Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms

Recent advances in isolation and physiological characterization of planktonic anaerobic ammonia-oxidizing bacteria

Anaerobic ammonia oxidation (anammox) is widely regarded as an efficient biological nitrogen removal technology and is increasingly applied in wastewater treatment processes. However, the long doubling time and sensitivity to environmental pressures of anaerobic ammonia-oxidizing bacteria (AnAOB) often lead to unstable nitrogen removal performance. Various combined processes are being explored to overcome these limitations, providing insights into the ecological, physiological, and biochemical characteristics of AnAOB. Nevertheless, due to the lack of AnAOB pure cultures, the mechanisms of nitrogen metabolism, growth regulation, and cell communication remain unclear. This review highlights the unique physiological structures of AnAOB, current techniques for isolating and enriching planktonic AnAOB, and the associated challenges. A deeper understanding of these aspects offers guidance for improving planktonic AnAOB enrichment and incubation.

Microbial extracellular polymeric substances in the environment, technology and medicine

Microbial biofilms exhibit a self-produced matrix of extracellular polymeric substances (EPS), including polysaccharides, proteins, extracellular DNA and lipids. EPS promote interactions of the biofilm with other cells and sorption of organics, metals and chemical pollutants, and they facilitate cell adhesion at interfaces and ensure matrix cohesion. EPS have roles in various natural environments, such as soils, sediments and marine habitats. In addition, EPS are relevant in technical environments, such as wastewater and drinking water treatment facilities, and water distribution systems, and they contribute to biofouling and microbially influenced corrosion. In medicine, EPS protect pathogens within the biofilm against the host immune system and antimicrobials, and emerging evidence suggests that EPS can represent potential virulence factors. By contrast, EPS yield a wide range of valuable products that include their role in self-repairing concrete. In this Review, we aim to explore EPS as a functional unit of biofilms in the environment, in technology and in medicine.

Deciphering intricate associations between vigorous development and novel metabolic preferences of partial denitrification/anammox granular consortia within mainstream municipal wastewater

There is limited understanding of the granular partial denitrification/anammox (PD/A) microbiota and metabolic hierarchy specific to municipal wastewater treatment, particularly concerning the multi-mechanisms of functional differentiation and granulation tendencies under high-loading shocks. Therefore, this study utilized fragmented mature biofilm as the exclusive inoculum to rapidly establish a granular PD/A system. Following long-term feeding with municipal wastewater, PD/A process reached a total nitrogen removal efficiency of 97.7%, with anammox contributing over 93%. The dominant filamentous bacteria that supported the granular structure underwent significant changes throughout the operational period. Notably, the mature granular PD/A process demonstrated a distinct metabolic preference for recalcitrant, labile, and xenobiotic organics found in municipal wastewater. The biosynthesis of quorum sensing signaling molecules and core cofactors further enhanced the re-development and substrate metabolic adaptations of PD/A granules in real wastewater environments. This research illuminates the micro-ecological succession and metabolic heterogeneity of the granular PD/A process under mainstream loading.

The role of the proteosurfaceome and exoproteome in bacterial coaggregation

Bacterial coaggregation is a critical process in multispecies biofilm formation, driven by specific molecular interactions that facilitate the adhesion and aggregation of bacterial cells. These interactions are essential for the development and persistence of complex microbial communities. This review provides a comprehensive analysis of the roles of the proteosurfaceome and exoproteome in bacterial coaggregation. The proteosurfaceome, comprising surface-bound molecules such as adhesins, drives species-specific interactions crucial for partner recognition and adhesion. In parallel, the exoproteome, particularly extracellular polymeric substances (EPS), enhances aggregate stability by reinforcing structural integrity and facilitating intercellular communication, although its direct role in coaggregation remains to be fully clarified. By integrating these perspectives, this review aims to elucidate how the proteosurfaceome and exoproteome influence bacterial coaggregation, offering insights into their combined impact on microbial community structure and function. Furthermore, we highlight existing knowledge gaps and propose directions for future research.

Novel ellipsoid-like granules exhibit enhanced anammox performance compared to sphere-like granules

Anammox granular sludge (AnGS) serves as an important platform for cost-effective nitrogen removal from wastewater. Different to the traditionally sphere-like granules, a novel type of AnGS in a unique ellipsoid-like shape was obtained through enhancing shear force. The ellipsoid-like AnGS significantly exhibited a smaller aspect ratio (-25.1 %) and granular size (-11.8 %), compared to traditional sphere-like AnGS (p < 0.01). Comprehensive comparisons showed that ellipsoid-like AnGS possessed a significantly higher extracellular polymeric substances (EPS) content and strength, as well as an enhanced mass transfer and a higher viable bacteria proportion due to the larger substrate permeable zone (p < 0.01). Additionally, the anammox bacterial abundance (Candidatus Kuenenia) was 12.2 % higher in ellipsoid-like AnGS than in sphere-like AnGS. All these characteristics of ellipsoid-like AnGS jointly increased the specific anammox activity by 29.0 % and nitrogen removal capacity by 22.6 %, compared to sphere-like AnGS. Further fluid field simulation suggested the enhanced flow shear on the side surface of AnGS likely drove the formation of ellipsoid-like AnGS. The higher shear force on the side surface led to an increase of EPS content (especially hydrophobic protein) and elastic modulus, thus constraining lateral expansion. This study sheds light on impacts of granular shape, an overlooked morphological factor, on anammox performance. The ellipsoid-like AnGS presented herein also offers a unique and promising aggregate to enhance anammox performance.

A novel strategy for waste activated sludge treatment: Recovery of structural extracellular polymeric substances and fermentative production of volatile fatty acids

Structural extracellular polymeric substances (SEPS) as valuable biopolymers, can be extracted from waste activated sludge (WAS). However, the extraction yield is typically low, and detailed information on SEPS characterizations, as well as proper treatment of the sludge after SEPS extraction, remains limited. This study aimed to optimize the conditions of heating-Na2CO3 extraction process to increase the yield of SEPS extracted from WAS. Subsequently, SEPS were characterized, and, for the first time, insights into their protein composition were uncovered by using proteomics. A maximum SEPS yield of 209 mg g-1 volatile solid (VS) was obtained under optimal conditions: temperature of 90 °C, heating time of 60 min, Na+ dosage of 8.0 mmol/g VS, and pH required to precipitation of 4.0, which was comparable to that from the aerobic granular sludge reported in literature. Proteomics analysis unveiled that the proteins in SEPS primarily originated from microorganisms involved in nitrogen fixation and organic matter degradation, including their intracellular and membrane-associated regions. These proteins exhibited various catalytic activities and played crucial roles in aggregation processes. Besides, the process of SEPS extraction significantly enhanced volatile fatty acid (VFA) production during the anaerobic fermentation of residual WAS after SEPS extraction. A maximum VFA yield of 420 ± 14 mg COD/g VSadded was observed in anaerobic fermentation of 10 d, which was 77.2 ± 0.1 % higher than that from raw sludge. Mechanism analysis revealed that SEPS extraction not only improved WAS disintegration and solubilization but also reduced the relative activity of methanogens during anaerobic fermentation. Moreover, SEPS extraction shifted the microbial population during anaerobic fermentation in the direction towards hydrolysis and acidification such as Fermentimonas sp. and Soehngenia sp. This study proposed a novel strategy based on SEPS extraction and VFA production for sludge treatment, offering potential benefits for resource recovery and improved process efficiency.

Enhancing the performance of microalgal-bacterial systems with sodium bicarbonate: A step forward to carbon neutrality of municipal wastewater treatment

The microalgal-bacterial granular sludge (MBGS) process, enhanced with sodium bicarbonate (NaHCO3), offers a sustainable alternative for wastewater treatment aiming for carbon neutrality. This study demonstrates that NaHCO3, which can be derived from the flue gases and alkaline textile wastewater, significantly enhances pollutant removal and biomass production. Optimal addition of NaHCO3 was found to achieve an inorganic-to-organic carbon ratio of 1.0 and a total carbon-to-nitrogen ratio of 5.0. Metagenomic analysis and structural equation modeling showed that NaHCO3 addition increased dissolved oxygen concentrations and pH levels, creating a more favorable environment for key microbial communities, including Proteobacteria, Chloroflexi, and Cyanobacteria. Confocal laser scanning microscopy further confirmed enhanced interactions between Cyanobacteria and Proteobacteria/Chloroflexi, facilitating the MBGS process. These microbes harbored functional genes (gap2, GLU, and ppk) critical for removing organics, nitrogen, and phosphorus. Carbon footprint analysis revealed significant reductions in CO2 emissions by the NaHCO3-added MBGS process in representative countries (China, Australia, Canada, Germany, and Morocco), compared to the conventional activated sludge process. These findings highlight the effectiveness of NaHCO3 in optimizing MBGS process, establishing it as a key strategy in achieving carbon-neutral wastewater treatment globally.

A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota

Research on the microbial community and function of the anammox process for environmentally friendly wastewater treatment has achieved certain success, which may mean more universal insights are needed. However, the comprehensive understanding of the anammox process is constrained by the limited taxonomic assignment and functional characterization of anammox microbiota, primarily due to the scarcity of high-quality genomes for most organisms. This study reported a global genome catalog of anammox microbiotas based on numerous metagenomes obtained from both lab- and full-scale systems. A total of 1376 candidate species from 7474 metagenome-assembled genomes were used to construct the genome catalog, providing extensive microbial coverage (averaged of 92.40 %) of anammox microbiota. Moreover, a total of 64 core genera and 44 core species were identified, accounting for approximately 64.25 % and 43.97 %, respectively, of anammox microbiota. The strict core genera encompassed not only functional bacteria (e.g., Brocadia, Desulfobacillus, Zeimonas, and Nitrosomonas) but also two candidate genera (UBA12294 and OLB14) affiliated with the order Anaerolineales. In particular, core denitrifying bacteria with observably taxonomic diversity exhibited diverse functional profiles; for instance, the potential of carbohydrate metabolism in Desulfobacillus and Zeimonas likely improves the mixotrophic lifestyle of anammox microbiota. Besides, a noteworthy association was detected between anammox microbiota and system type. Microbiota in coupling system exhibited complex diversity and interspecies interactions by limiting numerous core denitrifying bacteria. In summary, the constructed catalog substantially expands our understanding of the core community and their functions of anammox microbiota, providing a valuable resource for future studies on anammox systems.

Illuminating microbial mat assembly: Cyanobacteria and Chloroflexota cooperate to structure light-responsive biofilms

Microbial mats are stratified communities often dominated by unicellular and filamentous phototrophs within an exopolymer matrix. It is challenging to quantify the dynamic responses of community members in situ as they experience steep gradients and rapid fluctuations of light. To address this, we developed a binary consortium using two representative isolates from hot spring mats: the unicellular oxygenic phototrophic cyanobacterium Synechococcus OS-B' (Syn OS-B') and the filamentous anoxygenic phototroph Chloroflexus MS-CIW-1 (Chfl MS-1). We quantified the motility of individual cells and entire colonies and demonstrated that Chfl MS-1 formed bundles of filaments that moved in all directions with no directional bias to light. Syn OS-B' was slightly less motile but exhibited positive phototaxis. This binary consortium displayed cooperative behavior by moving further than either species alone and formed ordered arrays where both species aligned with the light source. No cooperative motility was observed when a non-motile pilB mutant of Syn OS-B' was used instead of Syn OS-B'. The binary consortium also produced more adherent biofilm than individual species, consistent with the close interspecies association revealed by electron microscopy. We propose that cyanobacteria and Chloroflexota cooperate in forming natural microbial mats, by colonizing new niches and building robust biofilms.

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.

Life history strategies determine response to SRT driven crash in anammox bioreactors

Anaerobic ammonium oxidation (anammox) is a biological process often applied in wastewater treatment plants for nitrogen removal from highly concentrated side-stream effluents from anaerobic digesters. However, they are vulnerable to process instability prompted by operational shocks and microbial community imbalances, resulting in lengthy recovery times. These issues are further compounded by a lack of understanding of how sustained press disturbances influence the microbial ecology of the system. Here we investigate the response and recovery of an anammox membrane bioreactor to a solids retention time (SRT)-induced reactor crash using 16S rRNA gene and shotgun metagenomic sequencing. We observed a strong selection of bacterial groups based on reproduction strategies, with the Orders Rhodospirillales and Sphingobacteriales increasing from 1.0 % and 11.9 % prior to the crash to 31.9 % and 18.1 % during the crash respectively. The Orders Brocadiales and Anaerolineales decreased from 17.3 % and 28.3 % to 7.3 % and 1.4 % over the same time period, respectively. Metagenomic and metatranscriptomic analyses revealed differential crash responses in metabolically distinct groups of bacteria, with increased expression of genes for extracellular carbohydrate active enzymes, peptidases and membrane transporters. Following the crash, the reactor recovered to its prior state of nitrogen removal performance and pathway analysis demonstrated increased expression of genes related to exopolysaccharide biosynthesis and quorum sensing during the reactor recovery period. This study highlights the effects of reactor perturbations on microbial community dynamics in anammox bioreactors and provides insight into potential recovery mechanisms from severe disturbance.

Differentiation of the Anammox core microbiome: Unraveling the evolutionary impetus of scalable gene flow

Anaerobic ammonium oxidation bacteria (AAOB), distinguished by their unique autotrophic nitrogen metabolism, hold pivotal positions in the global nitrogen cycle and environmental biotechnologies. However, the ecophysiology and evolution of AAOB remain poorly understood, attributed to the absence of monocultures. Hence, a comprehensive elucidation of the AAOB-dominated core microbiome, anammox core, is imperative to further completing the theory of engineered nitrogen removal and ecological roles of anammox. Performing taxonomic and phylogenetic analyses on collected genome repertoires, we show here that Candidatus Brocadia and Candidatus Kuenenia possesses a more compact core than Candidatus Jettenia, which partly explains why the latter has a less common ecological presence. Evidence of gene flow is particularly striking in functions related to biosynthesis and oxygen detoxification, underscoring the evolutionary forces driving lineage and core differentiation. Furthermore, CRISPR spacer traceback of the AAOB metagenome-assembled genomes (MAGs) reveals a series of genetic traces for the concealed phages. By reconceptualizing the functional divergence of AAOB with the historical role of phages, we ultimately propose a coevolutionary framework to understand the evolutionary trajectory of anammox microecology. The discoveries provided in this study offer new insights into understanding the evolution of AAOB and the ecology of anammox.

Rethinking characterization, application, and importance of extracellular polymeric substances in water technologies

Biofilms play important roles in water technologies such as membrane treatments and activated sludge. The extracellular polymeric substances (EPS) are key components of biofilms. However, the precise nature of these substances and how they influence biofilm formation and behavior remain critical knowledge gaps. EPS are produced by many different microorganisms and span multiple biopolymer classes, which each require distinct strategies for characterization. The biopolymers additionally associate with each other to form insoluble complexes. Here, we explore recent progress toward resolving the structures and functions of EPS, where a shift towards direct functional assessments and advanced characterization techniques is necessary. This will enable integration with better microbial community and omics analyses to understand EPS biosynthesis pathways and create further opportunities for EPS control and valorization.

Mechanisms of microbial co-aggregation in mixed anaerobic cultures

Co-aggregation of anaerobic microorganisms into suspended microbial biofilms (aggregates) serves ecological and biotechnological functions. Tightly packed aggregates of metabolically interdependent bacteria and archaea play key roles in cycling of carbon and nitrogen. Additionally, in biotechnological applications, such as wastewater treatment, microbial aggregates provide a complete metabolic network to convert complex organic material. Currently, experimental data explaining the mechanisms behind microbial co-aggregation in anoxic environments is scarce and scattered across the literature. To what extent does this process resemble co-aggregation in aerobic environments? Does the limited availability of terminal electron acceptors drive mutualistic microbial relationships, contrary to the commensal relationships observed in oxygen-rich environments? And do co-aggregating bacteria and archaea, which depend on each other to harvest the bare minimum Gibbs energy from energy-poor substrates, use similar cellular mechanisms as those used by pathogenic bacteria that form biofilms? Here, we provide an overview of the current understanding of why and how mixed anaerobic microbial communities co-aggregate and discuss potential future scientific advancements that could improve the study of anaerobic suspended aggregates. KEY POINTS: • Metabolic dependency promotes aggregation of anaerobic bacteria and archaea • Flagella, pili, and adhesins play a role in the formation of anaerobic aggregates • Cyclic di-GMP/AMP signaling may trigger the polysaccharides production in anaerobes.

Novel anammox granules formation from conventional activated sludge for municipal wastewater treatment through flocs management

The direct integration of anammox process into municipal wastewater treatment has caused widespread concern, but the lack of anammox seeds limited its real application. This study successfully cultivated anammox granules (322.0 μm) from conventional activated sludge treating municipal wastewater. Through ultra-low floc sludge retention times of 8d, nitrifiers on flocs were eliminated and partial nitrification was realized. Furthermore, highly bacteria-enriched granules were initially formed, with Nitrosomonas and Ca. Competibacter 4-fold higher than that of flocs. Specific staining results revealed the microbial interaction with Ca. Brocadia, considering that Ca. Competibacter and Nitrosomonas correspondingly identified in the inner and outer layers of granules. The percentage of Ca. Brocadia present on the granules increased substantially from 0.0 % to 3.0 %, accompanied by a nitrogen removal rate of 0.3 kg·m-3·d-1. Our findings revealed a valuable reference for the anammox bacteria in-situ enrichment under mainstream conditions, which provides theoretical guidance for anammox-based processes practical application.

Iron-modified carriers accelerate biofilm formation and resist anammox bacteria loss in biofilm reactors for partial denitrification-anammox

The slow formation of anammox biofilms presents a bottleneck for resolving anammox bacterial loss and achieving stable performance in biofilm-based partial denitrification-anammox (PD-A) processes. This study utilized iron-modified (K1/Fe3O4 NPs) carriers, which were prepared and used for the first time in PD-A processes. Parallel moving bed biofilm reactors (MBBRs) indicated that iron-modified carriers facilitated the formation of biofilms at a faster rate than K1 carriers, consequently improving the nitrogen removal performance of the process by over 40 %. 16S rDNA analysis showed that anammox bacteria were approximately four times more abundant in the iron-modified carrier biofilm than in the K1 carrier biofilm. XPS and zeta potential analysis suggested that the improved microbial affinity of the iron-modified carrier surface caused this. As a result, the iron-modified carriers facilitated the formation of anammox biofilms and enhanced PD-A performance.

Quest for Nitrous Oxide-reducing Bacteria Present in an Anammox Biofilm Fed with Nitrous Oxide

N2O-reducing bacteria have been examined and harnessed to develop technologies that reduce the emission of N2O, a greenhouse gas produced by biological nitrogen removal. Recent investigations using omics and physiological activity approaches have revealed the ecophysiologies of these bacteria during nitrogen removal. Nevertheless, their involvement in‍ ‍anammox processes remain unclear. Therefore, the present study investigated the identity, genetic potential, and activity‍ ‍of N2O reducers in an anammox reactor. We hypothesized that N2O is limiting for N2O-reducing bacteria‍ ‍and an‍ ‍exogeneous N2O supply enriches as-yet-uncultured N2O-reducing bacteria. We conducted a 1200-day incubation of N2O-reducing bacteria in an anammox consortium using gas-permeable membrane biofilm reactors (MBfRs), which efficiently supply N2O in a bubbleless form directly to a biofilm grown on a gas-permeable membrane. A 15N tracer test indicated that the supply of N2O resulted in an enriched biomass with a higher N2O sink potential. Quantitative PCR and 16S rRNA amplicon sequencing revealed Clade II nosZ type-carrying N2O-reducing bacteria as protagonists of N2O sinks. Shotgun metagenomics showed the genetic potentials of the predominant Clade II nosZ-carrying bacteria, Anaerolineae and Ignavibacteria in MBfRs. Gemmatimonadota and non-anammox Planctomycetota increased their abundance in MBfRs despite their overall lower abundance. The implication of N2O as an inhibitory compound scavenging vitamin B12, which is essential for the synthesis of methionine, suggested its limited suppressive effect on the growth of B12-dependent bacteria, including N2O reducers. We identified Dehalococcoidia and Clostridia as predominant N2O sinks in an anammox consortium fed exogenous N2O because of the higher metabolic potential of vitamin B12-dependent biosynthesis.

Strengthen high-loading operation of wastewater treatment plants by composite micron powder carrier: Microscale control of carbon, nitrogen, and sulfur metabolic pathways

The concentration of activated sludge is a crucial factor influencing the capacity and efficiency of sewage wastewater treatment plants (WWTPs). However, high sludge concentrations can lead to sludge loss in the secondary sedimentation tank, resulting in reduced processing capacity, particularly during low-temperature stages and sludge bulking. This study investigated the impact of adding composite micron powder carriers (CMPC) in high-concentration powder carrier biofluidized bed (HPB) technology to the biochemical units of WWTPs on sludge concentration and settling performance. For the traditional activated sludge method (ASM), its hydraulic retention time (HRT) was 8 h, with an average effluent total nitrogen (TN) of 15.14 mg/L. Sludge bulking was prone to occur in low-temperature environments, resulting in a high average sludge volume index (SVI) of 560 mL/g. Conversely, with a CMPC dosage of 4 g/L, the HRT of HPB technology was 4.8 h, and the average effluent TN was 11.40 mg/L, with a removal efficiency of 67.43 %. During operation of HPB technology under high sludge concentration conditions (8 g/L), the average SVI remained at 85 mL/g, indicating excellent settling characteristics. Moreover, in the sequencing batch reactor (SBR), the SVI value of bulking sludge decreased from the original 695 to 111 mL/g by the 9th day of operation with the CMPC dosage of 2 g/L. At the same time, the filamentous bacteria almost disappeared, suggesting that CMPC inhibit the growth of filamentous bacteria. Metagenomic analysis demonstrated that CPMC enhance the utilization of small molecular fatty acids in activated sludge and promote electron transfer between nitrate and nitrite, thereby improving wastewater treatment capacity. Additionally, CMPC enhanced the relative abundance of Saprospiraceae in sludge, which accelerate the degradation of polysaccharides in extracellular polymeric substances, weaken sludge's hydrophilic properties, and improve sludge's settling performance. Overall, these findings suggested that CMPC effectively strengthen the high-loading operation of WWTPs by improving sludge concentration and sedimentation performance.

Cross-Feeding between Filamentous Cyanobacteria and Symbiotic Bacteria Favors Rapid Photogranulation

Photogranules are dense algal-bacterial aggregates used in aeration-free and carbon-negative wastewater treatment, wherein filamentous cyanobacteria (FC) are essential components. However, little is known about the functional role of symbiotic bacteria in photogranulation. Herein, we combined cyanobacterial isolation, reactor operation, and multiomics analysis to investigate the cyanobacterial-bacterial interaction during photogranulation. The addition of FC to the inoculated sludge achieved a 1.4-fold higher granule size than the control, and the aggregation capacity of FC-dominant photogranules was closely related to the extracellular polysaccharide (PS) concentration (R = 0.86). Importantly, we found that cross-feeding between FC and symbiotic bacteria for macromolecular PS synthesis is at the heart of photogranulation and substantially enhanced the granular stability. Chloroflexi-affiliated bacteria intertwined with FC throughout the photogranules and promoted PS biosynthesis using the partial nucleotide sugars produced by FC. Proteobacteria-affiliated bacteria were spatially close to FC, and highly expressed genes for vitamin B1 and B12 synthesis, contributing the necessary cofactors to promote FC proliferation. In addition, Bacteroidetes-affiliated bacteria degraded FC-derived carbohydrates and influenced granules development. Our metabolic characterization identified the functional role of symbiotic bacteria of FC during photogranulation and shed light on the critical cyanobacterial-bacterial interactions in photogranules from the viewpoint of cross-feeding.