The role of quorum sensing signalling in EPS production and the assembly of a sludge community into aerobic granules

Methanogenic partner influences cell aggregation and signalling of Syntrophobacterium fumaroxidans

For several decades, the formation of microbial self-aggregates, known as granules, has been extensively documented in the context of anaerobic digestion. However, current understanding of the underlying microbial-associated mechanisms responsible for this phenomenon remains limited. This study examined morphological and biochemical changes associated with cell aggregation in model co-cultures of the syntrophic propionate oxidizing bacterium Syntrophobacterium fumaroxidans and hydrogenotrophic methanogens, Methanospirillum hungatei or Methanobacterium formicicum. Formerly, we observed that when syntrophs grow for long periods with methanogens, cultures tend to form aggregates visible to the eye. In this study, we maintained syntrophic co-cultures of S. fumaroxidans with either M. hungatei or M. formicicum for a year in a fed-batch growth mode to stimulate aggregation. Millimeter-scale aggregates were observed in both co-cultures within the first 5 months of cultivation. In addition, we detected quorum sensing molecules, specifically N-acyl homoserine lactones, in co-culture supernatants preceding the formation of macro-aggregates (with diameter of more than 20 μm). Comparative transcriptomics revealed higher expression of genes related to signal transduction, polysaccharide secretion and metal transporters in the late-aggregation state co-cultures, compared to the initial ones. This is the first study to report in detail both biochemical and physiological changes associated with the aggregate formation in syntrophic methanogenic co-cultures. KEYPOINTS: • Syntrophic co-cultures formed mm-scale aggregates within 5 months of fed-batch cultivation. • N-acyl homoserine lactones were detected during the formation of aggregates. • Aggregated co-cultures exhibited upregulated expression of adhesins- and polysaccharide-associated genes.

Effects of the quorum sensing related luxS gene and lsr operon on Klebsiella michiganensis resisting copper stress

Industrial wastewater is a major environmental concern due to its high copper content, which poses significant toxicity to microbial life. Autoinducer-2 (AI-2) can participate in the inter- and intra-species communication and regulate the physiological functions of different bacterial species by producing AI-2 signal molecules. However, there are few research reports on the luxS gene and lsr operon functions for AI-2 in bacteria with a certain tolerance to copper. This study delves into the potential of quorum sensing mechanisms, particularly the AI-2 system, for enhancing microbial resistance to copper toxicity in Klebsiella michiganensis (KM). We detail the critical roles of the luxS gene in AI-2 synthesis and the lsr operon in AI-2 uptake, demonstrating their collective impact on enhancing copper resistance. Our findings show that mutations in the lsr operon, alongside the knockout of the luxS gene in KM strain (KMΔluxSΔlsr), significantly impair the strain's motility (p < 0.0001) and biofilm formation (p < 0.01), underscoring the operon's role in AI-2 transport. These genetic insights are pivotal for developing bioremediation strategies aimed at mitigating copper pollution in wastewater. By elucidating the mechanisms through which KM modulates copper resistance, this study highlights the broader ecological significance of leveraging microbial quorum sensing pathways for sustainable wastewater management.

Unveiling the common laws of extracellular polymeric substances (EPS) properties on short-chain fatty acids production from sludge by EPS disintegration pretreatment

The production of short-chain fatty acids (SCFAs) from sludge is promising, but the efficiency and product quality often vary because of extracellular polymeric substances (EPS) characteristics and pretreatment principles. This study adopted specific EPS disintegration pretreatment to treat different types of sludge. By correlation coefficient matrix analysis and correlation dynamics change resolution, the intrinsic relationships between the nature of EPS and the production of SCFAs from sludge was unveiled. We demonstrate that tight-bound EPS (TB-EPS) is a principal carbon reservoir, positively impacting SCFAs yields, in the fermentation system with EPS as the main fermentation substrate, it can contribute about 29.2 % for SCFAs growth during fermentation. Conversely, TB-EPS exhibits a negative correlation during fermentation due to EPS-SCFAs interconversion, while loosely bound EPS (LB-EPS) correlates positively. Proteins and polysaccharides in TB-EPS, especially proteins, significantly enhance individual SCFAs yields, predominantly acetic, propionic, and isovaleric acids. The findings would provide a theoretical basis for developing pretreatments and process-control technologies aimed at improving SCFAs production efficiency and quality.

Regulation and application of quorum sensing on anaerobic digestion system

Quorum sensing (QS) plays an important role in the social behavior of microbial communities. Anaerobic digestion (AD) is a biological process using anaerobic microorganisms to degrade organic macromolecules into small molecules for biogas and biofertilizer production. In AD, the QS signaling molecule N-acyl homoserine lactones (AHLs) induces bacterial metabolism, improving AD process efficiency. However, there are fewer systematic reports about QS regulation of microbial behavior in AD. In this report, the effects of signaling molecules on extracellular polymer secretion, biofilm formation, granulation of granular sludge and bacterial metabolism in AD were investigated in detail. At present, the regulation behavior of QS on AD is a group phenomenon, and there are few in-depth studies on the regulation pathway. Therefore, we conducted an in-depth analysis of the pure culture system, granular sludge and reactor in the AD. Then we pointed out that the future application potential of QS in the AD may be combined with quorum quenching (QQ) and omics technology, which is of great significance for the future application of AD.

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.

Enhancement of Biological Nitrogen Removal System Resilience to Chronic Exposure of Zinc Oxide Nanoparticles by Quorum Sensing Modulation: Physiochemical, Microbial, and Metabolic Insights

The effects of three typical N-acyl-homoserine lactones (AHLs) on the tolerance of biological nitrogen removal (BNR) system to chronic exposure of zinc oxide nanoparticles (NPs) were investigated. C4-HSL successfully delayed the crash time of nitrogen removal performances in the NP-stressed system, while C6-HSL and C10-HSL maintained total nitrogen removal efficiencies throughout the 90-day NP exposure. All three AHLs increased NPs' contents captured in extracellular polymeric substances, alleviating membrane damage and preserving floc structure. The activities of tricarboxylic acid cycle-related enzymes and the relative abundances of BNR-related functional genes and genera were significantly enhanced. Besides, C6-HSL and C10-HSL augmented antioxidant enzyme activities and the abundances of functional genes and metabolites related to antioxidation, flagellar assembly, and chemotaxis, which synergistically reduced the reactive oxygen species' excessive accumulation. The tested AHLs effectively enhanced BNR systems' tolerance to chronic NP exposure, providing inspiration for quorum sensing applications in emerging contaminant removal.

Screening and identification of functional bacterial attachment genes in aerobic granular sludge

The screening and identification of attachment genes is important to exploring the formation mechanism of biofilms at the gene level. It is helpful to the development of key culture technologies for aerobic granular sludge (AGS). In this study, genome-wide sequencing and gene editing were employed for the first time to investigate the effects and functions of attachment genes in AGS. With the help of whole-genome analysis, ten attachment genes were screened from thirteen genes, and the efficiency of gene screening was greatly improved. Then, two attachment genes were selected as examples to further confirm the gene functions by constructing gene-knockout recombinant mutants of Stenotrophomonas maltophilia; when the two attachment genes were knocked out, the attachment potential was reduced by 50.67% and 43.93%, respectively. The results provide a new theoretical principle and efficient method for the development of AGS from the perspective of attachment genes.

The effect of quorum sensing on cadmium- and lead-containing wastewater treatment using activated sludge: Removal efficiency, enzyme activity, and microbial community

Quorum sensing (QS) is prevalent in activated sludge processes; however, its essential role in the treatment of heavy metal wastewater has rarely been studied. Therefore, in this study, acyl homoserine lactone (AHL)-mediated QS was used to regulate the removal performance, enzyme activity, and microbial community of Cd- and Pb-containing wastewater in a sequencing batch reactor (SBR) over 30 cycles. The results showed that exogenous AHL strengthened the removal of Cd(II) and Pb(II) in their coexistence wastewater during the entire period. The removal of NH4+-N, total phosphorus, and chemical oxygen demand (COD) was also enhanced by the addition of AHL despite the coexistence of Cd(II) and Pb(II). Meanwhile, the protein content of extracellular polymeric substances was elevated and the microbial metabolism and antioxidative response were stimulated by the addition of AHL, which was beneficial for resistance to heavy metal stress and promoted pollutant removal by activated sludge. Microbial sequencing indicated that AHL optimized the microbial community structure, with the abundance of dominant taxa Proteobacteria and Unclassified_f_Enterobacteriaceae increasing by 73.9% and 59.2% maximally, respectively. This study offers valuable insights into the mechanisms underlying Cd(II) and Pb(II) removal as well as microbial community succession under AHL availability in industrial wastewater.

Protective effects of antibiotic resistant bacteria on susceptibles in biofilm: Influential factors, mechanism, and modeling

In environmental biofilms, antibiotic-resistant bacteria facilitate the persistence of susceptible counterparts under antibiotic stresses, contributing to increased community-level resistance. However, there is a lack of quantitative understanding of this protective effect and its influential factors, hindering accurate risk assessment of biofilm resistance in diverse environment. This study isolated an opportunistic Escherichia coli pathogen from soil, and engineered it with plasmids conferring antibiotic resistance. Protective effects of the ampicillin resistant strain (AmpR) on their susceptible counterparts (AmpS) were observed in ampicillin-stress colony biofilms. The concentration of ampicillin delineated protective effects into 3 zones: continuous protection (<1 MIC of AmpS), initial AmpS/R dependent (1-8 MIC of AmpS), and ineffective (>8 MIC of AmpS). Intriguingly, Zone 2 exhibited a surprising "less is more" phenomenon tuned by the initial AmpS/R ratio, where biofilm with an initially lower AmpR (1:50 vs 50:1) harbored 30-90 % more AmpR after 24 h growth under antibiotic stress. Compared to AmpS, AmpR displayed superiority in adhesion, antibiotic degradation, motility, and quorum sensing, allowing them to preferentially colonize biofilm edge and areas with higher ampicillin. An agent-based model incorporating protective effects successfully simulated tempo-spatial dynamics of AmpR and AmpS influenced by antibiotic stress and initial AmpS/R. This study provides a holistic view on the pervasive but poorly understood protective effects in biofilm, enabling development of better risk assessment and precisely targeted control strategies of biofilm resistance in diverse environment.

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.

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.

A novel photoelectrochemical self-screening aptamer biosensor based on CAU-17-derived Bi2WO6/Bi2S3 for rapid detection of quorum sensing signal molecules

Quorum sensing signal molecule is an important biomarker released by some microorganisms, which can regulate the adhesion and aggregation of marine microorganisms on the surface of engineering facilities. Thus, it is significant to exploit a convenient method that can effectively monitor the formation and development of marine biofouling. In this work, an advanced photoelectrochemical (PEC) aptamer biosensing platform was established and firstly applied for the rapid and ultrasensitive determination of N-(3-Oxodecanoyl)-l-homoserine lactone (3-O-C10-HL) released from marine fouling microorganism Ponticoccus sp. PD-2. The visible-light-driven Bi2WO6/Bi2S3 heterojunction derived from metal-organic frameworks (MOFs) CAU-17 and self-screened aptamer were employed as the photoactive materials and bioidentification elements, respectively. Appropriate amount of MoS2 quantum dots (QDs) conjugated with single-stranded DNA were introduced by hybridization to enhance the photocurrent response of the PEC biosensor. The self-screening aptamer can specifically recognize 3-O-C10-HL, accompanied by increasing the steric hindrance and forcing MoS2 QDs to leave the electrode surface, resulting in an obvious reduction of photocurrent and achieving a dual-inhibition signal amplification effect. Under the optimized conditions, the photocurrent response of PEC aptasensor was linear with 3-O-C10-HL concentration from 1 nM to 10 μM, and the detection limit was as low as 0.26 nM. The detection strategy also showed a high reproducibility, superior specificity and good stability. This work not only provides a simple, rapid and ultrasensitive PEC aptamer biosensing strategy for monitoring quorum sensing signal molecules in marine biofouling, but also broadens the application of MOFs-based heterojunctions in PEC sensors.

Decoding Microcystis aeruginosa quorum sensing through AHL-mediated transcriptomic molecular regulation mechanisms

Acyl-homoserine lactone (AHL) serves as a key signaling molecule for quorum sensing (QS) in bacteria. QS-related genes and physiological processes in Microcystis aeruginosa remain elusive. In this study, we elucidated the regulatory role of AHL-mediated QS in M. aeruginosa. Using AHL activity extract and transcriptomic analysis, we revealed significant effects of the AHL on growth and photosynthesis. AHL significantly increased chlorophyll a (Chl-a) content and accelerated photosynthetic rate thereby promoting growth. Transcriptome analysis revealed that AHL stimulated the up-regulation of photosynthesis-related genes (apcABF, petE, psaBFK, psbUV, etc.) as well as nitrogen metabolism and ribosomal metabolism. In addition, AHL-regulated pathways are associated with lipopolysaccharide and phenazine synthesis. Our findings deepen the understanding of the QS system in M. aeruginosa and are important for gaining insights into the role of QS in Microcystis bloom formation. It also provides new insights into the prevalence of M. aeruginosa in water blooms.

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

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

Quorum sensing bacteria improve microbial networks stability and complexity in wastewater treatment plants

Quorum-sensing bacteria (QSB) are crucial factors for microbial communication, yet their ecological role in wastewater treatment plants (WWTPs) remains unclear. Here, we developed a method to identify QSB by comparing 16S rRNA gene sequences. QSB in 388 activated sludge samples collected from 130 WWTPs across China primarily were identified as rare taxa and conditionally rare taxa. A co-occurrence network shared by all sludge communities revealed that QSB exhibited higher average clustering coefficient (0.46) than non-QSB (0.15). Individual sludge networks demonstrated that quorum sensing microbiomes were positively correlated with network robustness and network complexity, including average clustering coefficient and link density. We confirmed that QSB keystones and QSB nodes have a positive impact on network complexity by influencing network modularity through a structural equation model. Meanwhile, QSB communities directly contributed to maintaining network robustness (r = 0.29, P < 0.05). Hence, QSB play an important role in promoting network complexity and stability. Furthermore, QSB communities were positively associated with the functional composition of activated sludge communities (r = 0.33, P < 0.01), especially the denitrification capacity (r = 0.45, P < 0.001). Overall, we elucidated the ecological significance of QSB and provided support for QS-based regulation of activated sludge microbial communities.

Plant-microbe interactions through a lens: tales from the mycorrhizosphere

BACKGROUND

The soil microbiome plays a pivotal role in maintaining ecological balance, supporting food production, preserving water quality and safeguarding human health. Understanding the intricate dynamics within the soil microbiome necessitates unravelling complex bacterial-fungal interactions (BFIs). BFIs occur in diverse habitats, such as the phyllosphere, rhizosphere and bulk soil, where they exert substantial influence on plant-microbe associations, nutrient cycling and overall ecosystem functions. In various symbiotic associations, fungi form mycorrhizal connections with plant roots, enhancing nutrient uptake through the root and mycorrhizal pathways. Concurrently, specific soil bacteria, including mycorrhiza helper bacteria, play a pivotal role in nutrient acquisition and promoting plant growth. Chemical communication and biofilm formation further shape plant-microbial interactions, affecting plant growth, disease resistance and nutrient acquisition processes.

SCOPE

Promoting synergistic interactions between mycorrhizal fungi and soil microbes holds immense potential for advancing ecological knowledge and conservation. However, despite the significant progress, gaps remain in our understanding of the evolutionary significance, perception, functional traits and ecological relevance of BFIs. Here we review recent findings obtained with respect to complex microbial communities - particularly in the mycorrhizosphere - and include the latest advances in the field, outlining their profound impacts on our understanding of ecosystem dynamics and plant physiology and function.

CONCLUSIONS

Deepening our understanding of plant BFIs can help assess their capabilities with regard to ecological and agricultural safe-guarding, in particular buffering soil stresses, and ensuring sustainable land management practices. Preserving and enhancing soil biodiversity emerge as critical imperatives in sustaining life on Earth amidst pressures of anthropogenic climate change. A holistic approach integrates scientific knowledge on bacteria and fungi, which includes their potential to foster resilient soil ecosystems for present and future generations.

Regulation of quorum sensing activities by the stringent response gene rsh in sphingomonads is species-specific and culture condition dependent

Stringent response and quorum sensing (QS) are two essential mechanisms that control bacterial global metabolism for better survival. Sphingomonads are a clade of bacteria that survive successfully in diverse ecosystems. In silico survey indicated that 36 out of 79 investigated sphingomonads strains contained more than one luxI homolog, the gene responsible for the biosynthesis of QS signal acyl homoserine lactones (AHLs). Investigation of the regulatory effects of the stringent response gene rsh on QS related bioactivities were carried out using rsh mutants of Sphingobium japonicum UT26 and Sphingobium sp. SYK-6, both had three luxI homologs. Results indicated that deletion of rsh upregulated the overall production of AHLs and extracellular polymeric substances (EPS) in both UT26 and SYK-6 in rich medium, but affected expressions of these luxI/luxR homologs in different ways. In the poor medium (1% LB), rsh mutant of SYK-6 significantly lost AHLs production in broth cultivation but not in biofilm cultivation. The regulatory effects of rsh on QS activities were growth phase dependent in UT26 and culture condition dependent in SYK-6. Our results demonstrated the negative regulatory effect of rsh on QS activities in sphingomonads, which were very different from the positive effect found in sphingomonads containing only one luxI/R circuit. This study extends the current knowledge on the intricate networks between stringent response and QS system in sphingomonads, which would help to understand their survival advantage.

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.

Enhanced granulation of activated sludge in an airlift reactor for organic carbon removal and ammonia retention from industrial fermentation wastewater: A comparative study

Ammonia retention and recovery from high-nitrogenous wastewater are new concepts being used for nitrogen management. A microaerophilic activated sludge system was developed to convert organic nitrogen into ammonia and retain it for its recovery; however, the settleability of activated sludge remains a challenge. Therefore, this study proposed an aerobic granular sludge system as a potential solution. Two types of sequencing batch reactors-airlift and upflow reactors-were operated to investigate the feasibility of fast granule formation, the performance of organic carbon removal and ammonia retention, and the dynamics of microbial community composition. The operation fed with industrial fermentation wastewater demonstrated that the airlift reactor ensured a more rapid granule formation than the upflow reactor because of the high shear force, and it maintained a superior ammonia retention stability of approximately 85 %. Throughout the operational period, changes in hydraulic retention time (HRT), settling time, and exchange ratio altered the granular particle sizes and microbial community compositions. Rhodocyclaceae were replaced with Comamonadaceae, Methylophilaceae, Xanthomonadaceae, and Chitinophagaceae as core taxa instrumental in granulation, likely because of their extracellular polymeric substance secretion. As the granulation process progressed, a significant decrease in the relative abundances of nitrifying bacteria-Nitrospiraceae and Nitrosomonadaceae-was observed. The reduction of settling time and HRT enhanced granulation and inhibited the activity of nitrifying bacteria. The success in granulation for ammonia conversion and retention in this study accelerates the paradigm shift from ammonia removal to ammonia recovery from industrial fermentation wastewater.

Effects of exogenous N-acyl homoserine lactones (AHLs) on methanogenic activities and microbial community differences during anaerobic digestion

N-acyl homoserine lactones (AHLs) function as signaling molecules influencing microbial community dynamics. This study investigates the impact of exogenously applied AHLs on methane production during waste-activated sludge (WAS) anaerobic digestion (AD). Nine AHL types, ranging from 10-4 to 10 μg/g VSS, were applied, comparing microbial community composition under optimal AHL concentrations. Firmicutes, Bacteroidetes, Chloroflexi, and Proteobacteria were identified in anaerobic digesters with C4-HSL, C6-HSL, and C8-HSL. Compared to the control, Halobacterota increased by 19.25%, 20.87%, and 9.33% with C7-HSL, C10-HSL, and C12-HSL. Exogenous C7-HSL enhanced the relative abundance of Methanosarcina, Romboutsia, Sedimentibacter, Proteiniclasticum, Christensenellaceae_R-7_group. C10-HSL increased Methanosarcina abundance. C4-HSL, C6-HSL, C8-HSL, C10-HSL, and C12-HSL showed potential to increase unclassified_Firmicutes. Functional Annotation of Prokaryotic Taxa (FAPROTAX) predicted AHLs' impact on related functional genes, providing insights into their role in AD methanogenesis regulation. This study aimed to enhance the understanding of the influence of different types of exogenous AHLs on AD and provide technical support for regulating the methanogenesis efficiency of AD by exogenous AHLs.

Regulation of extracellular polymers based on quorum sensing in wastewater biological treatment from mechanisms to applications: A critical review

Extracellular polymeric substances (EPS) regulated by quorum sensing (QS) could directly mediate adhesion between microorganisms and form tight microbial aggregates. Besides, EPS have redox properties, which can facilitate electron transfer for promoting electroactive bacteria. Currently, the applications research on improving wastewater biological treatment performance based on QS regulated EPS have been widely reported, but reviews on the level of QS regulated EPS to enhance EPS function in microbial systems are still lacking. This work proposes the potential mechanisms of EPS synthesis by QS regulation from the viewpoint of material metabolism and energy metabolism, and summarizes the effects of QS on EPS synthesis. By synthesizing the role of QS in EPS regulation, we further point out the applications of QS-regulated EPS in wastewater biological treatment, which involve a series of aspects such as strengthening microbial colonization, mitigating membrane biofouling, improving the shock resistance of microbial metabolic systems, and strengthening the electron transfer capacity of microbial metabolic systems. According to this comprehensive review, future research on QS-regulated EPS should focus on the exploration of the micro-mechanisms, and economic regulation strategies for QS-regulated EPS should be developed, while the stability of QS-regulated EPS in long-term production experimental research should be further demonstrated.

Combined recovery of polyhydroxyalkanoates and reclaimed water in the mainstream of a WWTP for agro-food industrial wastewater valorisation by membrane bioreactor technology

The present study investigated the combined production of reclaimed water for reuse purposes and polyhydroxyalkanoates (PHA) from an agro-food industrial wastewater. A pilot plant implementing a two-stage process for PHA production was studied. It consisted of a mainstream sequencing batch membrane bioreactor (SBMBR) in which selection of PHA-accumulating organisms and wastewater treatment were carried out in, and a side-stream fed-batch reactor (FBR) where the excess sludge from the SBMBR was used for PHA accumulation. The performance of the SBMBR was compared with that of a conventional sequencing batch reactor (SBR) treating the same wastewater under different food to microorganisms' ratios (F/M) ranging between 0.125 and 0.650 kgCOD kgTSS-3 d-1. The SBMBR enabled to obtain very high-quality effluent in compliance with the relevant national (Italy) and European regulations (Italian DM 185/03 and EU, 2020/741) in the field of wastewater reclamation, whereas the performances in the SBR collapsed at F/M higher than 0.50 kgCOD kgTSS-1d-1. A maximum intracellular storage of 45% (w/w) and a production yield of 0.63 gPHA L-1h-1 were achieved when the SBMBR system was operated with a F/M ratio close to 0.50 kgCOD kgTSS-1d-1. This resulted approximately 35% higher than those observed in the SBR, since the ultrafiltration membrane avoided the washout of dispersed and filamentous bacteria capable of storing PHA. Furthermore, while maximizing PHA productivity in conventional SBR systems led to process dysfunctions, in the SBMBR system it helped mitigate these issues by reducing membrane fouling behaviour. The results of this study supported the possibility to achieve combined recovery of reclaimed water and high-value added bioproducts using membrane technology, leading the way for agro-food industrial wastewater valorization in the frame of a circular economy model.

Comprehensive analysis of effects of magnetic nanoparticles on aerobic granulation and microbial community composition: From the perspective of acyl-homoserine lactones mediated communication

As dosing additives benefit for aerobic granular sludge (AGS) cultivation, effects of different concentrations (0, 10, 50 and 100 mg/L) of magnetic nanoparticles (Fe3O4 NPs) on aerobic granulation, contaminant removal and potential microbial community evolution related to acyl-homoserine lactones (AHLs) mediated bacterial communication were investigated with municipal wastewater. Results showed that the required time to achieve granulation ratio > 70 % was reduced by 60, 90 and 30 days in phase II with addition of 10, 50, 100 mg/L Fe3O4 NPs, respectively. 50 mg/L Fe3O4 NPs can improve contaminant removal efficiency. The promotion of relative abundance of AHLs-producing and AHLs-producing/quenching populations and AHLs-related functional genes accompanied with faster granulation. Iron-cycling-related bacteria were closely related with AHLs-related bacteria during AGS formation. Co-occurrence network analyses showed that AHLs-mediated communication may play an important role in coordinating microbial community composition and functional bacteria participating in nitrogen and polyphosphate metabolisms during aerobic granulation process.

Antibiofilm potential of nanonized eugenol against Pseudomonas aeruginosa

AIMS

The purpose of this study was to synthesize a nanoform of eugenol (an important phytochemical with various pharmacological potentials) and to investigate its antibiofilm efficacy on Pseudomonas aeruginosa biofilm.

METHODS AND RESULTS

Colloidal suspension of eugenol-nanoparticles (ENPs) was synthesized by the simple ultrasonic cavitation method through the emulsification of hydrophobic eugenol into hydrophilic gelatin. Thus, the nanonization process made water-insoluble eugenol into water-soluble nano-eugenol, making the nanoform bioavailable. The size of the ENPs was 20-30 nm, entrapment efficiency of eugenol within gelatin was 80%, and release of eugenol from the gelatin cap was slow and sustained over 5 days. Concerning the clinically relevant pathogen P. aeruginosa, ENPs had higher antibiofilm (for both formation and eradication) activities than free eugenol. Minimal biofilm inhibitory concentration and minimal biofilm eradication concentration of ENP on P. aeruginosa biofilm were 2.0 and 4.0 mM, respectively. In addition, the measurement of P. aeruginosa biofilm biomass, biofilm thickness, amount of biofilm extra-polymeric substance, cell surface hydrophobicity, cell swarming and twitching efficiencies, cellular morphology, and biofilm formation in catheter demonstrated that the antibiofilm efficacy of nano-eugenol was 30%-40% higher than that of bulk eugenol.

CONCLUSION

These results signify that future pharmacological and clinical studies are very much required to investigate whether ENPs can act as an effective drug against P. aeruginosa biofilm-mediated diseases. Thus, the problem of intrinsic antibiotic tolerance of biofilm-forming cells may be minimized by ENPs. Moreover, ENP may be used as a potential catheter-coating agent to inhibit pseudomonal colonization on catheter surfaces and, therefore, to reduce catheter-associated infections and complications.

Effect of thermal hydrolysis pretreatment on the occurrence of N-acyl homoserine lactone during anaerobic digestion of waste activated sludge

This study sought to investigate the relationship between N-acyl homoserine lactones (AHLs) and methanogenic microorganisms, focusing on endogenous AHLs in the anaerobic digestion (AD) process. By analyzing waste activated sludge (WAS) samples, we examine the changes in microbial communities and the AHLs-methanogens connection. The Mantel test and Spearman correlation analysis were conducted to gain novel insights into the AD process. Our findings demonstrate that thermal hydrolysis pretreatment (THP) modifies AHL concentrations during AD, thereby enhancing methanogenic bacteria activity and regulating social interactions among microorganisms. In the Eth group (AD of THP samples labeled Eth), Methanobacterium and Methanosarcina accounted for over 80% of the methanogenic bacteria, with correlation coefficients greater than 0.5 between these bacterial taxa and N-hexyl-l-homoserine lactone (C6-HSL) and N-enanthyl-l-homoserine lactone (C7-HSL).

Complete genome analysis reveals environmental adaptability of sulfur-oxidizing bacterium Thioclava nitratireducens M1-LQ-LJL-11 and symbiotic relationship with deep-sea hydrothermal vent Chrysomallon squamiferum

One sulfur-oxidizing bacterium Thioclava sp. M1-LQ-LJL-11 was isolated from the gill of Chrysomallon squamiferum collected from 2700 m deep hydrothermal named Longqi on the southwest Indian Ocean ridge. In order to understand its survival mechanism in hydrothermal extreme environment and symbiotic relationship with its host, the complete genome of strain M1-LQ-LJL-11 was sequenced and analyzed. A total of 6117 Mb of valid data was obtained, including 4096 coding genes, 61 non coding genes, including 9 rRNAs (among them, there are 3 in 23S rRNA, 3 in 5S rRNA, and 3 in 16S rRNA.), 52 tRNAs and 35 genomic islands. Strain M1-LQ-LJL-11 contains one chromosome and two plasmids. In the genome annotation information of the strain, we found 28 genes including cys sox, sor, sqr, tst related to sulfur metabolism and 17 metal resistance genes. Interestingly, a pair of quorum sensing system which probably regulating biofilm formation located in chromosome was found. These genes are critical for self-adaptation against severe environment as well as host survival. This study provides a basis understanding for the adaptive strategies of deep-sea hydrothermal bacteria and symbiotic relationship with its host in extreme environments through gene level.

Effect of quorum quenching on biofouling control and microbial community in membrane bioreactors by Brucella sp. ZJ1

Quorum quenching (QQ) has been demonstrated to be a novel technique for controlling biofouling in membrane bioreactors (MBRs), as it can significantly inhibit biofilm formation by disrupting quorum sensing (QS). The exploration of new QQ bacterial strains and the evaluation of their performance in mitigating membrane fouling in MBR systems is significant. In this study, an efficient QQ strain, Brucella sp. ZJ1 was encapsulated in alginate beads and evaluated for its ability to mitigate biofouling. The findings revealed that MBR with QQ beads extended the operation time by 2-3 times without affecting pollutant degradation. QQ beads maintained approximately 50% QQ activity after more than 50 days operation, indicating a long-lasting and endurable QQ effect. The QQ effect reduced extracellular polymeric substance (EPS) production especially in terms of polysaccharide and protein by more than 40%. QQ beads in the MBR also reduced the cake resistance and the irreversible resistance of membrane biofouling. Metagenomic sequencing suggests that QQ beads suppressed the QS effect and increased the abundance of QQ enzyme genes, ultimately inducing efficient membrane biofouling control.

Nitrite-resistance mechanisms on wastewater treatment in denitrifying phosphorus removal process revealed by machine learning, co-occurrence, and metagenomics analysis

Nitrite is a key intermediate in nitrogen metabolism that determines microbial transformations of N and P, greenhouse gas (N₂O) emissions, and system nutrient removal efficiency. However, nitrite also exerts toxic effects on microorganisms. A lack of understanding of high nitrite-resistance mechanisms at community- and genome-scale resolutions hinders the optimization for robustness of wastewater treatment systems. Here, we established nitrite-dependent denitrifying and phosphorus removal (DPR) systems under a gradient concentration of nitrite (0, 5, 10, 15, 20, and 25 mg N/L), relying on 16S rRNA gene amplicon and metagenomics to explore high nitrite-resistance mechanism. The results demonstrated that specific taxa were adopted to change the metabolic relationship of the community through phenotypic evolution to resist toxic nitrite contributing to the enhancement of denitrification and inhibition of nitrification and phosphorus removal. The key specific species, Thauera enhanced denitrification, whereas Candidatus Nitrotoga decreased in abundance to maintain partial nitrification. The extinction of Candidatus Nitrotoga induced a simpler restructuring-community, forcing high nitrite-stimulating microbiome to establish a more focused denitrification rather than nitrification or P metabolism in response to nitrite toxicity. Our work provides insights for understanding microbiome adaptation to toxic nitrite and giving theoretical support for operation strategy of nitrite-based wastewater treatment technology.

Understanding the cometabolic degradation of sulfadiazine by an enriched ammonia oxidizing bacteria culture from both extracellular and intracellular perspectives

Antibiotics are widely used drugs in the world and pose serious threats to ecosystems and human health. Although it has been reported that ammonia oxidizing bacteria (AOB) can cometabolize antibiotics, little has been reported on how AOB would respond to the exposure of antibiotics on extracellular and enzymatic levels, as well as the impact of antibiotics on the bioactivity of AOB. Therefore, in this study, a typical antibiotic, sulfadiazine (SDZ), was selected, and a series short-term batch tests using enriched AOB sludge were conducted to investigate the intracellular and extracellular responses of AOB along the cometabolic degradation process of SDZ. The results showed the cometabolic degradation of AOB made the main contribution to SDZ removal. When the enriched AOB sludge was exposed to SDZ, ammonium oxidation rate, ammonia monooxygenase activity, adenosine triphosphate concentration and dehydrogenases activity were negatively affected. The amoA gene abundance increased 1.5 folds within 24 h, which may enhance the uptake and utilization of substrates and maintain stable metabolic activity. In the tests with and without ammonium, the concentration of total EPS increased from 264.9 to 231.1 mg/gVSS to 607.7 and 538.2 mg/gVSS, respectively, under the exposure to SDZ, which was mainly contributed by the increase of proteins in tightly bound extracellular polymeric substances (EPS) and polysacharides in tightly bound EPS and soluble microbial products. The proportion of tryptophan-like protein and humic acid-like organics in EPS also increased. Moreover, SDZ stress stimulated the secretion of three quorum sensing signal molecules, C4-HSL (from 140.3 to 164.9 ng/L), 3OC6-HSL (from 17.8 to 42.4 ng/L) and C8-HSL (from 35.8 to 95.9 ng/L) in the enriched AOB sludge. Among them, C8-HSL may be a key signal molecule that promoted the secretion of EPS. The findings of this study could shed more light on the cometabolic degradation of antibiotics by AOB.

Environmentally relevant level of perfluorooctanoic acid affect the formation of aerobic granular sludge

The growing increasing occurrence of perfluorooctanoic acid (PFOA) in wastewater has raised concerns about its potential impact on the environment. Nevertheless, the impact of PFOA at environmentally relevant level on the formation of aerobic granular sludge (AGS) is still a 'black box'. This study thus aims to fill this gap by comprehensive investigation of sludge properties, reactor performance and microbial community during the formation of AGS. It was found that 0.1 mg/L PFOA delayed the formation of AGS, causing relatively lower proportion of large size AGS at the end of operation process. Interestingly, the microorganisms contribute to the reactor's tolerance to PFOA by secreting more extracellular polymeric substances (EPS) to slow or block the entry of toxic substances into the cells. During the granule maturation period, the reactor nutrient removal especially chemical oxygen demand (COD) and total nitrogen (TN) were affected by PFOA, decreasing the corresponding removal efficiencies to ∼81.2% and ∼69.8%, respectively. Microbial analysis further revealed that PFOA decreased the abundances of Plasticicumulans, Thauera, Flavobacterium and Cytophagaceae_uncultured, but it has promoted Zoogloea and Betaproteobacteria_unclassified growth, which maintained the structures and functions of AGS. The above results revealed that the intrinsic mechanism of PFOA on the macroscopic representation of sludge granulation process was revealed, and it is expected to provide theoretical insights and practical support for direct adoption of municipal or industrial wastewater containing perfluorinated compounds to cultivate AGS.

New insights into multi-strategies of sludge granulation in up-flow anaerobic sludge blanket reactors from community succession and interaction

This study aimed to elucidate the multiple strategies employed by anaerobes during granulation in a laboratory upflow anaerobic sludge blanket reactor, based on microbial succession and interactions. The anaerobic granulation process featured staged dominance of microbial genera, corresponding well with the environmental traits. Across the stages (selection, seeding, expansion, and maturation), chemotaxis attraction of nitrogen and/or carbon sources and flagellar motion were the primary strategy of microbial assembly. The second messengers - cyclic adenosine and guanosine monophosphates - partially regulated the agglomeration of filamentous Euryachaeota and Chloroflexi as the inner cores, while quorum sensing mediated the expansion of granules prior to maturation. Antagonism or competition governed the interactions within the phylogenetic molecular ecological network during sludge granulation, which were largely driven by the low-abundance (<1%) taxa. These new insights suggest that better engineering solutions to enhance chemotaxis attraction and species selection could achieve more efficient anaerobic granular sludge processes.

Microbial community evolution and functional trade-offs of biofilm in odor treatment biofilters

Biofilters inoculated with activated sludge are widely used for odor control in WWTP. In this process, biofilm community evolution plays an important role in the function of reactor and is closely related to reactor performance. However, the trade-offs in biofilm community and bioreactor function during the operation are still unclear. Herein, an artificially constructed biofilter for odorous gas treatment was operated for 105 days to study the trade-offs in the biofilm community and function. Biofilm colonization was found to drive community evolution during the start-up phase (phase 1, days 0-25). Although the removal efficiency of the biofilter was unsatisfactory at this phase, the microbial genera related to quorum sensing and extracellular polymeric substance secretion led to the rapid accumulation of the biofilm (2.3 kg biomass/m³ filter bed /day). During the stable operation phase (phase 2, days 26-80), genera related to target-pollutant degradation showed increases in relative abundance, which accompanied a high removal efficiency and a stable accumulation of biofilm (1.1 kg biomass/m³ filter bed/day). At the clogging phase (phase 3, days 81-105), a sharp decline in the biofilm accumulation rate (0.5 kg biomass/m³ filter bed /day) and fluctuating removal efficiency were observed. The quorum quenching-related genera and quenching genes of signal molecules increased, and competition for resources among species drove the evolution of the community in this phase. The results of this study highlight the trade-offs in biofilm community and functions during the operation of bioreactors, which could help improve bioreactor performance from a biofilm community perspective.

Celebrating 50 years of microbial granulation technologies: From canonical wastewater management to bio-product recovery

Microbial granulation technologies (MGT) in wastewater management are widely practised for more than fifty years. MGT can be considered a fine example of human innovativeness-driven nature wherein the manmade forces applied during operational controls in the biological process of wastewater treatment drive the microbial communities to modify their biofilms into granules. Mankind, over the past half a century, has been refining the knowledge of triggering biofilm into granules with some definite success. This review captures the journey of MGT from inception to maturation providing meaningful insights into the process development of MGT-based wastewater management. The full-scale application of MGT-based wastewater management is discussed with an understanding of functional microbial interactions within the granule. The molecular mechanism of granulation through the secretion of extracellular polymeric substances (EPS) and signal molecules is also highlighted in detail. The recent research interest in the recovery of useful bioproducts from the granular EPS is also emphasized.

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.

Role of bacterial quorum sensing and quenching mechanism in the efficient operation of microbial electrochemical technologies: A state-of-the-art review

Microbial electrochemical technologies (METs) are a group of innovative technologies that produce valuables like bioelectricity and biofuels with the simultaneous treatment of wastewater from microorganisms known as electroactive microorganisms. The electroactive microorganisms are capable of transferring electrons to the anode of a MET through various metabolic pathways such as direct (via cytochrome or pili) or indirect (through transporters) transfer. Though this technology is promising, the inferior yield of valuables and the high cost of reactor fabrication are presently impeding the large-scale application of this technology. Therefore, to overcome these major bottlenecks, a lot of research has been dedicated to the application of bacterial signalling, for instance, quorum sensing (QS) and quorum quenching (QQ) mechanisms in METs to improve its efficacy in order to achieve a higher power density and to make it more cost-effective. The QS circuit in bacteria produces auto-inducer signal molecules, which enhances the biofilm-forming ability and regulates the bacterial attachment on the electrode of METs. On the other hand, the QQ circuit can effectively function as an antifouling agent for the membranes used in METs and microbial membrane bioreactors, which is imperative for their stable long-term operation. This state-of-the-art review thus distinctly describes in detail the interaction between the QQ and QS systems in bacteria employed in METs to generate value-added by-products, antifouling strategies, and the recent applications of the signalling mechanisms in METs to improve their yield. Further, the article also throws some light on the recent advancements and the challenges faced while incorporating QS and QQ mechanisms in various types of METs. Thus, this review article will help budding researchers in upscaling METs with the integration of the QS signalling mechanism in METs.

Hierarchical stringent response behaviors of activated sludge system to stressed conditions

The stringent response of activated sludge systems to either stressed or harmful environments is important for the stable operation of activated sludge, which is examined by taking copper ion (Cu²⁺) as a stress model in this study. When weak stress was employed (Cu²⁺ ≤ 2.5 mg/L), the N-acyl-homoserine lactones (AHLs) of C6-, C8-, and C10-HSL increased by 30 %, 13 %, and 127 %, respectively, while the redox sensor green (RSG) intensity decreased by 28 %. Encountering the increased stress (2.5 mg/L < Cu²⁺ ≤ 5 mg/L), bacteria concentration in the supernatant increased by 87 %. However, the respiration rates of autotrophic and heterotrophic bacteria (SOUR_a and SOUR_h) and adenosine triphosphate decreased by 52 %, 18 %, and 27 %, respectively, and the flocs disintegrated with a diameter decreasing from 57 to 51 μm. When the stress became more serious (Cu²⁺ > 5 mg/L), the respiration rates continued to decline, but the quasi-endogenous respiration ratio (R_q/t) increased from 31 % to 47 %. Negligible changes occurred in the endogenous respiration rate (SOUR_e), adenosine diphosphate, and adenosine monophosphate. Based on these results, a hierarchical stringent response model of the activated sludge system to stressed conditions was proposed, and these responses were evaluated by respirogram. The initial response to weak stress was related to the most sensitive signals of quorum sensing and RSG intensity, well described by the quasi-endogenous respiration rate. The adaptive response to increased stress was the proactive migrations of low- and high-nucleic-acid bacteria to the supernatant, causing the looseness and even disintegration of sludge flocs, well described by SOUR_a, SOUR_h, and R_q/t. The lethal response to lethal stress was related to endogenous metabolic processes, well described by SOUR_e. This work provides new insights into understanding the stringent response of activated sludge systems to some stressed conditions. It helps to regulate the stability of activated sludge systems with respirogram technology.

Metagenomic analysis reveals indole signaling effect on microbial community in sequencing batch reactors: Quorum sensing inhibition and antibiotic resistance enrichment

Indole is an essential signal molecule in microbial studies. However, its ecological role in biological wastewater treatments remains enigmatic. This study explores the links between indole and complex microbial communities using sequencing batch reactors exposed to 0, 15, and 150 mg/L indole concentrations. A concentration of 150 mg/L indole enriched indole degrader Burkholderiales, while pathogens, such as Giardia, Plasmodium, and Besnoitia were inhibited at 15 mg/L indole concentration. At the same time, indole reduced the abundance of predicted genes in the "signaling transduction mechanisms" pathway via the Non-supervised Orthologous Groups distributions analysis. Indole significantly decreased the concentration of homoserine lactones, especially C₁₄-HSL. Furthermore, the quorum-sensing signaling acceptors containing LuxR, the dCACHE domain, and RpfC showed negative distributions with indole and indole oxygenase genes. Signaling acceptors' potential origins were mainly Burkholderiales, Actinobacteria, and Xanthomonadales. Meanwhile, concentrated indole (150 mg/L) increased the total abundance of antibiotic resistance genes by 3.52 folds, especially on aminoglycoside, multidrug, tetracycline, and sulfonamide. Based on Spearman's correlation analysis, the homoserine lactone degradation genes which were significantly impacted by indole negatively correlated with the antibiotic resistance gene abundance. This study brings new insights into the effect of indole signaling on in biological wastewater treatment plants.

Microbial population properties in the hierarchically structured aerobic granular sludge: Phenotype and genotype

Aerobic granular sludge (AGS) is a layered microbial aggregate formed by the ordered self-assembly of different microbial populations. In this study, the outer layer (OL), middle layer (ML), and the inner layer (IL) of matured AGS were obtained by circular cutting. The adhesion of microorganisms in IL was significantly higher than that in OL and ML during the famine period, while the adhesion of microorganisms in ML and OL was significantly higher than that in IL during the feast period, confirming that the formation of AGS started in the famine period, and the feast period promoted the increase of particle size. Microorganisms in the three-layer structure were highly diverse and rich in genes for cytochrome c oxidase synthesis with oxygen as the electron acceptor. G_Pseudoxanthomonas was the dominant bacterium in OL. Its spatial distribution increased gradually from the inside to the outside. G_Rhodanobacter was the dominant bacterium in IL. Its spatial distribution gradually decreased from the inside to the outside. The microorganisms in IL contained abundant pili genes. During the self-assembly process of particle formation, G_ Rhodanobaker adhered stronger than G_ Pseudoxanthomonas. The interface between aerobic and anoxic was about 0.6 mm away from the granule surface. Combined with the electron mediator properties of the extracellular polymeric substance (EPS) in granules, it was speculated that the degradation of organic substrates located in the anoxic layer relied on EPS as a mediator for long-range electron transfer, and finally transferred electrons to O₂. This study provides a new viewpoint on the formation mechanism of AGS from the perspective of the ordered self-assembly of microorganisms, offering a theoretical basis for the optimal selection of culture conditions and the application of AGS technology.

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.

Non-gene-editing microbiome engineering of spontaneous food fermentation microbiota-Limitation control, design control, and integration

Non-gene-editing microbiome engineering (NgeME) is the rational design and control of natural microbial consortia to perform desired functions. Traditional NgeME approaches use selected environmental variables to force natural microbial consortia to perform the desired functions. Spontaneous food fermentation, the oldest kind of traditional NgeME, transforms foods into various fermented products using natural microbial networks. In traditional NgeME, spontaneous food fermentation microbiotas (SFFMs) are typically formed and controlled manually by the establishment of limiting factors in small batches with little mechanization. However, limitation control generally leads to trade-offs between efficiency and the quality of fermentation. Modern NgeME approaches based on synthetic microbial ecology have been developed using designed microbial communities to explore assembly mechanisms and target functional enhancement of SFFMs. This has greatly improved our understanding of microbiota control, but such approaches still have shortcomings compared to traditional NgeME. Here, we comprehensively describe research on mechanisms and control strategies for SFFMs based on traditional and modern NgeME. We discuss the ecological and engineering principles of the two approaches to enhance the understanding of how best to control SFFM. We also review recent applied and theoretical research on modern NgeME and propose an integrated in vitro synthetic microbiota model to bridge gaps between limitation control and design control for SFFM.

New insight into soluble extracellular metabolites during sludge bulking process based on excitation-emission matrix spectroscopy and ultrahigh-performance liquid chromatography-mass spectrometry

Soluble extracellular metabolites (SEM) produced by microorganisms might significantly change during sludge bulking, which is a major operational problem caused by the excessive growth of filamentous bacteria. However, knowledge remains limited about the dynamics and potential role of SEM in the bulking of sludge. In this study, filamentous bulking was simulated in a laboratory-scale reactor and changes to SEM characteristics during the bulking process were investigated using excitation-emission matrix spectroscopy and ultrahigh-performance liquid chromatography-mass spectrometry. SEM components changed significantly at different phases of sludge bulking. Changes in SEM were closely correlated with the structure of the bacterial community. Based on the EEM profiles, significant increases in fulvic acid-like and humic acid-like substances in SEM were observed with the development of filamentous bulking. The degree of humification in SEM showed a clear increasing trend. Untargeted extracellular metabolomic analysis showed that the intensity of berberine and isorhamnetin in SEM increased significantly during the bulking phase, which might synergistically facilitate the development of filamentous bulking.

Challenges of aerobic granular sludge utilization: Fast start-up strategies and cationic pollutant removal

Aerobic granular sludge (AGS) is a self-aggregated microorganism consortium with pollutant removal properties. The aim of this work is to study and review the application of aerobic granules for water treatment with special focus on new applications and methodologies. Carbon-nitrogen containing pollutants are the classic targets of AGS technology. Carbon and nitrogen removal of AGS are classified as a biodegradation process. More recently, the AGS granules have been studied as sorbent materials for wastewater treatment. In particular, the sorption of cationic pollutants has been studied through biosorption and bioaccumulation mechanisms without distinguishing when one or the other process is involved. AGS conformation made them suitable for complex wastewater treatment. Indeed, several studies have demonstrated the removal of polyvalent cationic pollutants even with higher capacity than conventional sorbent materials. However, this was achieved almost exclusively for synthetic substrates, with single cation evaluation and using in some cases only qualitative measures. For successful industrial AGS application in complex substrates, it is necessary to evaluate and demonstrate the technology in real industrial conditions and reduce the currently long start-up times which limits its utility. Two new strategies have been proposed: autoinducer molecules and the production of artificial granular from common active sludge with commercial alginate. Finally, the increase of research on AGS cations assimilation properties will allow a new point of view, where granules will be materials for the recovery of valuable metals from industrial wastewater streams.

Understanding the N-acylated homoserine lactones(AHLs)-based quorum sensing for the stability of aerobic granular sludge in the aspect of substrate hydrolysis enhancement

Efficient substrate metabolism is the premise for stable operation of aerobic granular sludge and can be regulated by quorum sensing (QS). In this study, starch and acetate were selected to represent complex and simple substrates to provide comparable amount of metabolic energy for granules cultivation. Starch-fed granules were larger in size and contained higher EPS content than acetate-fed granules, though both granules exhibited similar substrate-degradation rates during sequencing batch reactor (SBR) cycle. Three N-acylhomoserine lactones (AHLs), including C8-HSL, 3OHC8-HSL and 3OHC12-HSL, were detected as dominant autoinducers in granules. They accumulated more in starch-fed granules than acetate-fed granules. The batch experiments were implemented to investigate QS regulation for granular stability in terms of substrate hydrolysis and transformation. The addition of three AHLs increased the activity of α-amylase, the main starch hydrolase, 4-6 times, significantly (p < 0.01) higher than the control treatment without AHLs amendment. While activity of dehydrogenase, the main simple substrate degradation enzyme, was increased only 1-2 times. Higher enzyme activity, especially α-amylase, significantly (p < 0.05) promoted the substrate-degradation rate (65 % than control group) and EPS yield in starch-fed system. Overall, QS can facilitate complex substrate uptake via hydrolysis enhancement and EPS secretion, which together promote sludge granulation and stability.

Quorum sensing unveils the sludge floccule-assisted stabilization of aerobic granules in granule-dominated sequencing batch reactors

Floccules are another major form of microbial aggregates in aerobic granular sludge systems. Previous studies mainly attributed the persistence of floccules to their relatively faster nutrient uptake and higher growth rate over aerobic granules; however, they failed to unravel the underlying mechanism of the long-term coexistence of these two aggregates. In this work, the existence and function of the floccules in an aerobic granule-dominated sequencing batch reactor were investigated from the view of quorum sensing (QS) and quorum quenching (QQ). The results showed that though the floccules were closely associated with the granules in terms of similar community structures (including the QS- and QQ-related ones), they exhibited a relatively higher QQ-related activity but a lower QS-related activity. A compatible proportion of floccules might be helpful to maintain the QS-related activity and keep the granules stable. In addition, the structure difference was demonstrated to diversify the QS- and QQ-related activities of the floccules and the aerobic granules. These findings could broaden our understanding of the interactions between the coexistent floccules and granules in aerobic granule-dominated systems and would be instructive for the development of the aerobic granular sludge process.

Quorum sensing responses of r-/K-strategists Nitrospira in continuous flow and sequencing batch nitrifying biofilm reactors

A better understanding of r-/K-strategists nitrifiers will help to balance the design and operation of bioprocesses for efficient pollution removal from wastewater. The objectives of study were to investigate the nitrite oxidation biokinetics, biofilm property, microbial community and quorum sensing (QS) of nitrifying biofilm in a continuously flow reactor (CFR) and a sequencing batch reactor (SBR). Results showed that nitrite-oxidizing bacteria were estimated to have a nitrite half saturation constant of 76.23 and 224.73 μM in CFR and SBR, respectively. High-throughput and metagenomic sequencing results showed that Nitrospira and Candidatus Nitrospira defluvii were the dominated nitrite-oxidizing taxa performing nitrite oxidation in both reactors. Nitrifying biofilm developed in CFR and SBR showed obviously different properties. Biofilm in SBR had an obviously higher ratio of polysaccharide and protein in extracellular polymeric substances, and higher thickness than in CFR. Metagenomics and chemical analysis revealed various types of acyl-homoserine lactone (AHL) circuit genes (e.g., luxI, lasI, hdtS) and four types of AHL signaling substances (e.g., C₆-HSL, C₈-HSL, C₁₀-HSL and 3-oxo-C₁₀-HSL) in nitrifying biofilm. The concentrations of these AHLs in biomass and water phases were obviously higher in SBR than that in CFR. Together, AHLs-based QS might affect the formation of nitrifying biofilm and thus contribute to the different biokinetics of Nitrospira in CFR and SBR. Our insights may reveal the molecular mechanism of Nitrospira for different biokinetics, and indicate the AHL association with Nitrospira adaptation to various conditions.

Evidence for Complex Interplay between Quorum Sensing and Antibiotic Resistance in Pseudomonas aeruginosa

Quorum sensing (QS) is a cell-density-dependent, intercellular communication system mediated by small diffusible signaling molecules. QS regulates a range of bacterial behaviors, including biofilm formation, virulence, drug resistance mechanisms, and antibiotic tolerance. Enzymes capable of degrading signaling molecules can interfere in QS-a process termed as quorum quenching (QQ). Remarkably, previous work reported some cases where enzymatic interference in QS was synergistic to antibiotics against Pseudomonas aeruginosa. The premise of combination therapy is attractive to fight against multidrug-resistant bacteria, yet comprehensive studies are lacking. Here, we evaluate the effects of QS signal disruption on the antibiotic resistance profile of P. aeruginosa by testing 222 antibiotics and antibacterial compounds from 15 different classes. We found compelling evidence that QS signal disruption does indeed affect antibiotic resistance (40% of all tested compounds; 89/222), albeit not always synergistically (not synergistic for 19% of compounds; 43/222). For some tested antibiotics, such as sulfathiazole and trimethoprim, we were able to relate the changes in resistance caused by QS signal disruption to the modulation of the expression of key genes of the folate biosynthetic pathway. Moreover, using a P. aeruginosa-based Caenorhabditis elegans killing model, we confirmed that enzymatic QQ modulates the effects of antibiotics on P. aeruginosa's pathogenicity in vivo. Altogether, these results show that signal disruption has profound and complex effects on the antibiotic resistance profile of P. aeruginosa. This work suggests that combination therapy including QQ and antibiotics should be discussed not globally but, rather, in case-by-case studies. IMPORTANCE Quorum sensing (QS) is a cell-density-dependent communication system used by a wide range of bacteria to coordinate behaviors. Strategies pertaining to the interference in QS are appealing approaches to control microbial behaviors that depend on QS, including virulence and biofilms. Interference in QS was previously reported to be synergistic with antibiotics, yet no systematic assessment exists. Here, we evaluate the potential of combination treatments using the model opportunistic human pathogen Pseudomonas aeruginosa PA14. In this model, collected data demonstrate that QS largely modulates the antibiotic resistance profile of PA14 (for more than 40% of the tested drugs). However, the outcome of combination treatments is synergistic for only 19% of them. This research demonstrates the complex relationship between QS and antibiotic resistance and suggests that combination therapy including QS inhibitors and antibiotics should be discussed not globally but, rather, in case-by-case studies.

The role of immobilized quorum sensing strain in promoting biofilm formation of Moving Bed Biofilm Reactor during long-term stable operation

Quorum sensing (QS) signaling plays a significant role in the natural regulation of biofilm formation. Multiple species QS systems in wastewater treatment processes have received significant attention in recent years and this study presents a long-term analysis of QS signaling, bacterial structures and extracellular polymeric substance (EPS) during biofilm formation, detachment and reformation processes. Six types of Acyl homoserine lactones (AHLs) were found to be closely related to different phases of biofilm development, with both QS and quorum quenching (QQ) strains being identified as drivers of various biofilm phases and 10 strains presenting a close relationship with AHLs (p < 0.05). Meanwhile, QS strain Sphingomonas rubra was immobilized and added into reactor systems, resulting in significant increase in AHL content, EPS production, and adhesion strength of biofilm (p < 0.05), which might promote biofilm formation processes during long-term stable operation. This study provides a potentially simple and economical way to improve activity and stability of MBBR in complex wastewater systems.

Formation, application, and storage-reactivation of aerobic granular sludge: A review

It was an important discovery in wastewater treatment that the microorganisms in the traditional activated sludge can form aerobic granular sludge (AGS) by self-aggregation under appropriate water quality and operation conditions. With a typical three-dimensional spherical structure, AGS has high sludge-water separation efficiency, great treatment capacity, and strong tolerance to toxic and harmful substances, so it has been considered to be one of the most promising wastewater treatment technologies. This paper comprehensively reviewed AGS from multiple perspectives over the past two decades, including the culture conditions, granulation mechanisms, metabolic and structural stability, storage, and its diverse applications. Some important issues, such as the reproducibility of culture conditions and the structural and functional stability during application and storage, were also summarized, and the research prospects were put forward. The aggregation behavior of microorganisms in AGS was explained from the perspectives of physiology and ecology of complex populations. The storage of AGS is considered to have large commercial potential value with the increase of large-scale applications. The purpose of this paper is to provide a reference for the systematic and in-depth study on the sludge aerobic granulation process.

Inhibition of growth, biofilm formation, virulence, and surface attachment of Agrobacterium tumefaciens by cinnamaldehyde derivatives

Agrobacterium tumefaciens, a soil-borne, saprophytic plant pathogen that colonizes plant surfaces and induces tumors in a wide range of dicotyledonous plants by transferring and expressing its T-DNA genes. The limited availabilities and efficacies of current treatments necessitate the exploration of new anti-Agrobacterium agents. We examined the effects of trans-cinnamaldehyde (t-CNMA) and its derivatives on the cell surface hydrophobicity, exopolysaccharide and exo-protease production, swimming motility on agar, and biofilm forming ability of A. tumefaciens. Based on initial biofilm inhibition results and minimum inhibitory concentration (MIC) data, 4-nitro, 4-chloro, and 4-fluoro CNMAs were further tested. 4-Nitro, 4-chloro, and 4-fluoro CNMA at ≥150 μg/ml significantly inhibited biofilm formation by 94–99%. Similarly, biofilm formation on polystyrene or nylon was substantially reduced by 4-nitro and 4-chloro CNMAs as determined by optical microscopy and scanning electron microscopy (SEM) and 3-D spectrum plots. 4-Nitro and 4-chloro CNMAs induced cell shortening and concentration- and time-dependently reduced cell growth. Virulence factors were significantly and dose-dependently suppressed by 4-nitro and 4-chloro CNMAs (P ≤ 0.05). Gene expressional changes were greater after 4-nitro CNMA than t-CNMA treatment, as determined by qRT-PCR. Furthermore, some genes essential for biofilm formation, motility, and virulence genes significantly downregulated by 4-nitro CNMA. Seed germination of Raphanus sativus was not hindered by 4-nitro or 4-fluoro CNMA at concentrations ≤200 μg/ml, but root surface biofilm formation was severely inhibited. This study is the first to report the anti-Agrobacterium biofilm and anti-virulence effects of 4-nitro, 4-chloro, and 4-fluoro CNMAs and t-CNMA and indicates that they should be considered starting points for the development of anti-Agrobacterium agents.