Potential bacterial isolation by dosing metabolites in cross-feedings

Metabolic and ecological responses of denitrifying consortia to different carbon source strategies under fluctuating C/N conditions

Frequent fluctuations in the carbon-to-nitrogen (C/N) ratio of urban wastewater influent can undermine denitrification performance, posing challenges for stable nitrogen removal. Although supplying additional carbon sources is a recognized strategy to mitigate these issues, the underlying microbial interactions and metabolic reconfigurations triggered by changing C/N ratios remain incompletely understood. Here, we employed methanol, glycerol, sodium acetate, and glucose in long-term denitrification reactors and integrated denitrification kinetics, 16S rRNA gene amplicon sequencing, metagenomic binning, and metabolic modeling to elucidate how these systems respond to a declining C/N ratio. Our results show that lower C/N ratios diminished denitrification efficiency in all treatments, with each carbon source eliciting distinct shifts in microbial assemblages. Fluctuations in the C/N ratio determine the extent of directional selection of microbial communities based on carbon source metabolism and induce significant changes in non-dominant microorganisms. Throughout the process, the synthesis potential of PHA is closely linked to the system's ability to withstand fluctuations. Notably, metabolic modeling indicated that heightened tricarboxylic acid (TCA) cycle activity in the methanol- and glucose-fed communities was associated with suboptimal nitrogen removal. These findings offer novel insights into the metabolic and ecological mechanisms governing carbon source-driven denitrification under fluctuating C/N conditions, providing a valuable framework for optimizing nitrogen removal in urban wastewater treatment systems.

Insights into the influence of organic and salinity on the two-stage partial nitritation/anammox process in treating food waste digestate

ABSTRACTFood waste digestate (FWD), which contains significant levels of ammonium, organic matter, and salinity, can interfere with treatment performance of the anammox process. In this study, a two-stage partial nitritation/anammox (PN/A) process was established to investigate nitrogen removal and microbial response in treating FWD at a nitrogen loading rate (NLR) of 0.27 ± 0.02 gN/L/d. High concentrations of free ammonia (58 mg/L) and free nitrous acid (0.3 mg/L) facilitated the initiation of the partial nitritation (PN) process, achieving an average NO2-/NH4+ ratio of 1.28 ± 0.08. For the anammox process, a nitrogen removal rate (NRR) of 0.72 ± 0.13 gN/L/d was achieved. Free ammonia (NH3) stripping, Anammox pathway, and denitrification pathway contributed 4.1 ± 0.3%, 5.1 ± 0.2%, and 84.0 ± 1.5% of the total nitrogen removal, respectively. Nitrosomonas, a salt-tolerant ammonia-oxidizing bacteria (AOB), was enriched to 1.0%, while Nitrospira, a nitrite-oxidizing bacteria (NOB), was effectively suppressed to 0.003%. The salt-tolerant anammox genera unclassified_f__Brocadiaceae (13.9%) and Candidatus_Kuenenia (4.8%) dominated the nitrogen removal pathway. The high enrichment of unclassified_f__Brocadiaceae ensured stable operation of the anammox process at 0.62 ± 0.11% salinity, even with a high initial FA inhibition concentration of 40 mg/L. Additionally, norank_f_A4b (1.34%) and norank_f_norank_o_SBR1031 (52.1%) facilitated the hydrolysis of refractory organic matter. Denitrifying bacteria, including Hyphomicrobium, Truepera, and unclassified_c__Alphaproteobacteria, played significant roles in nitrate removal, with a CODconsumed/NO3-removed ratio of 2.7 ± 0.2. This study highlights the application of a two-stage PN/A process for rapid startup and effective nitrogen removal from FWD.

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 regulation of interspecific interaction and metabolism in anammox process to achieve coadaptation to artificial sweeteners

Artificial sweeteners (ASs) were frequently detectable in wastewater, which pose high risks to human health and ecological security. The feasibility of anaerobic ammonium oxidation (anammox) process for treatment of ASs-containing wastewater was evaluated in this study. The 86-d continuous flow experiment results showed that 0-30 μg L-1 cyclamate and acesulfame did not significantly affect the nitrogen removal efficiency (NRE) of anammox processes, which were 94.5 ± 3.0 % and 96.6 ± 2.5 %, respectively. Simultaneously, specific anammox activity (SAA) was inhibited by 15 μg L-1 ASs. Fortunately, anammox consortia adapted to the ASs stress by secreting extracellular polymeric substance (EPS). The relative abundances of Candidatus Kuenenia slightly decreased by 0.2 % and 2.3 % under stress of two ASs, and the microbial diversity increased. In addition, the anammox consortia regulated metabolites expression by cell energy allocation. The dominant metabolic pathways were amino acid metabolism, lipid metabolism and nucleotide metabolism. Particularly, the abundances of 5-hydroxylysinonorleucine and L-hypoglycin A significantly increased with ASs concentrations, which were crucial for bacterial proliferation. The co-metabolism between different bacteria might contribute to the biodegradation of ASs. This work demonstrates the feasibility of anammox process to treat the ASs-containing wastewater and reveals the regulation and adaptation mechanism of anammox microbiota, which further drives the implementation and development of anammox process.

Adjusted bacterial cooperation in anammox community to adapt to high ammonium in wastewater treatment plant

Bacterial cooperation is very important for anammox bacteria which perform low-carbon and energy-efficient nitrogen removal, yet its variation to adapt to high NH4 +-N concentration in actual wastewater treatment plants (WWTPs) remains unclear. Here, we found wide and varied cross-feedings of anammox bacteria and symbiotic bacteria in the two series connected full-scale reactors with different NH4 +-N concentrations (297.95 ± 54.84 and 76.03 ± 34.01 mg/L) treating sludge digester liquor. The uptake of vitamin B6 as highly effective antioxidants secreted by the symbiotic bacteria was beneficial for anammox bacteria to resist the high NH4 +-N concentration and varied dissolved oxygen (DO). When NH4 +-N concentration in influent (1785.46 ± 228.5 mg/L) increased, anammox bacteria tended to reduce the amino acids supply to symbiotic bacteria to save metabolic costs. A total of 26.1% bacterial generalists switched to specialists to increase the stability and functional heterogeneity of the microbial community at high NH4 +-N conditions. V/A-type ATPase for anammox bacteria to adapt to the change of NH4 +-N was highly important to strive against cellular alkalization caused by free ammonia. This study expands the understanding of the adjusted bacterial cooperation within anammox consortia at high NH4 +-N conditions, providing new insights into bacterial adaptation to adverse environments from a sociomicrobiology perspective.

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

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

Efficient alleviation granular sludge floatation in a high-rate anammox reactor by dosing folate

Although granular floatation has been recognized as a significant issue hindering the application of high-rate anammox biotechnology, limited knowledge is available about its causes and control strategies. This study proposed a novel control strategy by adding folate, and demonstrated its role in the granular floatation alleviation through long-term operation and granular characterizations. It was found that the floatation of anammox granular sludge was obviously relieved with the decreased sludge floatation potential by 67.1% after dosing with folate (8 mg/L) at a high nitrogen loading rate of 12.3 kg-N/(m3·d). Physiochemical analyses showed that the decrease of extracellular polymeric substances (EPS) content (mainly protein), the alleviation of granular surface pore plugging in conjunction with the smooth discharge of generated nitrogen gas were collectively responsible for efficient floatation control. Moreover, metagenomic analysis suggested that the synergistic interactions between anammox bacteria and their symbionts were attenuated after dosing exogenous folate. Anammox bacteria would reduce their synergistic dependence on the symbionts, and decline the supply of metabolites (e.g., amino acids and carbohydrates in EPS) to symbiotic bacteria. The declined EPS excretion contributed to the alleviation of granular floatation by dredging pores blockage, thus leading to a stable system performance. The findings not only offer insights into the role of microbial interaction in granular sludge floatation, but also provide a feasible approach for controlling the floatation issue in anammox granular-based processes.

Monitoring the Biochemical Activity of Single Anammox Granules with Microbarometers

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

Principles, challenges, and optimization of indigenous microalgae-bacteria consortium for sustainable swine wastewater treatment

Indigenous microalgae-bacteria consortium (IMBC) offers significant advantages for swine wastewater (SW) treatment including enhanced adaptability and resource recovery. In this review, the approaches for enriching IMBC both in situ and ex situ were comprehensively described, followed by symbiotic mechanisms for IMBC which involve metabolic cross-feeding and signal transmission. Strategies for enhancing treatment efficiencies of SW-originated IMBC were then introduced, including improving SW quality, optimizing system operating conditions, and adjusting microbial activities. Recommendations for maximizing treatment efficiencies were particularly proposed using a decision tree approach. Moreover, removal/recovery mechanisms for typical pollutants in SW using IMBC were critically discussed. Ultimately, a technical route termed SW-IMBC-Crop-Pig was proposed, to achieve a closed-loop economy for pig farms by integrating SW treatment with crop cultivation. This review provides a deeper understanding of the mechanism and strategies for IMBC's resource recovery from SW.

MAGs-centric crack: how long will, spore-positive Frankia and most Protofrankia, microsymbionts remain recalcitrant to axenic growth?

Nearly 50 years after the ground-breaking isolation of the primary Comptonia peregrina microsymbiont under axenic conditions, efforts to isolate a substantial number of Protofrankia and Frankia strains continue with enduring challenges and complexities. This study aimed to streamline genomic insights through comparative and predictive tools to extract traits crucial for isolating specific Frankia in axenic conditions. Pangenome analysis unveiled significant genetic diversity, suggesting untapped potential for cultivation strategies. Shared metabolic strategies in cellular components, central metabolic pathways, and resource acquisition traits offered promising avenues for cultivation. Ecological trait extraction indicated that most uncultured strains exhibit no apparent barriers to axenic growth. Despite ongoing challenges, potential caveats, and errors that could bias predictive analyses, this study provides a nuanced perspective. It highlights potential breakthroughs and guides refined cultivation strategies for these yet-uncultured strains. We advocate for tailored media formulations enriched with simple carbon sources in aerobic environments, with atmospheric nitrogen optionally sufficient to minimize contamination risks. Temperature adjustments should align with strain preferences-28-29°C for Frankia and 32-35°C for Protofrankia-while maintaining an alkaline pH. Given potential extended incubation periods (predicted doubling times ranging from 3.26 to 9.60 days, possibly up to 21.98 days), patience and rigorous contamination monitoring are crucial for optimizing cultivation conditions.

A typical acidic extracellular polysaccharide alludes to algae-bacteria-collaboration in microalgal-bacterial symbiosis

Microalgal-bacterial symbioses are prevalent in aquatic ecosystems and play a pivotal role in carbon sequestration, significantly contributing to global carbon cycling. The understanding of the contribution of exopolysaccharides (EPSs), a crucial carbon-based component, to the structural integrity of microalgal-bacterial symbioses remains insufficiently elucidated. To address this gap, our study aims to enhance our comprehension of the composition and primary structure of EPSs within a specific type of granular microalgal-bacterial symbiosis named microalgal-bacterial granular sludge (MBGS). Our investigation reveals that the acidic EPSs characteristic of this symbiosis have molecular weights ranging from several hundred thousand to over one million Daltons, including components like glucopyranose, galactopyranose, mannose, and rhamnose. Our elucidation of the backbone linkage of a representative exopolysaccharide revealed a →3)-β-D-Galp-(1→4)-β-D-Glcp-(1→ glycosidic linkage. This linear structure closely resembles bacterial xanthan, while the branched chain structure bears similarities to algal EPSs. Our findings highlight the collaborative synthesis of acidic EPSs by both microalgae and bacteria, emphasizing their joint contribution in the production of macromolecules within microalgal-bacterial symbiosis. This collaborative synthesis underscores the intricate molecular interactions contributing to the stability and function of these symbiotic relationships.

Enhancing anammox process with granular activated carbon: A study on Microbial Extracellular Secretions (MESs)

Granular activated carbon (GAC), a porous carbon-based material, provides increased attachment space for functional microorganisms and enhances nitrogen removal by facilitating extracellular electron transfer in the anammox process. This study investigates the effects of GAC on the biosynthesis of microbial extracellular secretions (MESs) and explores the roles of these secretions in anammox activities. Four lab-scale reactors were operated: two downstream UASB reactors (D1 and D2) receiving effluents from the upstream UASB reactors (U1: no-GAC, U2: yes-GAC). Our results indicate that MESs were enhanced with the addition of GAC. The effluent from U2 exhibited a 59.62 % higher amino acid content than that from U1. These secretions contributed to an increase in the nitrogen loading rate (NLR) in the downstream reactors. Specifically, NLR in D1 increased from 130.5 to 142.7 g N/m3/day, and in D2, it escalated from 137.5 to 202.8 g N/m3/day, likely through acting as cross-feeding substrates or vital nutrients. D2 also showed increased anammox bacterial activity, enriched Ca. Brocadia population and hao gene abundance. Furthermore, this study revealed that D2 sludge has significantly higher extracellular polymeric substances (EPS) (48.71 mg/g VSS) and a larger average granule size (1.201 ± 0.119 mm) compared to D1 sludge. Overall, GAC-stimulated MESs may have contributed to the enhanced performance of the anammox process.

Multi-omics analysis reveals the collaboration and metabolisms of the anammox consortia driven by soluble/non-soluble Fe(III) as the sole iron element

Iron is recognized as a physiological requirement for anammox bacteria (AnAOB), with Fe(II) considered to be the most effective form. However, Fe(III), instead of Fe(II) is the common iron form in natural and artificial ecosystems. In this study, the nitrogen removal performance and metabolic mechanisms in anammox consortia with soluble and non-soluble Fe(III) as the sole iron element were investigated. After the 150-day operation, the soluble (FeCl3) and insoluble (Fe2O3) Fe(III)-fed anammox systems reached nitrogen removal rates of 71.84 ± 0.80% and 50.20 ± 0.98%, respectively. AnAOB could survive with soluble (FeCl3) or insoluble (Fe2O3) Fe(III) as the sole iron element, reaching relative abundances of 18.49% and 13.16%, respectively. The results show that the formation of anammox core consortia can enable AnAOB's survival to adverse external conditions of Fe(II) deficiency. Metagenomic and metatranscriptomic analysis reveal that Ca. Kuenenia can only uptake Fe(II) into the cell for metabolisms either independently through the extracellular electron transfer or with the cross-feeding of symbiotic microbes. This study provides insight into the utilization and metabolic mechanisms of Fe(III) in Ca. Kuenenia-dominated consortia, and deepens the understanding of anammox core consortia in the nitrogen, carbon, and iron cycling, further promoting the practical applications of anammox processes.

Degradation of polycyclic aromatic hydrocarbons in aquatic environments by a symbiotic system consisting of algae and bacteria: green and sustainable technology

Polycyclic aromatic hydrocarbons (PAHs) are genotoxic, carcinogenic, and persistent in the environment and are therefore of great concern in the environmental protection field. Due to the inherent recalcitrance, persistence and nonreactivity of PAHs, they are difficult to remediate via traditional water treatment methods. In recent years, microbial remediation has been widely used as an economical and environmentally friendly degradation technology for the treatment of PAH-contaminated water. Various bacterial and microalgal strains are capable of potentially degrading or transforming PAHs through intrinsic metabolic pathways. However, their biodegradation potential is limited by the cytotoxic effects of petroleum hydrocarbons, unfavourable environmental conditions, and biometabolic limitations. To address this limitation, microbial communities, biochemical pathways, enzyme systems, gene organization, and genetic regulation related to PAH degradation have been intensively investigated. The advantages of algal-bacterial cocultivation have been explored, and the limitations of PAHs degradation by monocultures of algae or bacteria have been overcome by algal-bacterial interactions. Therefore, a new model consisting of a "microalgal-bacterial consortium" is becoming a new management strategy for the effective degradation and removal of PAHs. This review first describes PAH pollution control technologies (physical remediation, chemical remediation, bioremediation, etc.) and proposes an algal-bacterial symbiotic system for the degradation of PAHs by analysing the advantages, disadvantages, and PAH degradation performance in this system to fill existing research gaps. Additionally, an algal-bacterial system is systematically developed, and the effects of environmental conditions are explored to optimize the degradation process and improve its technical feasibility. The aim of this paper is to provide readers with an effective green and sustainable remediation technology for removing PAHs from aquatic environments.

Combination of Sequencing Batch Operation and A/O Process to Achieve Partial Mainstream Anammox: Pilot-Scale Demonstration and Microbial Ecological Mechanism

In this study, sequencing batch operation was successfully combined with a pilot-scale anaerobic biofilm-modified anaerobic/aerobic membrane bioreactor to achieve anaerobic ammonium oxidation (anammox) without inoculation of anammox aggregates for municipal wastewater treatment. Both total nitrogen and phosphorus removal efficiencies of the reactor reached up to 80% in the 250-day operation, with effluent concentrations of 4.95 mg-N/L and 0.48 mg-P/L. In situ enrichment of anammox bacteria with a maximum relative abundance of 7.86% was observed in the anaerobic biofilm, contributing to 18.81% of nitrogen removal, with denitrification being the primary removal pathway (38.41%). Denitrifying phosphorus removal (DPR) (40.54%) and aerobic phosphorus uptake (48.40%) played comparable roles in phosphorus removal. Metagenomic sequencing results showed that the biofilm contained significantly lower abundances of NO-reducing functional genes than the bulk sludge (p < 0.01), favoring anammox catabolism in the former. Interactions between the anammox bacteria and flanking community were dominated by cooperation behaviors (e.g., nitrite supply, amino acids/vitamins exchange) in the anaerobic biofilm community network. Moreover, the hydrolytic/fermentative bacteria and endogenous heterotrophic bacteria (Dechloromonas, Candidatus competibacter) were substantially enriched under sequencing batch operation, which could alleviate the inhibition of anammox bacteria by complex organics. Overall, this study provides a feasible and promising strategy for substantially enriching anammox bacteria and achieving partial mainstream anammox as well as DPR.

Anammox bacteria adapt to long-term light irradiation in photogranules

Photogranules composed of algae, nitrifiers, and anammox bacteria are promising for nitrogen removal from wastewater with reduced aeration and carbon emissions. However, it is difficult to be achieved as the potential inhibition of anammox bacteria by light. In this study, a syntrophic algal-partial nitrification/anammox granular sludge process was developed, with a nitrogen removal rate of 294.5 mg N/(L·d). We found the symbiosis in the community promoted the adaptation of anammox bacteria under light, and cross-feeding played an important role. Microalgae in the outer layers of photogranules sheltered most of the light and supplied cofactors and amino acids to promote nitrogen removal. In particular, Myxococcota MYX1 degraded the extracellular proteins produced by microalgae, providing amino acids to the entire bacterial community, which helped anammox bacteria save metabolic energy and adapt to light. Notably, the anammox bacteria Candidatus Brocadia exhibited unique light-sensing potential and adaptations to light irradiation compared with Candidatus Jettenia, including diverse DNA repair, scavenging of reactive oxygen species, cell movement. The phytochrome-like proteins encoded by Candidatus Brocadia further facilitated their spatial positioning and niche partitioning in photogranules. This study provides insights into the response of anammox bacteria in the algae-bacteria symbiosis system and suggests its potential application for carbon-negative nitrogen removal.