Metabolic network analysis reveals microbial community interactions in anammox granules

Gut microbiome drives individual memory variation in bumblebees

The potential of the gut microbiome as a driver of individual cognitive differences in natural populations of animals remains unexplored. Here, using metagenomic sequencing of individual bumblebee hindguts, we find a positive correlation between the abundance of Lactobacillus Firm-5 cluster and memory retention on a visual discrimination task. Supplementation with the Firm-5 species Lactobacillus apis, but not other non-Firm-5 bacterial species, enhances bees' memory. Untargeted metabolomics after L. apis supplementation show increased LPA (14:0) glycerophospholipid in the haemolymph. Oral administration of the LPA increases long-term memory significantly. Based on our findings and metagenomic/metabolomic analyses, we propose a molecular pathway for this gut-brain interaction. Our results provide insights into proximate and ultimate causes of cognitive differences in natural bumblebee populations.

Classification of uncultivated anammox bacteria and Candidatus Uabimicrobium into new classes and provisional nomenclature as Candidatus Brocadiia classis nov. and Candidatus Uabimicrobiia classis nov. of the phylum Planctomycetes and novel family Candidatus Scalinduaceae fam. nov to accommodate the genus Candidatus Scalindua

The phylum Planctomycetes is metabolically unique group of bacteria divided in two classes Planctomycetia and Phycisphaerae. Anaerobic ammonia-oxidizing (anammox) bacteria are the uncultured representatives of the phylum Planctomycetes. Anammox bacterial genera are placed in the family Candidatus (Ca.) Brocadiaceae of the order Ca. Brocadiales, assigned to the class Planctomycetia. Phylogenetic analysis, showed that the anammox bacteria and Ca. Uabimicrobium form a divergent clade from the rest of the cultured representatives of the phylum Planctomycetes. The phylogenetic study, pairwise distance and Average Amino acid Identity (AAI) showed that anammox bacteria don't belong to the classes Planctomycetia and Phycisphaerae. Anammox bacteria and Ca. Uabimicrobium form a deep-branching third clade in the phylogenetic analysis indicating that it is the most ancient third class within the phylum Planctomycetes. Phenotypic characters also separate anammox bacteria from classes Planctomycetia and Phycisphaerae. Therefore, based on phenotypic, phylogenetic, pairwise distance, AAI and phylogenomic analysis we propose a novel class Ca. Brocadiia to accommodate the order Ca. Brocadiales of anammox bacteria except Ca. Anammoximicrobium. Genera Ca. Jettenia, Ca. Anammoxoglobus, Ca. Kuenenia and Ca. Brocadia show their phylogenetic affiliation to the family Ca. Brocadiaceae. However, Ca. Scalindua showed a distant relationship with the family Ca. Brocadiaceae. Therefore, we suggest the exclusion of the genus Ca. Scalindua from the family Ca. Brocadiaceae; and propose its inclusion under a novel family with a provisional name as Ca. Scalinduaceae fam. nov. Similarly, Ca. Uabimicrobium amporphum showed distinct phylogenetic affiliation, therefore we propose a novel class Ca. Uabimicrobiia classis nov. to accommodate the genus Ca. Uabimicrobium.

Efficient nitrogen removal from mainstream wastewater through coupling Partial Nitritation, Anammox and Methane-dependent nitrite/nitrate reduction (PNAM)

The application of partial nitritation and anammox to remove nitrogen from mainstream wastewater is of great interest because of the potential to reduce energy cost and carbon dosage. However, this process confronts a dilemma of relatively high effluent nitrogen concentration (>10 mg N/L), owning to the unwanted prevalence of nitrite-oxidizing bacteria (NOB) and the intrinsic nitrate production by anammox bacteria. Here, a novel technology, named the one-stage PNAM, that integrates Partial Nitritation, Anammox and Methane-dependent nitrite/nitrate reduction reactions, was developed in a single membrane biofilm reactor (MBfR). With feeding of synthetic mainstream wastewater containing ∼50 mg NH₄⁺-N/L at a hydraulic retention time of 12 h, more than 95% nitrogen was removed in the established one-stage PNAM process at a practically useful rate of 0.1 kg N/m³/d. Microbial community characterization and in-situ batch tests revealed a sophisticated microbial structure consisting of ammonia-oxidizing bacteria (AOB), anammox bacteria, nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) bacteria and archaea, and a small fraction of NOB and aerobic methanotrophs. The role of methane in removing nitrate was confirmed by switching on/off the methane supply, which relaxed the requirement for NOB suppression. In addition, the established system was relatively robust against temperature variations, evidenced by a total nitrogen removal efficiency above 80% at temperature as low as 14 ℃. The results provide a promising alternative for efficient nitrogen removal from domestic wastewater using methane as the sole carbon source.

Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome

Microorganisms must respond to environmental changes to survive, often by controlling transcription initiation. Intermittent aeration during wastewater treatment presents a cyclically changing environment to which microorganisms must react. We used an intermittently aerated bioreactor performing partial nitritation and anammox (PNA) to investigate how the microbiome responds to recurring change. Meta-transcriptomic analysis revealed a dramatic disconnect between the relative DNA abundance and gene expression within the metagenome-assembled genomes (MAGs) of community members, suggesting the importance of transcriptional regulation in this microbiome. To explore how community members responded to cyclic aeration via transcriptional regulation, we searched for homologs of the catabolite repressor protein/fumarate and nitrate reductase regulatory protein (CRP/FNR) family of transcription factors (TFs) within the MAGs. Using phylogenetic analyses, evaluation of sequence conservation in important amino acid residues, and prediction of genes regulated by TFs in the MAGs, we identified homologs of the oxygen-sensing FNR in Nitrosomonas and Rhodocyclaceae, nitrogen-sensing dissimilative nitrate respiration regulator that responds to nitrogen species (DNR) in Rhodocyclaceae, and nitrogen-sensing nitrite and nitric oxide reductase regulator that responds to nitrogen species (NnrR) in Nitrospira MAGs. Our data also predict that CRP/FNR homologs in Ignavibacteria, Flavobacteriales, and Saprospiraceae MAGs sense carbon availability. In addition, a CRP/FNR homolog in a Brocadia MAG was most closely related to CRP TFs known to sense carbon sources in well-studied organisms. However, we predict that in autotrophic Brocadia, this TF most likely regulates a diverse set of functions, including a response to stress during the cyclic aerobic/anoxic conditions. Overall, this analysis allowed us to define a meta-regulon of the PNA microbiome that explains functions and interactions of the most active community members.

IMPORTANCE Microbiomes are important contributors to many ecosystems, including ones where nutrient cycling is stimulated by aeration control. Optimizing cyclic aeration helps reduce energy needs and maximize microbiome performance during wastewater treatment; however, little is known about how most microbial community members respond to these alternating conditions. We defined the meta-regulon of a PNA microbiome by combining existing knowledge of how the CRP/FNR family of bacterial TFs respond to stimuli, with metatranscriptomic analyses to characterize gene expression changes during aeration cycles. Our results indicated that, for some members of the community, prior knowledge is sufficient for high-confidence assignments of TF function, whereas other community members have CRP/FNR TFs for which inferences of function are limited by lack of prior knowledge. This study provides a framework to begin elucidating meta-regulons in microbiomes, where pure cultures are not available for traditional transcriptional regulation studies. Defining the meta-regulon can help in optimizing microbiome performance.

Prospects for multi-omics in the microbial ecology of water engineering

Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.

Key microorganisms mediate soil carbon-climate feedbacks in forest ecosystems

Soil microorganisms are known to significantly contribute to climate change through soil carbon (C) cycle feedbacks. However, it is challenging to incorporate these feedbacks into predictions of future patterns of terrestrial C cycling, largely because of the vast diversity of soil microorganisms and their responses to environmental conditions. Here, we show that the composition of the bacterial community can provide information about the microbial community-level thermal response (MCTR), which drives ecosystem-scale soil C-climate feedbacks. The dominant taxa from 169 sites representing a gradient from tropical to boreal forest mainly belonged to the phyla Actinobacteria and Acidobacteria. Moreover, we show that the MCTR in warm biomes and acidic soils was linked primarily to bacteria, whereas the MCTR in cold biomes and alkaline soils was primarily associated with fungi. Our results provide strong empirical evidence of linkages between microbial composition and the MCTR across a wide range of forests, and suggest the importance of specific microorganisms in regulating soil C-climate feedbacks.

Comparative Metagenomics Reveals Microbial Communities and Their Associated Functions in Two Types of Fuzhuan Brick Tea

Fuzhuan brick tea (FBT) is a unique post-fermented tea product, naturally co-fermented by microorganisms, and has gained global popularity due to its potential health benefits for humans. Considerable efforts have been made toward elucidating the microbial diversity within FBT, but an understanding of the underlying FBT community interactions and functions remains poorly studied. Consequently, the microbial communities of two types of FBT, originating from Hunan and Shaanxi provinces, were investigated using comparative shotgun metagenomic sequencing and functional annotations. Metagenomic analysis indicated that two communities shared similar taxonomic and functional attributes. Two samples shared 486 genera, in which Pseudomonas contributed most to the abundant functions within the two samples. The carbohydrate active enzyme functions of the communities primarily comprised GH (32.92%), GT (26.8%), CEs (20.43%), and AAs (18.04%). Furthermore, the overall metabolic pathways encoded by the metagenomes were largely associated with carbohydrate and amino acid metabolism, with nine metabolic pathways that were differential between two groups including penicillin and cephalosporin biosynthesis. Significantly, a total of 35 potential probiotics were inferred, with Pseudomonas putida being the most abundant inferred probiotic (80%) within the FBT communities. This study provides new insights into FBT microbial communities on their potential functions and roles in FBT characteristics.

High nitrogen removal performance of anaerobically treated fish processing wastewater by one-stage partial nitritation and anammox process with hydroxyapatite (HAP)-based syntrophic granules and granule structure

The one-stage partial nitritation and anammox process with the hydroxyapatite (HAP)-based syntrophic granules was studied for the ammonium nitrogen removal from the effluents of a self-agitated anaerobic baffled reactor treating the fish processing wastewater. When the ammonium in the influent was 1140 mg N·L^-1, a high nitrogen removal rate and nitrogen removal efficiency of 1.51 ± 0.10 kg N·m^-3·d^-1 and 88.2% were obtained, respectively. Anammox bacteria of Candidatus Kuenenia stuttgartiensis and ammonium oxidizing bacteria of Nitrosomonas were the two most predominant bacteria, while nitrite oxidizing bacteria activity was low and could be neglected during the treatment. The inorganic element properties of the sludge were analyzed by several methods to confirm the existence of HAP granules. Optical microscopic observation and scanning electron microscopy analysis revealed the structure of the granular sludge.This study supports the feasibility and potential of this process for high-efficiency nitrogen removal from fish processing wastewater.

Machine learning-assisted single-cell Raman fingerprinting for in situ and nondestructive classification of prokaryotes

Accessing enormous uncultivated microorganisms (microbial dark matter) in various Earth environments requires accurate, nondestructive classification, and molecular understanding of the microorganisms in in situ and at the single-cell level. Here we demonstrate a combined approach of random forest (RF) machine learning and single-cell Raman microspectroscopy for accurate classification of phylogenetically diverse prokaryotes (three bacterial and three archaeal species from different phyla). Our RF classifier achieved a 98.8 ± 1.9% classification accuracy among the six species in pure populations and 98.4% for three species in an artificially mixed population. Feature importance scores against each wavenumber reveal that the presence of carotenoids and structure of membrane lipids play key roles in distinguishing the prokaryotic species. We also find unique Raman markers for an ammonia-oxidizing archaeon. Our approach with moderate data pretreatment and intuitive visualization of feature importance is easy to use for non-spectroscopists, and thus offers microbiologists a new single-cell tool for shedding light on microbial dark matter.

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Random forest models classify prokaryotic species with high accuracy of >98%

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Both bacteria and archaea are classified using minimally preprocessed Raman data

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Feature importance reveals what biomolecules contribute to species classification

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Raman marker bands for some archaeal species are discovered

Metabolic potential of microbial community and distribution mechanism of Staphylococcus species during broad bean paste fermentation

Although the microbial diversity and structure in bean-based fermented foods have been widely studied, systematic studies on functional microbiota and mechanism of community forms in multi-microbial fermentation systems were still lacking. In this work, the metabolic pathway and functional potential of microbial community in broad bean paste (BBP) were investigated by metagenomics approach, and Staphylococcus, Bacillus, Weissella, Aspergillus and Zygosaccharomyces were found to be the potential predominant populations responsible for substrate alteration and flavor biosynthesis. Among them, Staphylococcus was the most abundant and widespread functional microbe, and closely related Staphylococcus species were diverse and ubiquitously distributed, with the opportunistic pathogen S. gallinarum being the most abundant Staphylococcus specie isolated from BBP. To explain the dominance status of S. gallinarum and species distributions of Staphylococcus genus, we tested the effects of abiotic and biotic factors on three Staphylococcus species using a tractable BBP model, demonstrating that adaptation to environmental conditions (environmental parameters and other functional microbes) led to the dominant position and species coexistence of Staphylococcus, and congeneric competition among Staphylococcus species further shaped ecological distributions of closely related Staphylococcus species. In general, this work revealed the metabolic potential of microbial community and distribution mechanism of Staphylococcus species during BBP fermentation, which could help traditional factories to more precisely control the safety and quality of bean-based fermented foods.

Soil type shapes the antibiotic resistome profiles of long-term manured soil

Animal manure fertilization facilitates the proliferation and dissemination of antibiotic resistance genes (ARGs) in soil, posing high risks to humans and ecosystem health. Although studies suggest that soil types could shape the ARG profiles in greenhouse soil, there is still a lack of comparative studies on the fate of ARGs in different types of manured soils under field trials. Thus, a metagenomic approach was used to decipher the fate of ARGs in 12-year long-term fertilized (inorganic fertilizer, compost manure and a mix of them) acidic, near-neutral and alkaline soils. A total of 408 unique ARG subtypes with multidrug, glycopeptide, beta-lactam and aminoglycoside resistance genes were identified as the most universal ARG types in all soil samples. Genes conferred to beta-lactam was the predominant ARG type in all the manure-amended soils. Genomic and statistical analyses showed that manure application caused the enrichment of 98 and 91 ARG subtypes in acidic and near-neutral soils, respectively, and 8 ARG subtypes in alkaline soil. The abundances of Proteobacteria (acidic and near-neutral soils) and Actinobacteria (alkaline soil), which are the potential hosts of ARGs, were clearly increased in manured soils. Random forest modelling and Pearson correlation analysis revealed that the soil properties (pH and bio-available Zn) and mobile genetic elements had considerable impacts on the transmission of ARGs. A structural equation model further indicated that soil types shaped the ARG profiles by significantly (P < 0.01) influencing the soil properties, bacterial abundance and bacterial diversity, where bacterial abundance was the major factor influencing the ARG profiles. This study systematically explored the mechanisms shaping the ARG profiles of long-term manured soils, and this information could support strategies to manage the dissemination of ARGs in different soil types.

Ecological Linkages between a Biofilm Ecosystem and Reactor Performance: The Specificity of Biofilm Development Phases

In biofilm-based engineered ecosystems, the reactor performance was closely linked to interspecies interactions within a biofilm ecosystem, whereas the ecological processes underpinning such linkage were still unenlightened. Herein, the principles of community succession and assembly were integrated to capture the ecological laws of biofilm development by molecular ecological networks and assembly model analysis based on the 16S rRNA sequencing analysis and metagenomics in a well-controlled moving bed biofilm reactor. At the initial colonization phase (days 0-2, driven by initial colonizers), interspecific cooperation (74.18%) facilitated initial biofilm formation, whereas some pioneers, and keystone species disappeared at later phases. At the accumulation phase (days 3-30, rapid biofilm development), interspecific cooperation (81.41 ± 5.07%) contributed to rapid biofilm development and keystone species were mainly involved in quorum sensing or positively correlated with extracellular polymeric substance production. At the maturation phase (days 31-106, a well-adapted quasi-equilibrium state), increased interspecific competition (32.74 ± 4.77%) and higher small-world property facilitated the rapid information transportation and pollutant treatment, and keystone species were positively correlated with the removal of COD and NH₄⁺-N. Homogenizing dispersal diminished the contemporary community dissimilarities, while turnover but rather nestedness governed the temporal variations in the biofilm succession period. This study highlighted the specificity of ecological processes at distinct biofilm development phases, which would advance our understanding on the development-to-function linkages in biofilm-based treatment processes.

Deciphering the mechanism of medium size anammox granular sludge driving better nitrogen removal performance

In this study, an integrated investigation to the microbial activities, extracellular polymeric substance (EPS), microbial community and function of anammox granular sludge (AnGS) was performed.Results showed that AnGS at 0.5-1.0 mm had the highest average specific anammox activity (SAA) of 345.9 mg NH₄⁺-N·gVSS^-1·d^-1, but AnGS at 1.0-1.5 mm with higher SAA might lead to better nitrogen removal efficiency. The content of slime EPS and SAA achieved positively correlation with R² of 98.11%, while protein/polysaccharide ratio of slime EPS and sludge volume index achieved negatively correlation with R² of 99.13%. Cadidatus Broccadia and Denitratisoma were positive correlations and most abundant in AnGS 0.5-1.0 mm of 20% and AnGS 1.0-1.5 mm of 37%, respectively. AnGS at 0.5-1.0 mm exhibited higher energy metabolism which mostly contributed to produce protein. The study provides new insights into the mechanisms of AnGS about 1 mm playing more important role in nitrogen removal performance.

Nitrate removal by anammox biomass with intracellular carbon source as electron donors via DNRA pathway

In this work, a novel nitrate (NO₃^-) reduction pathway by anaerobic ammonium oxidation (anammox) biomass was firstly discovered with the intracellular carbon sources as the only electron donors. And the possible reaction mechanism was deduced to be intracellular dissimilatory nitrate reduction to ammonium (DNRA) pathway according to the experimental results. In batch experiments, without any external electron donors, NO₃^--N (about 50 mg/L) was reduced to N₂ within 48 h, and a small amount of NO₂^--N was detected (the maximum of 2 mg/L) with the anammox biomass concentration of 4400 mg/L. Acetylene (4.46 mmol/L) addition resulted in obvious NH₄⁺ accumulation during NO₃^- degradation by anammox biomass, since acetylene mainly interfered in hydrazine (N₂H₄) generation from NH₄⁺ and NO. Without HCO₃^- addition, the NO₃^--N degradation rate was slower than that with HCO₃^- addition. Simultaneously, glycogen contents inside anammox biomass decreased to 133.22 ± 1.21 mg/g VSS and 129.79 ± 1.21 mg/g VSS with and without HCO₃^-, respectively, from 142.20 ± 0.61 mg/g VSS. In the long-term experiment, anammox biomass stably degraded NO₃^--N without external electron donors addition, and the maximum removal efficiency of NO₃^--N reached 55.4%. The above results indicated the anammox bacteria utilized the DNRA pathway to reduce NO₃^- to NO₂^- and further NH₄⁺, then normal anammox metabolism would continue to convert the produced NO₂^- and NH₄⁺ to N₂. The intracellular stored carbon sources (e.g., glycogen) were supposed to be electron donors for NO₃^- degradation. This capability would enhance the viability and living space of anammox bacteria in different natural ecosystems, and make it plausible that complete nitrogen removal could be implemented only by the anammox process.

Fast start-up and enhancement of partial nitritation and anammox process for treating synthetic wastewater in a sequencing bath biofilm reactor: Strategy and function of nitric oxide

In this study, the partial nitritation and anammox (PN-A) process was initiated within 30 days in a sequencing batch biofilm reactor (SBBR) by employing pre non-aeration and post non-aeration with fixed aeration rates. The average ammonia removal efficiency (ARE), total nitrogen removal efficiency (TNRE) of 98.5 ± 1.5% and 89.5 ± 1.6% were achieved. By doubling aeration rate and agitation rate and adopting pre non-aeration, the TNRR was promoted from 0.135 ± 0.013 kg N·m^-3·d^-1 to 0.285 ± 0.015 kg N·m^-3·d^-1, obtaining an average ARE and TNRE of 97.5 ± 1.5% and 85.5 ± 2.6%. Nitric oxide might induce anaerobic ammonia oxidation bacteria (AnAOB) during the start-up stage, and could be an indicator for synergetic state between ammonia oxidation bacteria (AOB) and AnAOB. Lower nitrous oxide emission factor of 0.51% was obtained. The abundance of AOB, AnAOB and nitrite oxidation bacteria (NOB) accounted for 1.6%, 19.3% and 0.3%, respectively.

Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria

The discovery of anaerobic ammonia-oxidizing bacteria (Anammox) and, more recently, aerobic bacteria common in many natural and engineered systems that oxidize ammonia completely to nitrate (Comammox) have significantly altered our understanding of the global nitrogen cycle. A high affinity for ammonia (K_m(app),NH3 ≈ 63nM) and oxygen place Comammox Nitrospira inopinata, the first described isolate, in the same trophic category as organisms such as some ammonia-oxidizing archaea. However, N. inopinata has a relatively low affinity for nitrite (K_m,NO2 ≈ 449.2μM) suggesting it would be less competitive for nitrite than other nitrite-consuming aerobes and anaerobes. We examined the ecological relevance of the disparate substrate affinities by coupling it with the Anammox bacterium Candidatus Brocadia anammoxidans. Synthetic communities of the two were established in hydrogel granules in which Comammox grew in the aerobic outer layer to provide Anammox with nitrite in the inner anoxic core to form dinitrogen gas. This spatial organization was confirmed with FISH imaging, supporting a mutualistic or commensal relationship. The functional significance of interspecies spatial organization was informed by the hydrogel encapsulation format, broadening our limited understanding of the interplay between these two species. The resulting low nitrate formation and the competitiveness of Comammox over other aerobic ammonia- and nitrite-oxidizers sets this ecological cooperation apart and points to potential biotechnological applications. Since nitrate is an undesirable product of wastewater treatment effluents, the Comammox-Anammox symbiosis may be of economic and ecological importance to reduce nitrogen contamination of receiving waters.

Enhancing the in-situ enrichment of anammox bacteria in aerobic granules to achieve high-rate CANON at low temperatures

In this study, a high-rate CANON (Complete Autotrophic Nitrogen-removal Over Nitrite) process was started up successfully by enhancing the in-situ enrichment of anammox bacteria in aerobic granules at conditions relevant for mainstream wastewater treatment. Firstly, to provide nitrite for anammox bacteria growth efficient nitrite-oxidizing bacteria (NOB) repression was rapidly achieved and stably maintained. Both low dissolved oxygen (DO) and ammonium concentrations ratio (DO/NH₄⁺ <0.15) and selective washing-out of NOB-preferred smaller particles at short hydraulic retention time (HRT, 25-15 min) contributed to the NOB repression. Then the stepwise down-regulating DO concentrations from 2.8 to 1.2 mg/L enhanced the enrichment of anammox bacteria in the aerobic granules. The enriched anammox species was dominated by Ca. Brocadia sapporoensis with the estimated growth rate of 0.008-0.013 d^-1 at 15 °C. Chloroflexi and Chlorobi-affiliated bacteria were also significantly enriched in the granules, which may benefit the anammox bacteria activity and growth. At the end of this study, the average total nitrogen removal rate and efficiency of the granular CANON process respectively reached 1.26 kg N·m^-3·d^-1 and 68% treating low-strength ammonium (∼50 mg N·L^-1) wastewater under such aggressive conditions (DO = 0.8-1.5 mg/L, HRT< 1.0 h, and T = 15 °C). Overall, the aerobic granules provided a habitable niche for the proliferation and almost complete retention of the anammox bacteria. This study provides a roadmap for in-situ starting up of high-rate CANON process for mainstream wastewater treatment with aerobic granules as inoculum.

Operational mode affects the role of organic matter in granular anammox process

In the presence of organic matter, the granular anammox system under sequencing batch mode showed more robust anammox performance than that under completely mixed mode, which was attributed to the better biomass retention with high settling ability and stability of granular sludge. Based on the specific anammox activity test, stratified and mixed distribution of heterotrophic bacteria was found under completely mixed and sequencing batch mode, respectively. The stratified microbial distribution resulted in low enzyme activity of anammox bacteria and sludge disintegration by hindering substrate transfer with a large accumulation of EPS on the granular surface. Whereas the heterotrophic bacteria mixed in granules (mixed microbial distribution) act as a "skeleton", which increased the particle size, density, and stability of granular sludge. Compared with biokinetic-based selection, diffusion-based selection with high substrate penetration depth more likely resulted in the mixed granular structure and strong resistance to organic inhibition under sequencing batch mode.

Retooling Microbiome Engineering for a Sustainable Future

Microbial communities (microbiomes) have been harnessed in biotechnology applications such as wastewater treatment and bioremediation for over a century. Traditionally, engineering approaches have focused on shaping the environment to steer microbiome function versus direct manipulation of the microbiome's metabolic network. While these selection-based approaches have proven to be invaluable for guiding bioprocess engineering, they do not enable the precise manipulation and control of microbiomes required for unlocking their full potential. Over the past 2 decades, systems biology has revolutionized our understanding of the metabolic networks driving microbiome processes, and more recently genetic engineering tools have started to emerge for nonmodel microorganisms and microbiomes. In this commentary, I discuss how systems biology approaches are being used to generate actionable understanding of microbiome functions in engineered ecosystems. I also highlight how integrating synthetic biology, automation, and machine learning can accelerate microbiome engineering to meet the sustainability challenges of the future.

Startup of pilot-scale single-stage nitrogen removal using anammox and partial nitritation (SNAP) reactor for waste brine treatment using marine anammox bacteria

This study is the first to demonstrate the startup of a pilot-scale single-stage nitrogen removal using anammox and partial nitritation (SNAP) reactor utilizing marine anammox bacteria. A complete mixing type reactor, continuously fed with waste brine obtained from a natural gas plant (salinity 3%, NH₄⁺-N 130-180 mg/L) and having an effective volume of 2 m³, achieved stable operation at temperatures of 20-30°C with a maximum nitrogen removal rate of 1.43 kg-N/m³/day. During the startup process, along with a small amount of seed sludge, granular sludge was additionally inoculated as a biomass carrier for the enrichment of ammonia oxidizing bacteria (AOB), followed by the enrichment of anammox bacteria. A mesh screen equipped at the outlet of the reactor facilitated the successful sludge retention in the reactor. Analysis of bacterial community composition indicated that Candidatus Scalindua was successfully enriched in the pilot SNAP reactor. These methods for stable sludge retention in the reactor greatly contributed to the startup of the first pilot-scale SNAP reactor using marine anammox bacteria.

Characteristics of anammox granular sludge using color differentiation, and nitrogen removal performance of its immobilized fillers based on microbial succession

The characteristics of anammox granular sludge (AnGS) based on color differentiation, and the regulation mechanism of immobilized fillers in the system were investigated. The results showed that biomass content, EPS and activity of red AnGS (R1) were higher than those of brown AnGS (R2). Moreover, R1 showed nitrification, while R2 showed denitrification. Filamentous bacteria constituted the granule skeleton of R1, while R2 mainly constituted inorganic nucleation and granulation. Additionally, immobilization improved the contribution rate of Anammox, and involved different regulatory mechanisms. High-throughput sequencing analysis showed that R1 encapsulation biomass eliminated miscellaneous bacteria and established specific flora, while mixed encapsulated biomass of R1 and R2 re-formed a functional bacterial network, which strengthened interspecies cooperation. The R2 encapsulated biomass and AnAOB copy numbers were inferior and the interspecific cooperation was weak, resulting in an unsatisfactory nitrogen removal performance. These results can strengthen the understanding and optimization of AnGS and its immobilization system.

Metabolic potential of the imperfect denitrifier Candidatus Desulfobacillus denitrificans in an anammox bioreactor

The imperfect denitrifier, Candidatus (Ca.) Desulfobacillus denitrificans, which lacks nitric oxide (NO) reductase, frequently appears in anammox bioreactors depending on the operating conditions. We used genomic and metatranscriptomic analyses to evaluate the metabolic potential of Ca. D. denitrificans and deduce its functional relationships to anammox bacteria (i.e., Ca. Brocadia pituitae). Although Ca. D. denitrificans is hypothesized to supply NO to Ca. B. pituitae as a byproduct of imperfect denitrification, this microbe also possesses hydroxylamine oxidoreductase, which catalyzes the oxidation of hydroxylamine to NO and potentially the reverse reaction. Ca. D. denitrificans can use a range of electron donors for denitrification, including aromatic compounds, glucose, sulfur compounds, and hydrogen, but metatranscriptomic analysis suggested that the major electron donors are aromatic compounds, which inhibit anammox activity. The interrelationship between Ca. D. denitirificans and Ca. B. pituitae via the metabolism of aromatic compounds may govern the population balance of both species. Ca. D. denitrificans also has the potential to fix CO2 via an irregular Calvin cycle and couple denitrification to the oxidation of hydrogen and sulfur compounds under chemolithoautotrophic conditions. This metabolic versatility, which suggests a mixotrophic lifestyle, would facilitate the growth of Ca. D. denitrificans in the anammox bioreactor.

Metabolic patterns reveal enhanced anammox activity at low nitrogen conditions in the integrated I-ABR

Substrate concentrations greatly influence bacterial growth and metabolism. However, optimal nitrogen concentrations for anammox bacteria in nitrogen-limited environments remain unclear. Here, we observed enhanced nitrogen metabolism and anabolism of anammox bacteria at low nitrogen conditions. Efficient nitrogen removal was achieved at ammonium and nitrite influent concentration of 30 mg/L under HRT of 1 hr, with an average nitrogen removal rate (NRR) of 0.73 kg N/(m³ ·day) in I-ABR composed of four compartments. The highest anammox activity of 6.25 mmol N/ (gVSS·hr) was observed in the fourth compartment (C4) with the lowest substrate levels (ammonium and nitrite of 11.6 mg/L and 7 mg/L). This could be resulted from the highest expression level of genes involved in nitrogen metabolism in C4, which was 1.49-1.67 times higher than that in other compartments. Besides, the second compartment (C2) exhibited the most active anabolism at ammonium and nitrite of 17 mg/L and 13 mg/L, respectively, which contributed to the most active amino acid synthesis and thus the highest EPS (1.35 times higher) in C2. This enhanced amino acid auxotrophy between anammox bacteria with heterotrophs, and consequently, heterotrophs thrived and competed for nitrite. These results hint at the potential application of anammox process in micro-polluted water. PRACTITIONER POINTS: High nitrogen removal and efficient biomass retention at low nitrogen concentrations under short HRT was achieved in I-ABR. Optimal concentrations for anammox nitrogen removal and anabolism were discussed under low nitrogen concentrations. More active anabolism contributed to enhanced amino acid synthesis and thus higher EPS contents. Low substrate levels led to enhanced expression of genes involved in nitrogen metabolism and thus high anammox activity.

Distinct growth stages controlled by the interplay of deterministic and stochastic processes in functional anammox biofilms

Mainstream anaerobic ammonium oxidation (anammox) represents one of the most promising energy-efficient mechanisms of fixed nitrogen elimination from wastewaters. However, little is known about the exact processes and drivers of microbial community assembly within the complex microbial biofilms that support anammox in engineered ecosystems. Here, we followed anammox biofilm development on fresh carriers in an established 8m³ mainstream anammox reactor that is exposed to seasonal temperature changes (~25-12°C) and varying NH₄⁺ concentrations (5-25 mg/L). We use fluorescence in situ hybridization and 16S rRNA gene sequencing to show that three distinct stages of biofilm development emerge naturally from microbial community composition and biofilm structure. Neutral modelling and network analysis are employed to elucidate the relative importance of stochastic versus deterministic processes and synergistic and antagonistic interactions in the biofilms during their development. We find that the different phases are characterized by a dynamic succession and an interplay of both stochastic and deterministic processes. The observed growth stages (Colonization, Succession and Maturation) appear to be the prerequisite for the anticipated growth of anammox bacteria and for reaching a biofilm community structure that supports the desired metabolic and functional capacities observed for biofilm carriers already present in the system (~100g_NH4-N m³ d^-1). We discuss the relevance of this improved understanding of anammox-community ecology and biofilm development in the context of its practical application in the start-up, configuration, and optimization of anammox biofilm reactors.

Responses of anammox process to elevated Fe(III) stress: Reactor performance, microbial community and functional genes

The aim of present study was to re-evaluate the impacts of elevated Fe(III) stress on anaerobic ammonium oxidation (anammox) process. The results indicated that long-term low concentration Fe(III) (5 and 10 mg/L) exposure significantly improved the nitrogen removal efficiency of anammox process, while high concentration Fe(III) (50 and 100 mg/L) significantly deteriorated the reactor performance. Batch assays showed that the specific anammox activity, heme c content and hydrazine dehydrogenase activity were significantly increased and decreased under low and high concentration Fe(III) exposure, respectively, indicating an enhancement and inhibition of anammox activity. Moreover, the presence of high concentration Fe(III) significantly shifted the anammox community structure. Ca. Brocadia was the predominant anammox genus, whose abundance decreased from 14.26% to 8.13% as Fe(III) concentration increased from 0 to 100 mg/L. In comparison, the abundance of denitrifiers progressively increased from 3.70% to 6.68% with increasing Fe(III) concentration. These suggested that different functional bacteria differed in their responses to Fe(III) stress. Furthermore, long-term Fe(III) exposure significantly up-regulated the abundances of genes associated with nitrogen metabolism and Fe(III) reduction. Overall, the obtained findings are expected to advances our understanding of the responses of anammox process to elevated Fe(III) stress.

Achieving superior nitrogen removal performance in low-strength ammonium wastewater treatment by cultivating concentrated, highly dispersive, and easily settleable granule sludge in a one-stage partial nitritation/anammox-HAP reactor

In low-strength ammonium wastewater (LSAWW) treatment, the application of anammox-based process is still limited due to extreme instability and the poor nitrogen removal rate (NRR). In this work, granule sludge, comprised of functional microbes and hydroxyapatite (HAP), was inoculated and cultivated in a one-stage partial nitritation/anammox (PNA) reactor for LSAWW treatment. The results showed that at the hydraulic retention time (HRT) of about 1.0 h and the influent ammonium concentration of 63.0 mg/L, an average NRR of 1.28 kg/m³/d was achieved, which far exceeds that reported in similar studies. The main inorganic matter in sludge was identified as HAP through the X-ray diffractometer and Raman spectrum analysis. The tomographic images of wet granule created through computed tomography revealed that the interior density of the granules was uneven and many hollow structures existed in the granule interior. Combined with the Scanning Electron Microscope images of dry granules, it was found that the granules were comprised of hollow sub-granules. Since the biomass in the reactor increased with no obvious increase in the granule size, it was inferred that the hollow sub-granules had fragile connections with each other and that granules division occurred easily, resulting in the high dispersity of sludge. Florescence in situ hybridization results also showed that the ammonium-oxidizing bacteria and anammox bacteria were mainly distributed in the two sides of the sub-granule shells and the HAP in the middle. This kind of structure raised the density of granules and improved the settleability of sludge, which made it possible to achieve a high biomass in the reactor at a short HRT. Therefore, the sludge formed in the reactor was concentrated, highly dispersive and easily settleable. These factors appear to be crucial for achieving the desired nitrogen removal performance. This study marks a big leap in LSAWW treatment through the one-stage PNA process and has great potential in actual applications.

Metagenomic Insight of a Full Scale Eco-Friendly Treatment System of Textile Dye Wastewater Using Bioaugmentation of the Composite Culture CES-1

Effects of bioaugmentation of the composite microbial culture CES-1 on a full scale textile dye wastewater treatment process were investigated in terms of water quality, sludge reduction, dynamics of microbial community structures and their functional genes responsible for degradation of azo dye, and other chemicals. The removal efficiencies for Chemical Oxygen Demand (COD), Total Nitrogen (T-N), Total Phosphorus (T-P), Suspended Solids (SS), and color intensity (96.4%, 78.4, 83.1, 84.4, and 92.0, respectively) 300-531 days after the augmentation were generally improved after bioaugmentation. The denitrification linked to T-N removal appeared to contribute to the concomitant COD removal that triggered a reduction of sludge (up to 22%) in the same period of augmentation. Azo dye and aromatic compound degradation and other downstream pathways were highly metabolically interrelated. Augmentation of CES-1 increased microbial diversity in the later stages of augmentation when a strong microbial community selection of Acinetobacterparvus, Acinetobacterjohnsonii, Marinobacter manganoxydans, Verminephrobacter sp., and Arcobacter sp. occurred. Herein, there might be a possibility that the CES-1 augmentation could facilitate the indigenous microbial community successions so that the selected communities made the augmentation successful. The metagenomic analysis turned out to be a reasonable and powerful tool to provide with new insights and useful biomarkers for the complex environmental conditions, such as the full scale dye wastewater treatment system undergoing bioaugmentation.

Flexible electrocatalysts: interfacial-assembly of iron nanoparticles for nitrate reduction

We report a novel template-assisted epitaxial assembly strategy to assemble carbon-coated iron nanoparticles on a functionalized carbon cloth (CC/Fe@C). This delicate assembled architecture provides a useful guideline for designing flexible iron-based electrocatalysts.

Combination of 15N Tracer and Microbial Analyses Discloses N2O Sink Potential of the Anammox Community

Although nitrogen removal by partial nitritation and anammox is more cost-effective than conventional nitrification and denitrification, one downside is the production and accumulation of nitrous oxide (N₂O). The potential exploitation of N₂O-reducing bacteria, which are resident members of anammox microbial communities, for N₂O mitigation would require more knowledge of their ecophysiology. This study investigated the phylogeny of resident N₂O-reducing bacteria in an anammox microbial community and quantified individually the processes of N₂O production and N₂O consumption. An up-flow column-bed anammox reactor, fed with NH₄⁺ and NO₂^- and devoid of oxygen, emitted N₂O at an average conversion ratio (produced N₂O: influent nitrogen) of 0.284%. Transcriptionally active and highly abundant nosZ genes in the reactor biomass belonged to the Burkholderiaceae (clade I type) and Chloroflexus genera (clade II type). Meanwhile, less abundant but actively transcribing nosZ strains were detected in the genera Rhodoferax, Azospirillum, Lautropia, and Bdellovibrio and likely act as an N₂O sink. A novel ¹⁵N tracer method was adapted to individually quantify N₂O production and N₂O consumption rates. The estimated true N₂O production rate and true N₂O consumption rate were 3.98 ± 0.15 and 3.03 ± 0.18 mg_N·g_VSS^-1·day^-1, respectively. The N₂O consumption rate could be increased by 51% (4.57 ± 0.51 mg_N·g_VSS^-1·day^-1) with elevated N₂O concentrations but kept comparable irrespective of the presence or absence of NO₂^-. Collectively, the approach allowed the quantification of N₂O-reducing activity and the identification of transcriptionally active N₂O reducers that may constitute as an N₂O sink in anammox-based processes.

The physiological potential of anammox bacteria as revealed by their core genome structure

We present here the second complete genome of anaerobic ammonium oxidation (anammox) bacterium, Candidatus (Ca.) Brocadia pituitae, along with those of a nitrite oxidizer and two incomplete denitrifiers from the anammox bacterial community (ABC) metagenome. Although NO2− reduction to NO is considered to be the first step in anammox, Ca. B. pituitae lacks nitrite reductase genes (nirK and nirS) responsible for this reaction. Comparative genomics of Ca. B. pituitae with Ca. Kuenenia stuttgartiensis and six other anammox bacteria with nearly complete genomes revealed that their core genome structure contains 1,152 syntenic orthologues. But nitrite reductase genes were absent from the core, whereas two other Brocadia species possess nirK and these genes were horizontally acquired from multiple lineages. In contrast, at least five paralogous hydroxylamine oxidoreductase genes containing candidate ones (hao2 and hao3) encoding another nitrite reductase were observed in the core. Indeed, these two genes were also significantly expressed in Ca. B. pituitae as in other anammox bacteria. Because many nirS and nirK genes have been detected in the ABC metagenome, Ca. B. pituitae presumably utilises not only NO supplied by the ABC members but also NO and/or NH₂OH by self-production for anammox metabolism.

Insights into two stable mainstream deammonification process and different microbial community dynamics at ambient temperature

How to achieve stable mainstream deammonification is still a huge challenge. In this work, satisfactory nitrogen removal were achieved in a deammonification granular sludge reactor (R1, 0.42 ± 0.03 kg N / (m³·d)) and a mixed flocculent with granular sludge reactor (R2, 0.39 ± 0.04 kg N / (m³·d)) at ambient temperature (21-28 ℃) . The good adaptability of anammox bacteria (Candidatus Jettenia) to ambient temperature ensured its efficient activity (0.84-1.54 mg N/(g VSS·h)). The overexpression ammonia monooxygenase gene abundances in ammonia oxidizing bacteria (Nitrosomonas) was also predicted. The inhibition of hydrazine and the competition of denitrifying bacteria (Denitratisoma) to nitrite nitrogen, leading to a low Nitrospira relative abundances (0.2%-2.1%) . It was also found that R1 was more resistant to the unfavorable condition. For R2, higher Denitratisoma abundances (9.2%-18.5%) and predicted metabolic pathway abundances related to carbon metabolism were observed.

Distribution of antibiotic resistance genes and their association with bacteria and viruses in decentralized sewage treatment facilities

The distribution of antibiotic resistance genes (ARGs) has been intensively studied in large-scale wastewater treatment plants and livestock sources. However, small-scale decentralized sewage treatment facilities must also be explored due to their possible direct exposure to residents. In this study, six wastewater treatment facilities in developed rural areas in eastern China were investigated to understand their risks of spreading ARGs. Using metagenomics and network analysis tools, ARGs and bacterial and viral communities were identified in the influent (INF) and effluent (EFF) samples. The dominant ARGs belonged to the bacitracin class, which are different from most of municipal wastewater treatment plants (WWTPs). The dominant hosts of ARGs are Acidovorax in bacterial communities and Prymnesiovirus in viral communities. Furthermore, a positive relationship was found between ARGs and phages. The ARGs significantly correlated with phages were all hosted by specific genera of bacteria, indicating that phages had contributed to the ARG's proliferation in sewage treatment facilities. Paying significant concern on the possible enhanced risks caused by bacteria, viruses and their related ARGs in decentralized sewage treatment facilities is necessary.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material is available in the online version of this article at 10.1007/s11783-021-1469-4 and is accessible for authorized users.

Comparison of nitrogen and VFA removal pathways in autotrophic and organotrophic anammox reactors

Organotrophic anammox is a promising process for treating both nitrogen and organic containing wastewater than that of the traditional autotrophic anammox for sole nitrogen removal. However pathways of nitrogen removal particularly at metagenomic level in both processes are still unknown. Here we report, metabolic pathways of nitrogen removal in two lab-scale sequencing batch reactors (SBR), one autotrophic and another organotrophic (TOC/TN = 0.1) anammox bacteria incubated over 220 days. Both reactors showed satisfactory nitrogen removal with 840.31 mg N/L.d and 786.81 mg N/L.d for autotrophic and organotrophic anammox reactors respectively. Four anammox species namely Candidatus B. fulgida, B. sinica, J. caeni and Candidatus K. stuttgartiensis were identified in both reactors. The Candidatus K. stuttgartiensis (4%) was dominant in autotrophic reactor whereas Candidatus J. caeni (10%) in the organotrophic reactor. The supply of organic promoted the growth of anammox bacteria more than three times higher than that of the autotrophic anammox reactor. The functional genes related to the DNRA pathway was obtained in all anammox species except for Candidatus K. stuttgartiensis. The co-existence of other DNRA (Armatimonadetes and Thauera) and partial denitrifying bacteria (Chloroflexi) was also found in both reactors. Moreover, functional genes related to acetate metabolism by acetyl-CoA way were obtained in all anammox bacteria except Candidatus B. fulgida which showed alternative ackA/Pac-t pathways in organic anammox reactor. Overall current results suggest that the anammox, DNRA and partial denitrification were the key nitrogen transformation pathways, particularly in organotrophic anammox reactor. Our findings will improve understanding of the practical application of organotrophic anammox for wider wastewater treatment.

Coupling anammox with denitrification in a full-scale combined biological nitrogen removal process for swine wastewater treatment

In order to enhance nitrogen removal through anammox process in the full-scale swine wastewater treatment plant, an innovative regulation strategy of nitrate-based carbon dosage and intermittent aeration was developed to apply the combined biological nitrogen removal process in a full scale anaerobic-anoxic-oxic (A²/O) system. TN removal efficiency reached at 65.5 ± 6.0% in Phase 1 with decreasing external carbon dosage in influent due to the reduction of return nitrate concentration, and it increased to 83.5 ± 6.7% when intermittent aeration was adopted in oxic zone and external carbon source was stopped adding into influent in Phase 2. As a result, the energy consumption for the swine wastewater treatment decreased from 1.93 to 0.9 kW h/m³ and 4.18 to 2.57 kW h/kg N, respectively. Microbial community analysis revealed that the average abundances of Candidatus Brocadia increased from 0.76% to 2.43% and removal of TN through anammox increased from 39% to 77%.

Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity

Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.

Integrated omics analyses reveal differential gene expression and potential for cooperation between denitrifying polyphosphate and glycogen accumulating organisms

Unusually high accumulation of the potent greenhouse gas nitrous oxide (N₂ O) has previously been documented in denitrifying biological phosphorus (P) removal bioprocesses, but the roles of differential denitrification gene expression patterns and ecological interactions between key functional groups in driving these emissions are not well understood. To address these knowledge gaps, we applied genome-resolved metagenomics and metatranscriptomics to a denitrifying bioprocess enriched in as-yet-uncultivated denitrifying polyphosphate accumulating organisms (PAOs) affiliated with Candidatus Accumulibacter. The six transcriptionally most active populations in the community included three co-occurring Accumulibacter strains affiliated with clades IF (a novel clade identified in this study), IA and IC, a competing glycogen accumulating organism (GAO) affiliated with Competibacteraceae (GAO1), a Gammaproteobacteria PR6 and an Anaerolineae CH7. Strongly elevated expression of nitrite reductase genes compared to nitrous oxide reductase genes was observed in the overall community and in Accumulibacter populations, suggesting a strong role for differential gene expression in driving N₂ O accumulation. Surprisingly, while ~90% of the nirS gene transcripts were expressed by the three co-occurring PAO populations, ~93% of the norB gene transcripts were expressed by GAO1 and ~75% of the norZ gene transcripts were mapped to PR6 and several other non-PAO flanking populations. This suggests the potential for cooperation between flanking populations and PAOs in reducing denitrification intermediates. Such cooperation may benefit the community by reducing the accumulation of toxic nitric oxide.

Metagenomics analysis of the key functional genes related to biofouling aggravation of reverse osmosis membranes after chlorine disinfection

Chlorine disinfection is a common technology to control biofouling in the pretreatment of the reverse osmosis (RO) system for wastewater reclamation. However, chlorine disinfection could even aggravate the RO membrane biofouling because of the changes of microbial community structure. In this study, the mechanism of biofilm formation and EPS secretion after chlorine disinfection was investigated by analyzing the genes coding quorum sensing, exopolysaccharide biosynthesis, and amino acid biosynthesis. After 1, 5, and 15 mg-Cl₂/L chlorine disinfection, the relative abundances of the functional genes all increased significantly. Compared with the control group, chlorine-resistant bacteria (Acidovorax, Arenimonas, and Pseudomonas) also harbored higher relative abundances of these functional genes. The high relative abundances of these genes might provide the bacterial community after chlorine disinfection with high potential of biofilm formation and EPS secretion and then cause severe RO membrane biofouling. In the sample with 5 mg-Cl₂/L chlorine disinfection, the correlation coefficients (r) between each two of the three kinds of functional genes were more than 0.9 and much stronger than that in the control group. These results indicated that the bacterial community selected by chlorine disinfection could build more stable biofilm to resist chlorine but also could cause more severe RO membrane biofouling.

Insight into how high dissolved oxygen favors the startup of nitritation with aerobic granules

To elucidate how high dissolved oxygen (DO) favors the startup of nitritation with aerobic granular sludge, two granular reactors were operated under low (1-2 mg O₂·L^-1) and high DO (3-5 mg O₂·L^-1) conditions with similar effluent ammonium concentrations (>20 mg N·L^-1). The results showed that though nitritation with an average nitrite accumulation ratio of above 95% was finally achieved in both reactors, a five-fold start-up time (eleven weeks) was required for the low DO reactor compared to the high DO reactor. Moreover, the nitritation performance was positively correlated with the extent of nitrifiers stratification in granules. The faster startup of nitritation under high DO conditions mainly resulted from the faster formation of well-stratified nitrifiers, with ammonium oxidizing bacteria (AOB) dominating granule surface. High DO operation combined with sufficient ammonium supply ensured the faster growth of AOB, which should provide a competitive advantage to AOB in competing for habitable space (i.e., granule surface). Besides, the lower porosity, larger size, and more active extracellular polymeric substances (particularly proteins) production of granules was observed under the high DO condition. Overall, these findings supported the proposition that the switch from mixed to stratified distribution of nitrifiers in granule was primarily driven by their competition for habitable space rather than by oxygen-limitation.

Development of a novel denitrifying phosphorus removal and partial denitrification anammox (DPR + PDA) process for advanced nitrogen and phosphorus removal from domestic and nitrate wastewaters

A novel energy-efficient DPR + PDA (denitrifying phosphorus removal and partial denitrification anammox) process for enhanced nitrogen and phosphorus removal was developed in the combined ABR-CSTR reactor. After 220 days operation, excellent total inorganic nitrogen (TIN) and phosphorus removal (97.57% and 95.66%, respectively) were obtained under external C/NO₃^--N of 0.7, with the effluent TIN and PO₄^3--P concentrations of 3.51 mg/L and 0.28 mg/L, respectively. At the steady period, DPR contributed major TN removal (58.65%), while PDA mediated an increasingly considerable impact and finally achieved 37.07%, in which anammox accounted for a significant percentage. Batch tests demonstrated that efficient PD with nitrate-to-nitrite transformation ratio of 97.67% supplying stable nitrite for anammox, and phosphorus was mainly removed using nitrate as electron acceptor via DPR with the ideal phosphorus release/uptake rate (7.73/22.17 mgP/gVSS/h). Accumulibacter (6.24%) dominated high phosphorus removal performance, while Thauera (8.26%) and Candidatus Brocadia (2.57%) represented the superior nitrogen removal performance.

Glycogen metabolism of the anammox bacterium "Candidatus Brocadia sinica"

Presence of glycogen granules in anaerobic ammonium-oxidizing (anammox) bacteria has been reported so far. However, very little is known about their glycogen metabolism and the exact roles. Here, we studied the glycogen metabolism in "Ca. Brocadia sinica" growing in continuous retentostat cultures with bicarbonate as a carbon source. The effect of the culture growth phase was investigated. During the growing phase, intracellular glycogen content increased up to 32.6 mg-glucose (g-biomass dry wt)-1 while the specific growth rate and ATP/ADP ratio decreased. The accumulated glycogen begun to decrease at the onset of entering the near-zero growth phase and was consumed rapidly when substrates were depleted. This clearly indicates that glycogen was synthesized and utilized as an energy storage. The proteomic analysis revealed that "Ca. B. sinica" synthesized glycogen via three known glycogen biosynthesis pathways and simultaneously degraded during the progress of active anammox, implying that glycogen is being continuously recycled. When cells were starved, a part of stored glycogen was converted to trehalose, a potential stress protectant. This suggests that glycogen serves at least as a primary carbon source of trehalose synthesis for survival. This study provides the first physiological evidence of glycogen metabolism in anammox bacteria and its significance in survival under natural substrate-limited habitat.

Metagenomic Insights Into Functional and Taxonomic Compositions of an Activated Sludge Microbial Community Treating Leachate of a Completed Landfill: A Pathway-Based Analysis

Upcycling wastes into valuable products by mixed microbial communities has recently received considerable attention. Sustainable production of high-value substances from one-carbon (C1) compounds, e.g., methanol supplemented as an external electron donor in bioreactors for wastewater treatment, is a promising application of upcycling. This study undertook a gene-centric approach to screen valuable production potentials from mixed culture biomass, removing organic carbon and nitrogen from landfill leachate. To this end, the microbial community of the activated sludge from a landfill leachate treatment plant and its metabolic potential for the production of seven valuable products were investigated. The DNA extracted from the activated sludge was subjected to shotgun metagenome sequencing to analyze the microbial taxonomy and functions associated with producing the seven products. The functional analysis confirmed that the activated sludge could produce six of the valuable products, ectoine, polyhydroxybutyrate (PHB), zeaxanthin, astaxanthin, acetoin, and 2,3-butanediol. Quantification of the detected functional gene hit numbers for these valuable products as a primary trial identified a potential rate-limiting metabolic pathway, e.g., conversion of L-2,4-diaminobutyrate into N-γ-acetyl-L2,4,-diaminobutyrate during the ectoine biosynthesis. Overall, this study demonstrated that primary screening by the proposed gene-centric approach can be used to evaluate the potential for the production of valuable products using mixed culture or single microbe in engineered systems. The proposed approach can be expanded to sites where water purification is highly required, but resource recovery, or upcycling has not been implemented.

A review of quorum sensing improving partial nitritation-anammox process: Functions, mechanisms and prospects

Partial nitritation-anammox (PNA) is a promising and energy-efficient process for the sustainable nitrogen removal. However, its wide applications are still limited by the long start-up period and instability of long-term operation. Quorum sensing (QS), as a way of cell-to-cell communication generally regulating various microbial behaviors, has been increasingly investigated in PNA process, because QS may substantially manipulate the metabolism of microorganisms and overcome the limitations of PNA process. This critical review provides a comprehensive analysis of QS in PNA systems, and identifies the challenges and opportunities for the optimization of PNA process based on QS. The analysis is grouped based on the configurations of PNA process, including partial nitritation, anammox and single-stage PNA systems. QS is confirmed to regulate various properties of PNA systems, including microbial activity, microbial growth rate, microbial aggregation, microbial interactions and the robustness under adverse conditions. Major challenges in the mechanisms of QS, such as QS circuits, target genes and the response to environmental inputs, are identified. Potential applications of QS, such as short-term addition of certain acyl-homoserine lactones (AHLs) or substances containing AHLs, transient unfavorable conditions to stimulate the secretion of AHLs, are also proposed. This review focuses on the theoretical and practical cognation for QS in PNA systems, and serves as a stepping stone for further QS-based strategies to enhance nitrogen removal through PNA process.

Highly enriched anammox within anoxic biofilms by reducing suspended sludge biomass in a real-sewage A2/O process

This study proposes a novel strategy of stably enriching anammox in mainstream, based on the competitive difference to NO₂^- between anoxic biofilms and suspended sludge. A modified anaerobic-anoxic-oxic (A²/O) process run for 500 days with actual municipal wastewater. Microbial analysis revealed that anoxic-carrier biofilms had a significantly higher abundance of anammox (qPCR: 0.74% - 4.34%) than suspended sludge (P< 0.001). Batch tests showed that anammox within anoxic-carrier biofilms contributed to significant nitrogen removal, coupled with partial-denitrification (NO₃^- → NO₂^-). The anammox genus, Ca. Brocadia, was highly enriched when suspended sludge was accidentally lost. Further batch tests found that reducing suspended biomass helped anammox enrichment in anoxic-carrier biofilms, because the suspended sludge had strong NO₂^- competition (NO₂^- → N₂) with anammox (increased nirK). Metagenomic sequencing revealed that Ca. Brocadia dominates in the anoxic-carrier biofilms, and is the most important narG contributor to NO₃^- → NO₂^-, which could have promoted the competition of NO₂^- with heterotrophic bacteria. For this A²/O process, the low effluent total nitrogen (8.9 mg ± 1.0 mg N/L) was attributed to partial-denitrification coupling with anammox, demonstrating that this process is applicable to the general influent N-concentration range (30 mg - 50 mg NH₄⁺-N/L) of municipal wastewater treatment plants (WWTPs). Based on the special competitive preference of anammox for NO₂^-, this study provides a promising and practical alternative for enriching anammox bacteria in municipal WWTPs.

Rapid formation of granules coupling n-DAMO and anammox microorganisms to remove nitrogen

Granular sludge exhibits unique features, including rapid settling velocity, high loading rate and relative insensitivity against inhibitors, thus being a favorable platform for the cultivation of slow-growing and vulnerable microorganisms, such as anaerobic ammonium oxidation (anammox) bacteria and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) microorganisms. While anammox granules have been widely applied, little is known about how to speed up the granulation process of n-DAMO microorganisms, which grow even slower than anammox bacteria. In this study, we used mature anammox granules as biotic carriers to embed n-DAMO microorganisms, which obtained combined anammox + n-DAMO granules within 6 months. The results of whole-granule 16S rRNA gene amplicon sequencing showed the coexistence of anammox bacteria, n-DAMO bacteria and n-DAMO archaea. The microbial stratification along granule radius was further elucidated by cryosection-16S rRNA gene amplicon sequencing, showing the dominance of n-DAMO archaea and anammox bacteria at inner and outer layers, respectively. Moreover, the images of cryosection-fluorescence in situ hybridization (FISH) verified this stratification and also indicated a shift in microbial stratification. Specifically, n-DAMO bacteria and n-DAMO archaea attached to the anammox granule surface initially, which moved to the inner layer after 4-months operation. On the basis of combined anammox + n-DAMO granules, a practically useful nitrogen removal rate (1.0 kg N/m³/d) was obtained from sidestream wastewater, which provides new avenue to remove nitrogen from wastewater using methane as carbon source.

Nitrogen isotope effects can be used to diagnose N transformations in wastewater anammox systems

Anaerobic ammonium oxidation (anammox) plays an important role in aquatic systems as a sink of bioavailable nitrogen (N), and in engineered processes by removing ammonium from wastewater. The isotope effects anammox imparts in the N isotope signatures (¹⁵N/¹⁴N) of ammonium, nitrite, and nitrate can be used to estimate its role in environmental settings, to describe physiological and ecological variations in the anammox process, and possibly to optimize anammox-based wastewater treatment. We measured the stable N-isotope composition of ammonium, nitrite, and nitrate in wastewater cultivations of anammox bacteria. We find that the N isotope enrichment factor ¹⁵ε for the reduction of nitrite to N₂ is consistent across all experimental conditions (13.5‰ ± 3.7‰), suggesting it reflects the composition of the anammox bacteria community. Values of ¹⁵ε for the oxidation of nitrite to nitrate (inverse isotope effect, - 16 to - 43‰) and for the reduction of ammonium to N₂ (normal isotope effect, 19-32‰) are more variable, and likely controlled by experimental conditions. We argue that the variations in the isotope effects can be tied to the metabolism and physiology of anammox bacteria, and that the broad range of isotope effects observed for anammox introduces complications for analyzing N-isotope mass balances in natural systems.

Purification of the key enzyme complexes of the anammox pathway from DEMON sludge

Anaerobic Ammonium Oxidation ("anammox") is a bacterial process in which nitrite and ammonium are converted into nitrogen gas and water, yielding energy for the cell. Anammox is an important branch of the global biological nitrogen cycle, being responsible for up to 50% of the yearly nitrogen removal from the oceans. Strikingly, the anammox process uniquely relies on the extremely reactive and toxic compound hydrazine as a free intermediate. Given its global importance and biochemical novelty, there is considerable interest in the enzymes at the heart of the anammox pathway. Unfortunately, obtaining these enzymes in sufficiently large amounts for biochemical and structural studies is problematic, given the slow growth of pure cultures of anammox bacteria when high cell densities are required. However, the anammox process is being applied in wastewater treatment to remove nitrogenous waste in processes like DEamMONification (DEMON). In plants using such processes, which rely on a combination of aerobic ammonia-oxidizers and anammox organisms, kilogram amounts of anammox bacteria-containing sludge are readily available. Here, we report a protein isolation protocol starting from anammox cells present in DEMON sludge from a wastewater treatment plan that readily yields pure preparations of key anammox proteins in the tens of milligrams, including hydrazine synthase HZS and hydrazine dehydrogenase (HDH), as well as hydroxylamine oxidoreductase (HAO). HDH and HAO were active and of sufficient quality for biochemical studies and for HAO, the crystal structure could be determined. The method presented here provides a viable way to obtain materials for the study of proteins not only from the central anammox metabolism but also for the study of other exciting aspects of anammox bacteria, such as for example, their unusual ladderane lipids.

Calcium nitrate as a bio-stimulant for anaerobic ammonium oxidation process

This study explored the role of calcium nitrate as a bio-stimulant for anaerobic ammonium oxidation (anammox) process. The anaerobic sequencing batch reactor was firstly inoculated with malodorous river sediment and only fed with calcium nitrate until no marked endogenous release of ammonium in effluent (Phase 1). Subsequently, nitrite and ammonium were supplied to test the performance of anammox process (Phase 2). During the operation of Phase 1, the effluent ammonium increased firstly and then decreased. Additionally, continuous nitrite (about 1.54 mgN/L) was observed in the effluent. The microbial analysis showed the simultaneous increase of the relative abundance of heterotrophic denitrifier Denitratisoma and sulfur autotrophic denitrifier Thiobacillus from 0.15% to 5.37% and 0.21% to 4.19%, respectively. Besides, ¹⁵N isotopes trace and qPCR results showed that the contribution of anammox to total nitrogen (TN) removal increased from 3.07% to 27.6%, and that the anammox functional gene hzsB increased from 1.37 × 10⁵ to 2.90 × 10⁶ copies/g. These results indicated that calcium nitrate may induce partial mixotrophic denitrification (heterotrophic and sulfur autotrophic denitrification) to provide nitrite as electron acceptor for anammox, thus promoting the occurrence of anammox. In Phase 2, rapid ammonium and TN removal were accomplished in the initial operation with the reduction efficiency of 80.1% and 90.0%, respectively. The relative abundance of anammox bacteria Candidatus_Brocadia significantly increased from 0.01% to 7.15% during the operation of Phase 2. These findings further confirmed the above deduction. Taken together, calcium nitrate can be a promising bio-stimulant for anammox process by promoting the coupling of mixotrophic denitrification with anammox.

Metagenomics unveils microbial roles involved in metabolic network of flavor development in medium-temperature daqu starter

As a widely used Asian starter culture, the quality of daqu can significantly affect the organoleptic characteristics of the final products, yet the microbial metabolic network involved in flavor development remains unclear. This study aims to investigate that network based on the dynamics of physicochemical properties, microbial community, and volatile compounds in medium-temperature daqu (MT-daqu) during spontaneous fermentation. Analyses using the metagenomic data set facilitated the gene repertoire overview of this ecosystem, indicating that Lactobacillales (mainly Weissella, Lactobacillus, and Pediococcus), Mucorales (mainly Lichtheimia), and Eurotiales (mainly Aspergillus, Rasamsonia and Byssochlamys) were the potential predominant populations successively responsible for the production of lytic enzymes and flavor precursors/compounds in MT-daqu. Flavor-relevant pathways were found to exist in multiple species, but only bacteria showed the potential to participate in butane-2,3-diol (e.g. Weissella, Lactobacillus, and Staphylococcus) and butanoate (Thermoactinomyces) metabolism, and only fungi were potentially involved in biosynthesis of guaiacol (Byssochlamys) and 4-vinylguaiacol (Aspergillus). Furthermore, a combined analysis revealed that the acidic thermal environment present in early phases was mainly due to the catabolic activities of Lactobacillales and Lichtheimia, which could contribute to the effective self-domestication of microbiota. The study helps elucidate the different metabolic roles of microorganisms and disclose the formation mechanism of daqu's partial functions, namely providing various aromatic substances/precursors and enzymes.

Ferroferric oxide promotes metabolism in Anaerolineae other than microbial syntrophy in anaerobic methanogenesis of antibiotic fermentation residue

Antibiotic fermentation residue (AFR) is a kind of protein-rich biosolids that would be utilized as valuable substrates for biogas production. However, the effectiveness of conductive material supplementation and its effect on the microbiome in anaerobic digestion of AFR have not been fully elucidated. The objective of this study is to access the impact of Fe₃O₄ addition on anaerobic digestion of AFR and reveal its microbial mechanism. By adding Fe₃O₄ at concentration of 150 mg/gTS to two typical AFRs, the methane yield was decreased while the methane production rate was significantly enhanced by 48% and 21%, respectively. Genomic analyses revealed that the Fe₃O₄ addition altered the microbial community by selecting the unknown genus of Anaerolineae with the metabolic capacity of carbohydrate hydrolysis and proteolysis. Meanwhile, the hydrogenotrophic methanogenesis was the dominant pathway in the AFR digestion system, which was mostly contributed by the Methanoculleus and Methanolinea. More interestingly, Methanoculleus might possess fermentative capability involved in the versatile hydrolysis pathway. Although the genes related to electrically conductive pili were detected, the induction of direct interspecies electron transfer by Fe₃O₄ supplementation was not confirmed in this study. In summary, except the accelerated methane production rate, Fe₃O₄ addition functioned as biostimulator for Anaerolineae other than electron conduit in anaerobic methanogenesis in the AFR digestion system.

Impacts of organics on the microbial ecology of wastewater anammox processes: Recent advances and meta-analysis

Anaerobic ammonium oxidation (anammox) represents a promising technology for wastewater nitrogen removal. Organics management is critical to achieving efficient and stable performance of anammox or integrated processes, e.g., denitratation-anammox. The aim of this systematic review is to synthesize the state-of-the-art knowledge on the multifaceted impacts of organics on wastewater anammox community structure and function. Both exogenous and endogenous organics are discussed with respect to their effects on the biofilm/granule structure and function, as well as the interactions between anammox bacteria (AnAOB) and a broad range of coexisting functional groups. A global core community consisting of 19 taxa is identified and a co-occurrence network is constructed by meta-analysis on the 16S rDNA sequences of 149 wastewater anammox samples. Correlations between core taxa, keystone taxa, and environmental factors, including COD, nitrogen loading rate (NLR) and C/N ratio are obtained. This review provides a holistic understanding of the microbial responses to different origins and types of organics in wastewater anammox reactors, which will facilitate the design and operation of more efficient anammox-based wastewater nitrogen removal process.