synthesis bacteria as temperature declined, however, cooperation between NOB and DSF synthesis bacteria inclined to get weakening. According to the regulatory effects of signal pathways, bacterial survival strategies for self-protection were revealed. This study hints a potential way to govern niche differentiation in the microbiota by bacterial communication, contributing to forming an efficient artificial ecosystem.

Meta-analyzing the mechanism of pyrogenic biochar strengthens nitrogen removal performance in sulfur-driven autotrophic denitrification system: Evidence from metatranscriptomics

Sulfur-driven autotrophic denitrification (SAD) exhibits significant benefits in treating low carbon/nitrogen wastewater. This study presents an eco-friendly, cost-effective, and highly efficient method for enhancing nitrogen removal performance. The addition of biochar prepared at 300 °C (BC300) notably increased nitrogen removal efficiency by 31.60 %. BC300 concurrently enhanced electron production, the activities of the electron transfer system, and electron acceptors. With BC300, the ratio of NADH/NAD+ rose 2.00±0.11 times compared to without biochar, and the expression of NAD(P)H dehydrogenase genes was markedly up-regulated. In the electron transfer system, BC300 improved the electroactivity of extracellular polymeric substances and the activities of NADH dehydrogenase and complex III in intracellular electron transfer. Subsequently, electrons were directed into denitrification enzymes, where the nar, nir, nor, and nos related genes were highly expressed with BC300 addition. Significantly, BC300 activated the Clp and quorum sensing systems, positively influencing numerous gene expressions and microbial communication. Furthermore, the O%, H%, molar O/C, and aromaticity index in biochar were identified as crucial bioavailable parameters for enhancing nitrogen removal in the SAD process. This study not only confirms the application potential of biochar in SAD, but also advances our comprehension of its underlying mechanisms.

Granulation characteristics of anammox sludge in response to different signal-molecule-stimulants; mediated through programmed cell death

During the anammox process, mitigation of biomass washout to increase sludge retention is an important parameter of process efficiency. Signal molecular stimulants (SMS) initiate the sludge granulations controlled by programmed cell death (PCD) of microorganisms. In this study, the aerobic granular sludge (AGS), cell fragments, extracellular polymeric substances (EPS), and AGS process effluent were tested as SMS to identify their effect on anammox granulation. The results showed that the addition of SMS increased the nitrogen removal efficiency to varying degrees, whereas the addition of AGS process supernatant, as SMS, increased the ammonia removal efficiency up to 96%. The addition of SMS was also found to increase EPS production and contributed to sludge granulation. In this process, the proportion of PCD increased and both Gaiella and Denitratisoma abundance increased from 3.54% to 5.59%, and from 1.8% to 3.42%, respectively. In conclusion, PCD was found important to increase anaerobic ammonia oxidation performance through the granulation mechanism.

Nitrogen-loss and carbon-footprint reduction by plant-rhizosphere exudates

Low-carbon approaches to agriculture constitute a pivotal measure to address the challenge of global climate change. In agroecosystems, rhizosphere exudates are significantly involved in regulating the nitrogen (N) cycle and facilitating belowground chemical communication between plants and soil microbes to reduce direct and indirect emissions of greenhouse gases (GHGs) and control N runoff from cultivated sites into natural water bodies. Here, we discuss specific rhizosphere exudates from plants and microorganisms and the mechanisms by which they reduce N loss and subsequent N pollution in terrestrial and aquatic environments, including biological nitrification inhibitors (BNIs), biological denitrification inhibitors (BDIs), and biological denitrification promoters (BDPs). We also highlight promising application scenarios and challenges in relation to rhizosphere exudates in terrestrial and aquatic environments.

Regulatory Effects of Diverse DSF Family Quorum-Sensing Signals in Plant-Associated Bacteria

Numerous bacterial species employ diffusible signal factor (DSF)-based quorum sensing (QS) as a widely conserved cell-cell signaling communication system to collectively regulate various behaviors crucial for responding to environmental changes. cis-11-Methyl-dodecenoic acid, known as DSF, was first identified as a signaling molecule in Xanthomonas campestris pv. campestris. Subsequently, many structurally related molecules have been identified in different bacterial species. This review aims to provide an overview of current understanding regarding the biosynthesis and regulatory role of DSF signals in both pathogenic bacteria and a biocontrol bacterium. Recent studies have revealed that the DSF-based QS system regulates antimicrobial factor production in a cyclic dimeric GMP-independent manner in the biocontrol bacterium Lysobacter enzymogenes. Additionally, the DSF family signals have been found to be involved in suppressing plant innate immunity. The discovery of these diverse signaling mechanisms holds significant promise for developing novel strategies to combat stubborn plant pathogens. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Roles and regulation of quorum sensing in anaerobic granular sludge: Research status, challenges, and perspectives

Anaerobic granular sludge (AnGS) has a complex and important internal microbial communication system due to its unique microbial layered structure. As a concentration-dependent communication system between bacterial cells through signal molecules, QS (quorum sensing) is widespread in AnGS and exhibits great potential to regulate microbial behaviors. Therefore, the universal functions of QS in AnGS have been systematically summarized in this paper, including the influence on the metabolic activity, physicochemical properties, and microbial community of AnGS. Subsequently, the common QS-based AnGS regulation approaches are reviewed and analyzed comprehensively. The regulation mechanism of QS in AnGS is analyzed from two systems of single bacterium and mixed bacteria. This review can provide a comprehensive understanding of QS functions in AnGS systems, and promote the practical application of QS-based strategies in optimization of AnGS treatment process.

Chameleon-like Anammox Bacteria for Surface Color Change after Suffering Starvation

Bacteria are often exposed to long-term starvation during transportation and storage, during which a series of enzymes and metabolic pathways are activated to ensure survival. However, why the surface color of the bacteria changes during starvation is still not well-known. In this study, we found black anammox consortia suffering from long-term starvation contained 0.86 mmol gVSS-1 cytochrome c, which had no significant discrepancy compared with the red anammox consortia (P > 0.05), indicating cytochrome c was not the key issue for chromaticity change. Conversely, we found that under starvation conditions cysteine degradation is an important metabolic pathway for the blackening of the anammox consortia for H2S production. In particular, anammox bacteria contain large amounts of iron-rich nanoparticles, cytochrome c, and other iron-sulfur clusters that are converted to produce free iron. H2S combines with free iron in bacteria to form Fe-S compounds, which eventually exist stably as FeS2, mainly in the extracellular space. Interestingly, FeS2 could be oxidized by air aeration, which makes the consortia turn red again. The unique self-protection mechanism makes the whole consortia appear black, avoiding inhibition by high concentrations of H2S and achieving Fe storage. This study expands the understanding of the metabolites of anammox bacteria as well as the bacterial survival mechanism during starvation.

Extracellular polymeric substances and microbial community shift during the start-up of a single-stage partial nitritation/anammox process

A sequencing batch reactor (SBR) was operated to investigate variations of extracellular polymeric substances (EPS) and microbial community during the start-up of the single-stage partial nitritation/anammox (SPN/A) process at intermittent aeration mode. The SPN/A system was successfully started on day 34, and the nitrogen removal efficiency and total nitrogen loading rate were 82.29% and 0.31 kg N/(m3 ·day), respectively. Furthermore, the relationship between the protein secondary structures and microbial aggregation was strongly related. The α-helix/ (β-sheet + random coil) ratios increased obviously from 0.20 ± 0.03 to 0.23 ± 0.01, with the sludge aggregation mean size increased from 56 to 107 μm during the start-up of SPN/A. During the start-up of SPN/A, Candidatus Kuenenia was the primary anammox bacteria, whereas Nitrospira was the main functional bacteria of nitrite-oxidizing bacteria. Correlation between the microbial community and EPS components was performed. The EPS and microbial community played important roles in keeping stable nitrogen removal and the formation of sludge granules. PRACTITIONER POINTS: Intermittent aeration strategy promoted SPN/A system start-up. EPS composition and protein secondary structure were related with the sludge disintegration and aggregation. Microbial community shift existed and promoted the stability of sludge and reactor performance during SPN/A start-up.

Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor

To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.

A microbiological identification and recovery actions of critical symptoms of anammox image bacteria

Currently, the risks posed by bacteria are becoming increasingly important. It now appears that the cell wall of Anammox image bacteria is very different from what has been generally considered for many years. Not every textbook contains the peptidoglycan on the cell wall of Anammox image bacteria - the sugar-protein chain that strengthens the cells of most bacteria. Most researchers in this Anammox image bacteria diseased identification wanted to find out what gave the Anammox image cell its stability. It used powerful cryo-electron microscopes to examine the bacterial cell wall and find the exact structure of the peptidoglycan. A new algorithm is proposed to discover that Anammox image bacteria contain peptidoglycan, which completes a theory in microbiology. The identification of different diseases is listed, and the proposed model compares the exact results while comparing the parameters like accuracy, precision, recall, and F1-Score. Keywords: Anammox image bacteria, cell wall, cell stability, cryo-electron, microscope images, accuracy, precision, recall, F1-score.

Quorum sensing-mediated microbial interactions: Mechanisms, applications, challenges and perspectives

Microbial community in natural or artificial environments playes critical roles in substance cycles, products synthesis and species evolution. Although microbial community structures have been revealed via culture-dependent and culture-independent approaches, the hidden forces driving the microbial community are rarely systematically discussed. As a mode of cell-to-cell communication that modifies microbial interactions, quorum sensing can regulate biofilm formation, public goods secretion, and antimicrobial substances synthesis, directly or indirectly influencing microbial community to adapt to the changing environment. Therefore, the current review focuses on microbial community in the different habitats from the quorum sensing perspective. Firstly, the definition and classification of quorum sensing were simply introduced. Subsequently, the relationships between quorum sensing and microbial interactions were deeply explored. The latest progressives regarding the applications of quorum sensing in wastewater treatment, human health, food fermentation, and synthetic biology were summarized in detail. Finally, the bottlenecks and outlooks of quorum sensing driving microbial community were adequately discussed. To our knowledge, this current review is the first to reveal the driving force of microbial community from the quorum sensing perspective. Hopefully, this review provides a theoretical basis for developing effective and convenient approaches to control the microbial community with quorum sensing approaches.

Research advances in application of mainstream anammox processes: Roles of quorum sensing and microbial metabolism

Anaerobic ammonium oxidation (anammox) is a low-carbon biological nitrogen removal process, that has been widely applied to treat high-strength wastewater. However, the practical application of mainstream anammox treatment is limited due to the slow growth rate of anammox bacteria (AnAOB). Therefore, it is important to provide a comprehensive summary of the potential impacts and regulatory strategies for system stability. This article systematically reviewed the effects of environmental fluctuations on anammox systems, summarizing the bacterial metabolisms and the relationship between metabolite and microbial functional effects. To address the shortcoming of mainstream anammox process, molecular strategies based on quorum sensing (QS) were proposed. Sludge granulation, gel encapsulation and carrier-based biofilm technologies were adopted to enhance the QS function in microbial aggregation and reduction of biomass loss. Furthermore, this article discussed the application and progress of anammox-coupled processes. Valuable insights were provided for the stable operation and development of mainstream anammox process from the perspectives of QS and microbial metabolism.

Deciphering endogenous and exogenous regulations of anammox consortia in responding to lincomycin by multiomics: quorum sensing and CRISPR system

The widespread use of antibiotics has created an antibiotic resistance genes (ARGs)-enriched environment, which causes high risks on human and animal health. Although antibiotics can be partially adsorbed and degraded in wastewater treatment processes, striving for a complete understanding of the microbial adaptive mechanism to antibiotic stress remains urgent. Combined with metagenomics and metabolomics, this study revealed that anammox consortia could adapt to lincomycin by spontaneously changing the preference for metabolite utilization and establishing interactions with eukaryotes, such as Ascomycota and Basidiomycota. Specifically, quorum sensing (QS) based microbial regulation and the ARGs transfer mediated by clustered regularly interspaced short palindromic repeats (CRISPR) system and global regulatory genes were the principal adaptive strategies. Western blotting results validated that Cas9 and TrfA were mainly responsible for the alteration of ARGs transfer pathway. These findings highlight the potential adaptative mechanism of microbes to antibiotic stress and fill gaps in horizontal gene transfer pathways in the anammox process, further facilitating the ARGs control through molecular and synthetic biology techniques.

Insights into heavy metals shock on anammox systems: Cell structure-based mechanisms and new challenges

Anaerobic ammonium oxidation (anammox) as a low-carbon and energy-saving technology, has shown unique advantages in the treatment of high ammonia wastewater. However, wastewater usually contains complex heavy metals (HMs), which pose a potential risk to the stable operation of the anammox system. This review systematically re-evaluates the HMs toxicity level from the inhibition effects and the inhibition recovery process, which can provide a new reference for engineering. From the perspective of anammox cell structure (extracellular, anammoxosome membrane, anammoxosome), the mechanism of HMs effects on cellular substances and metabolism is expounded. Furthermore, the challenges and research gaps for HMs inhibition in anammox research are also discussed. The clarification of material flow, energy flow and community succession under HMs shock will help further reveal the inhibition mechanism. The development of new recovery strategies such as bio-accelerators and bio-augmentation is conductive to breaking through the engineered limitations of HMs on anammox. This review provides a new perspective on the recognition of toxicity and mechanism of HMs in the anammox process, as well as the promotion of engineering applicability.

Deciphering the role of granular activated carbon (GAC) in anammox: Effects on microbial succession and communication

Anaerobic ammonium oxidation (anammox) offered an energy-efficient option for nitrogen removal from wastewater. Granular activated carbon (GAC) addition has been reported that improved biomass immobilization, but the role of GAC in anammox reactors has not been sufficiently revealed. In this study, it was observed that GAC addition in an upflow anaerobic sludge blanket (UASB) reactor led to the significantly shortened anammox enrichment time (shortened by 45 days) than the reactor without GAC addition. The nitrogen removal rate was 0.83 kg N/m³/day versus 0.76 kg N/m³/day in GAC and non-GAC reactors, respectively after 255 days' operation. Acyl-homoserine lactone (AHL) quorum sensing signal molecule C8-HSL had comparable concentrations in both anammox reactors, whereas the signal molecule C12-HSL was more pervasive in the reactor containing GAC than the reactor without GAC. Microbial analysis revealed distinct anammox development in both reactors, with Candidatus Brocadia predominant in the reactor that did not contain GAC, and Candidatus Kuenenia predominant in the reactor that contained GAC. Denitrification bacteria likely supported anammox metabolism in both reactors. The analyses of microbial functions suggested that AHL-dependent quorum sensing was enhanced with the addition of GAC, and that GAC possibly augmented the extracellular electron transfer (EET)-dependent anammox reaction.

Metabolomics uncovers adaptation discrepancy among anammox granular sludge with different granule size: Metabolic pathway regulation by consortia cooperation

The relationship between granular size and anaerobic ammonium oxidation (anammox) performance in the anammox granular sludge (AnGS) system has been extensively observed. However, the metabolic pathways regulated by communication and cross-feedings among anammox consortia remain unclear. The reactor operation and metabolomics analyses were combined to explore the influence of microbiota cooperation on metabolic pathways and granule properties under low temperature (18 °C) and nitrite inhibition. Anammox activity was sustained under challenging circumstances by active quorum sensing among anammox consortia in AnGS with diameters larger than 1.4 mm, which promoted nucleotide metabolism. Cross-feedings among anammox consortia increased the levels of molybdopterin cofactor and folate meanwhile decreasing the cost of carbon fixation metabolism, which supported anabolism and maintained the content of heme c and extracellular polymeric substance. These metabolic insights into the AnGS system provide a new view for anammox process overcoming the low temperature and nitrite stress.

Bacterial Communication Coordinated Behaviors of Whole Communities to Cope with Environmental Changes

Bacterial communication plays an important role in coordinating microbial behaviors in a community. However, how bacterial communication organizes the entire community for anaerobes to cope with varied anaerobic-aerobic conditions remains unclear. We constructed a local bacterial communication gene (BCG) database comprising 19 BCG subtypes and 20279 protein sequences. BCGs in anammox-partial nitrification consortia coping with intermittent aerobic and anaerobic conditions as well as gene expressions of 19 species were inspected. We found that when suffering oxygen changes, intra- and interspecific communication by a diffusible signal factor (DSF) and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) changed first, which in turn induced changes of autoinducer-2 (AI-2)-based interspecific and acyl homoserine lactone (AHLs)-based intraspecific communication. DSF and c-di-GMP-based communication regulated 455 genes, which covered 13.64% of the genomes and were mainly involved in antioxidation and metabolite residue degradation. For anammox bacteria, oxygen influenced DSF and c-di-GMP-based communication through RpfR to upregulate antioxidant proteins, oxidative damage-repairing proteins, peptidases, and carbohydrate-active enzymes, which benefited their adaptation to oxygen changes. Meanwhile, other bacteria also enhanced DSF and c-di-GMP-based communication by synthesizing DSF, which helped anammox bacteria survive at aerobic conditions. This study evidences the role of bacterial communication as an "organizer" within consortia to cope with environmental changes and sheds light on understanding bacterial behaviors from the perspective of sociomicrobiology.

Recent Nanotechnologies to Overcome the Bacterial Biofilm Matrix Barriers

Bacterial biofilm-related infectious diseases severely influence human health. Under typical situations, pathogens can colonize inert or biological surfaces and form biofilms. Biofilms are functional aggregates that coat bacteria with extracellular polymeric substances (EPS). The main reason for the failure of biofilm infection treatment is the low permeability and enrichment of therapeutic agents within the biofilm, which results from the particular features of biofilm matrix barriers such as negatively charged biofilm components and highly viscous compact EPS structures. Hence, developing novel therapeutic strategies with enhanced biofilm penetrability is crucial. Herein, the current progress of nanotechnology methods to improve therapeutic agents' penetrability against biofilm matrix, such as regulating material morphology and surface properties, utilizing the physical penetration of nano/micromotors or microneedle patches, and equipping nanoparticles with EPS degradation enzymes or signal molecules, is first summarized. Finally, the challenges, perspectives, and future implementations of engineered delivery systems to manage biofilm infections are presented in detail.

Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia

Denitrifying bacteria with high abundances in anammox communities play crucial roles in achieving stable anammox-based systems. Despite the relative constant composition of denitrifying bacteria, their functional diversity remains to be explored in anammox communities. Herein, a total of 77 high-quality metagenome-assembled genomes (MAGs) of denitrifying bacteria were recovered from the anammox community in a full-scale swine wastewater treatment plant. Among these microbes, a total of 26 MAGs were affiliated with the seven dominant denitrifying genera that have total abundances higher than 1%. A meta-analysis of these species suggested that external organics reduced the abundances of genus Ignavibacterium and species MAG.305 of UTPRO2 in anammox communities. Comparative genome analysis revealed functional divergence across different denitrifying bacteria, largely owing to their distinct capabilities for carbohydrate (including endogenous and exogenous) utilization and vitamin (e.g., pantothenate and thiamine) biosynthesis. Serval microbes in this system contained fewer genes encoding biotin, pantothenate and methionine biosynthesis compared with their related species from other habitats. In addition, the genes encoding energy production and conversion (73 genes) and inorganic ion transport (53 genes) putatively transferred from other species to denitrifying bacteria, while these denitrifying bacteria (especially genera UTPRO2 and SCN-69-89) likely donated the genes encoding nutrients (e.g., inorganic ion and amino acid) transporter (64 genes) for other members to utilize new metabolites. Collectively, these findings highlighted the functional divergence of these denitrifying bacteria and speculated that the genetic interactions within anammox communities through horizontal gene transfer may be one of the reasons for their functional divergence.

Micron-scale biogeography reveals conservative intra anammox bacteria spatial co-associations

Micron-scale resolution can help to reliably identify true taxon-taxon interactions in complex microbial communities. Despite widespread recognition of the critical role of metabolic interactions in anaerobic ammonium oxidation (anammox) system performance, no studies have examined microbial interactions at the micron-scale in anammox consortia. To fill this gap, we extensively sampled (totally 242 samples) the consortia of a lab-scale anammox reactor at different length scales, including bulk-scale (∼cm), macro-scale (300-500 µm) and micron-scale (70-100 µm). We firstly observed evident micron-scale heterogeneity in anammox consortia, with the relative abundance of anammox bacteria fluctuated greatly across individual clusters (2.0%-79.3%), indicating that the biotic interactions play a significant role in the assembly of anammox communities under well-controlled and well-mixed condition. Importantly, by mapping the spatial associations in anammox consortia at micron-scale, we demonstrated that the conserved co-associations for anammox bacteria were restricted to three different Brocadia species over time, and their co-associations with heterotrophs were random, implying that there was no statistically significant symbiotic interaction between anammox bacteria and other heterotrophic populations. Further metagenomic binning revealed that the quorum sensing with secondary messenger c-di-GMP potentially holding on the conservative metabolic cooperation among Brocadia species. These results shed new light on the social behavior of the anammox community. Overall, delineating of biological structures at micron-scale opens a new way of monitoring the microbial spatial structure and interactions, paving the way for improved community engineering of biotreatment systems.

The counteraction of anammox community to long-term nitrite stress: Crucial roles of rare subcommunity

Understanding the temporal dynamics and recovery of anammox community under nitrite stress is critical for successful application of anammox-related processes. Here, the response behaviors of anammox community were investigated to characterize the reactor performance and ecological function under varied levels of nitrite stress (changing from 0, 50, 100, 200 to 0 mg-N/L) across a large temporal scale (588 days). The nitrogen removal rates decreased from 0.51 ± 0.02 to 0.16 ± 0.04 kg-N/(m³·d) under nitrite stress from 0 to 200 mg-N/L, while it was recovered to 0.29 ± 0.06 kg-N/(m³·d) as nitrite stress terminated. A strong community succession was driven by the initial nitrite stress of 50 mg-N/L, while the community dissimilarity mainly resulted from the increased beta diversity of rare subcommunity. Meanwhile, the rare subcommunity with high functional redundancy likely warranted the functional resilience of anammox community across the nitrite stress gradients. Moreover, the increased positive interactions between anammox bacteria and side populations supported the resilience of anammox after discontinuing nitrite stress, which facilitated the recovery of nitrogen removal efficiency. This study deciphers the interspecies interactions and functional redundancy of rare subcommunity in shaping the robustness and resilience of anammox-related processes when treating nitrite fluctuated wastewater.

Construction of Environmental Synthetic Microbial Consortia: Based on Engineering and Ecological Principles

In synthetic biology, engineering principles are applied to system design. The development of synthetic microbial consortia represents the intersection of synthetic biology and microbiology. Synthetic community systems are constructed by co-cultivating two or more microorganisms under certain environmental conditions, with broad applications in many fields including ecological restoration and ecological theory. Synthetic microbial consortia tend to have high biological processing efficiencies, because the division of labor reduces the metabolic burden of individual members. In this review, we focus on the environmental applications of synthetic microbial consortia. Although there are many strategies for the construction of synthetic microbial consortia, we mainly introduce the most widely used construction principles based on cross-feeding. Additionally, we propose methods for constructing synthetic microbial consortia based on traits and spatial structure from the perspective of ecology to provide a basis for future work.

Colonization of biofilm in wastewater treatment: A review

The attachment and colonization process of microorganisms on a carrier is an interdisciplinary research field. Through a series of physical, chemical, and biological actions, the microorganisms can eventually reproduce on the carrier. This article introduces biofilm start-up and its applications, and explores the current issues to look forward to future development directions. Firstly, the mechanism of microbial film formation is analyzed from the microbial community colonization and reproduction process. Secondly, when analyzing the factors influencing microbial membrane formation, the effect of microbial properties (e.g., genes, proteins, lipids) and external conditions (i.e., carrier, operating environment, and regulation mechanism among microbial communities) were discussed in depth. Aimed at exploring the mechanisms and influencing factors of biofilm start-up, this article proposes the application measures to strengthen this process. Finally, the problems encountered and the future development direction of the technology are analyzed and prospected.

Differences in the Effects of Calcium and Magnesium Ions on the Anammox Granular Properties to Alleviate Salinity Stress

Divalent cations were known to alleviate salinity stress on anammox bacteria. Understanding the mechanism of reducing the salinity stress on anammox granules is essential for the application of the anammox process for saline wastewater treatment. In this study, the effect of Ca2+ and Mg2+ augmentation on the recovery of the activity of freshwater anammox granules affected by salinity stress was evaluated. At the condition of a salinity stress of 5 g NaCl/L, the specific anammox activity (SAA) of the granule decreased to 50% of that of the SAA without NaCl treatment. Augmentation of Ca2+ at the optimum concentration of 200 mg/L increased the SAA up to 78% of the original activity, while the augmentation of Mg2+ at the optimum concentration of 70 mg/L increased the SAA up to 71%. EPS production in the granules was increased by the augmentation of divalent cations compared with the granules affected by salinity stress. In the soluble EPS, the ratio of protein to polysaccharides was higher in the granules augmented by Ca2+ than with Mg2+, and the functional groups of the EPS differed from each other. The amount of Na+ sequestered in the soluble EPS was increased by the augmentation of divalent cations, which seems to contribute to the alleviation of salinity stress. Ca. Kuenenia-like anammox bacteria, which were known to be salinity stress-tolerant, were predominant in the granules and there was no significant difference in the microbial community of the granules by the salinity stress treatment. Our results suggest that the alleviation effect of the divalent cations on the salinity stress on the anammox granules might be associated with the increased production of different EPS rather than in changes to the anammox bacteria.

Unravelling the importance of Ca2+ and Mg2+ as essential in anammox culture medium

The mechanism and nitrogen removal performance of anammox process under different concentrations of Ca²⁺ and Mg²⁺ were explored from the perspective of molecular biology analysis based on the metabolic changes of the second messenger cyclic diguanylate (c-di-GMP). After 100-day operation, reactor with 98 mg/L Ca²⁺ and 30 mg/L Mg²⁺ achieved a higher anammox performance with an average total nitrogen (TN) removal efficiency of 85.8%. Under the Mg²⁺concentration of 30 mg/L, a higher Ca²⁺ could accelerate anammox process by promoting the amplification of Candidatus Brocadia (0.62%) and production of Diguanylate cyclase (DGC-s: 6.54 × 10⁸ copies/μL DNA) which function was to synthesize c-di-GMP. While under the Ca²⁺concentration of 49 mg/L, Mg²⁺ concentration at appropriate rang could promote the degradation process of c-di-GMP. Since Ca²⁺ had positive linear relationship with TN removal (R² = 0.96), a higher Ca²⁺ concentration is recommended in the culture medium. This study provided a potential method for optimization of anammox process.