Genome-based analysis to understanding rapid resuscitation of cryopreserved anammox consortia via sequential supernatant addition

Self-regulatory mechanisms of anammox system in response to CuO nanoparticles revealed by microbial ecological networks and metagenomics

Anaerobic ammonia oxidation (Anammox) has attracted widespread attention as an advanced biological nitrogen removal technology. CuO nanoparticles (CuO NPs) is one of the most common nanomaterials widely used in industrial production. In this study, microbial network construction, metagenomics and binning analysis were integrated to elucidate the impact of CuO NPs on anammox system. Nitrogen removal efficiency initially fluctuated but eventually stabilized after the addition of 1 mg/L CuO NPs. Network analysis revealed a significant increase in cooperative associations between anammox bacteria (AnAOB: Candidatus_Kuenenia, Candidatus_Jettenia, and Candidatus_Brocadia) and Chloroflexi from 0 % to 75 %. Metagenomic and binning analysis elucidated the intricate metabolic interactions between AnAOB and Chloroflexi, particularly in the biosynthesis of polysaccharide, protein, and cofactors.The collaboration between AnAOB and Chloroflexi was crucial for maintaining the ecological balance of the community structure under CuO NPs stress in anammox system.

Enhancement of the reactivation process of long-term starved anammox granular sludge with gravel balls: Microbial succession and metabolic impact

Anaerobic ammonium oxidation (Anammox) process is an economical and energy-efficient method of wastewater nitrogen removal. However, they are highly susceptible to starvation stress caused by sudden environmental changes. Rapid reactivation of starved anammox sludge is a crucial method to address seed sludge shortages and expand practical applications. This study investigated the impact of gravel balls on the reactivation of long-term starved anammox granular sludge (628 days). The results showed that gravel balls enhanced the recovery of nitrogen removal performance in starved anammox sludge, with nitrogen removal efficiency being 19.88% higher than the control group at the end of the recovery phase. The gravel balls also increased extracellular polymeric substance (EPS) secretion, contributing to the stability of the anammox system. Furthermore, the gravel balls promoted the proliferation of anammox bacteria, with the relative abundance of anammox bacteria reaching 38.25% on the 80th day. The analyses of microbial functions indicated that gravel balls facilitated cross-feeding and co-metabolism among microbes, while enhancing quorum sensing associated with anammox bacteria, forming a multifunctional community network centered on anammox bacteria. This indicates that gravel balls can effectively accelerate the reactivation process of long-term starved anammox sludge, aiding the reutilization of long-term starved anammox sludge.

Deciphering the adaptation mechanism of anammox consortia under sulfamethoxazole stress: A model coupling resistance accumulation and interspecies-cooperation

Sulfamethoxazole (SMX) is frequently detected in wastewater where anammox applications are promising. While it has been demonstrated that anammox consortia can adapt to SMX stress, the underlying community adaptation strategy has not yet been fully addressed. Therefore, in this study, we initially ascertained anammox consortia's ability to co-metabolize SMX in batch tests. Then, a 200-day domestication process of anammox consortia under SMX stress was carried out with community variations and transcriptional activities monitored by metagenomic and metatranscriptomic sequencing techniques. Despite the initial drop to 41.88 %, the nitrogen removal efficiency of the anammox consortia rebounded to 84.64 % post-domestication under 5 mg/L SMX. Meanwhile, a 4.85-fold accumulation of antibiotic resistance genes (ARGs) under SMX stress was observed as compared to the control group. Interestingly, the anammox consortia may unlock the SMX-inhibited folate synthesis pathway through a novel interspecies cooperation triangle among Nitrospira (NAA), Desulfobacillus denitrificans (DSS1), and the core anammox population Candidatus Brocadia sinica (AMX1), in which the modified dihydropteroate synthase (encoded by sul1) of NAA reconnected the symbiotic cooperation between AMX1 and DSS1. Overall, this study provides a new model for the adaptation strategies of anammox consortia to SMX stress.

Feasibility of simultaneous optimization of Anammox start-up and nitrogen removal performance by intermittent dosing of nanoscale zero-valent iron

The long acclimation period and sensitivity to environmental conditions of Anammox are the bottlenecks for its promotion and application. An innovative strategy was adopted to accelerate functional microbial enhancement and improve nitrogen removal performance by inoculating cryopreserved Anammox sludge and activated sludge with intermittent dosing of nanoscale zero-valent iron (nZVI). The acclimation time was shortened by 76 days with nitrogen removal efficiency (NRE) reaching up to 91.07 %. Anammox, NDFO (nitrate/nitrite-dependent Fe(II) oxidation), Feammox (Fe(III) reduction coupled with anaerobic ammonium oxidation) and abiotic reactions were coupled in the system with nZVI, contributing to 69.79 %, 15.14 %, 9.84 % and 0.25 % of nitrogen removal, respectively. Further microbial analysis demonstrated significant enrichment of functional microorganisms, such as Candidatus Jettenia, Acidovorax and Comamonas. High-efficient nitrogen removal was attribute to the increase of functional genes involved in Anammox, electronic transfer, heme C synthesis and iron metabolism. This work provides an inspiring idea for the mainstream Anammox application.

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

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

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

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

A review of anammox metabolic response to environmental factors: Characteristics and mechanisms

Anaerobic ammonium oxidation (anammox) is a promising low carbon and economic biological nitrogen removal technology. Considering the anammox technology has been easily restricted by environmental factors in practical engineering applications, therefore, it is necessary to understand the metabolic response characteristics of anammox bacteria to different environmental factors, and then guide the application of the anammox process. This review presented the latest advances of the research progress of the effects of different environmental factors on the metabolic pathway of anammox bacteria. The effects as well as mechanisms of conventional environmental factors and emerging pollutants on the anammox metabolic processes were summarized. Also, the role of quorum sensing (QS) mediating the bacteria growth, gene expression and other metabolic process in the anammox system were also reviewed. Finally, interaction and cross-feeding mechanisms of microbial communities in the anammox system were discussed. This review systematically summarized the variations of metabolic mechanism response to the external environment and cross-feeding interactions in the anammox process, which would provide an in-depth understanding for the anammox metabolic process and a comprehensive guidance for future anammox-related metabolic studies and engineering applications.

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

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

Active assimilators of soluble microbial products produced by wastewater anammox bacteria and their roles revealed by DNA-SIP coupled to metagenomics

Heterotrophic bacteria grow on influent organics or soluble microbial products (SMP) in wastewater anammox processes, playing key roles in facilitating microbial aggregation and reducing excess nitrate. The overgrowth of heterotrophs represents one of the major causes of anammox process failure, while the metabolic functions of coexisting heterotrophs and their roles in anammox process remain vague. This study aimed at revealing metabolic interactions between AnAOB and active SMP assimilators by integrating ¹³C DNA-stable isotope probing, metabolomic and metagenomic approaches. Glycine, aspartate, and glutamate with low biosynthetic energy cost were the major SMP components produced by AnAOB (net yield: 44.8, 10.4, 8.1 mg·g NH₄⁺-N^-1). Glycine was likely synthesized by AnAOB via the reductive glycine pathway which is oxygen-tolerant, supporting heterotrophic growth. Fermentative Chloroflexi bacterium OLB13, denitrifying Gemmatimonadaceae and Burkholderiaceae bacterium JOSHI-001 were active SMP assimilators, which were prevalent in globally distributed wastewater anammox reactors as core taxa. They likely formed a mutualistic relationship with auxotrophic Ca. Kuenenia by providing necessities such as methionine, folate, 4'-phosphopantetheine, and molybdopterin cofactor, and receiving vitamin B₁₂ for methionine synthesis. For the first time, the identify and metabolic features of SMP assimilators in wastewater anammox communities were revealed. Supplying necessities secreted by heterotrophs could be helpful to the endeavor of AnAOB enrichment. Practically, maintaining active but not overgrown SMP assimilators is critical to efficient and stable operation of wastewater anammox processes.

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

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

The anammox coupled partial-denitrification process in an integrated granular sludge and fixed-biofilm reactor developed for mainstream wastewater treatment: Performance and community structure

This study describes an integrated granular sludge and fixed-biofilm (iGB) reactor innovatively designed to carry out the anammox/partial-denitrification (A/PD) process for nitrogen removal with mainstream municipal wastewater. The iGB-A/PD reactor consists of anammox granules inoculated in the lower region of reactor and an acclimated fixed-biofilm positioned in the upper region. Compared to the other reported A/PD systems for mainstream wastewater treatment, this iGB-A/PD reactor is notable due to its higher quality effluent with a total inorganic nitrogen (TIN) of ∼3 mg•L^-1 and operation at a high nitrogen removal rate (NRR) of 0.8 ± 0.1 kg-N•m^-3•d^-1. Reads-based metatranscriptomic analysis found that the expression values of hzsA and hdh, key genes associated with anammox, were much higher than other functional genes on nitrogen conversion, confirming the major roles of the anammox bacteria in nitrogen bio-removal. In both regions of the reactor, the nitrate reduction genes (napA/narG) had expression values of 56-99 RPM, which were similar to that of the nitrite reduction genes (nirS/nirK). The expression reads from genes for dissimilatory nitrate reduction to ammonium (DNRA), nrfA and nirB, were unexpectedly high, and were over the half of the levels of reads from genes required for nitrate reduction. Kinetic assays confirmed that the granules had an anammox activity of 16.2 g-NH₄⁺-N•kg^-1-VSS•d^-1 and a nitrate reduction activity of 4.1 g-N•kg^-1-VSS•d^-1. While these values were changed to be 4.9 g- NH₄⁺-N•kg^-1-VSS•d^-1and 4.3 g-N•kg^-1-VSS•d^-1 respectively in the fixed-biofilm. Mass flux determination found that PD and DNRA was responsible for ∼50% and ∼25% of nitrate reduction, respectively, in the whole reactor, consistent with high effluent quality and treatment efficiency via a nitrite loop. Metagenomic binning analysis revealed that new and unidentified anammox species, affiliated with Candidatus Brocadia, were the dominant anammox organisms. Myxococcota and Planctomycetota were the principal organisms associated with the PD and DNRA processes, respectively.

Metagenomics and metatranscriptomics uncover the microbial community associated with high S0 production in a denitrifying desulfurization granular sludge reactor

The denitrification desulfurization process is a promising technology for elemental sulfur (S⁰) production from sulfide containing wastewater. However, the microbial community associated with high S⁰ production still is not well studied. This study describes an efficient denitrification S⁰ production bioreactor based on inoculation with anaerobic granular sludge. At an optimal S/N molar ratio of 7:2, 80 % of the influent sulfide was transformed to high quality elemental sulfur with a purity of 92.5% while the total inorganic nitrogen removal efficiency was stable at ∼80%. Metatranscriptomic analysis found that community expression of the gene encoding the sulfide-quinone reductase (SQR) was 10-fold greater than that of the flavocytochrome-c sulfide dehydrogenase subunit B (fccB). Moreover, the expression level of SQR was also significantly higher than the Dsr gene encoding for dissimilatory sulfate reductase, which encodes a critical S⁰ oxidation enzyme. Metagenomic binning analysis confirmed that sulfide-oxidizing bacteria (SOB) utilizing SQR were common in the community and most likely accounted for high S⁰ production. An unexpected enrichment in methanogens and high expression activity of bacteria carrying out Stickland fermentation as well as in other bacteria with reduced genomes indicated a complex community supporting stable sulfide oxidation to S⁰, likely aiding in performance stability. This study establishes this treatment approach as an alternative biotechnology for sulfide containing wastewater treatment and sheds light on the microbial interactions associated with high S⁰ production.

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

Both the benefits of bacterial quorum sensing (QS) and cross-feeding for bio-reactor performance in wastewater treatment have been recently reported. As the social traits of microbial communities, how bacterial QS regulating bacterial trade-off by cross-feeding remains unclear. Here, we find diffusion signal factor (DSF), a kind of QS molecules, can bridge bacterial interactions through regulating public goods (extracellular polymeric substances (EPS), amino acids) for metabolic cross-feedings. It showed that exogenous DSF-addition leads to change of public goods level and community structure dynamics in the anammox consortia. Approaches involving meta-omics clarified that anammox and a Lautropia-affiliated species in the phylum Proteobacteria can supply costly public goods for DSF-Secretor species via secondary messenger c-di-GMP regulator (Clp) after sensing DSF. Meanwhile, DSF-Secretor species help anammox bacteria scavenge extracellular detritus, which creates a more suitable environment for the anammox species, enhances the anammox activity, and improves the nitrogen removal rate of anammox reactor. The trade-off induces discrepant metabolic loads of different microbial clusters, which were responsible for the community succession. It illustrated the potential to artificially alleviate metabolic loads for certain bacteria. Deciphering microbial interactions via QS not only provides insights for understanding the social behavior of microbial community, but also creates new thought for enhancing treatment performance through regulating bacterial social traits via quorum sensing-mediated public goods.