Cometabolism of the Superphylum Patescibacteria with Anammox Bacteria in a Long-Term Freshwater Anammox Column Reactor

Strengthening nitrogen removal of rural wastewater treatment in humus biochemical system under low dissolved oxygen conditions: Sludge and microbial characteristics

To achieve efficient and cost-effective treatment for the rural wastewater, a novel humus biochemical system (HBS) process derived from humus bio-functional material was proposed to treat rural wastewater under low dissolved oxygen (DO) conditions, and the operational performance, sludge characteristics, and microbial community in HBS were systematically investigated in this study. The results indicated that the HBS reactor could be operated stably under low DO levels of 0.2-0.8 mg/L, and maintained high removal efficiencies of 96.4%, 96.0%, and 88.2% for chemical oxygen demand, ammonia nitrogen, and total nitrogen, with corresponding effluent concentrations of 11.0, 1.7, and 5.1 mg/L, respectively. The sludge produced from HBS was characterized by relatively large particle size, complex structural morphology, and abundant humic substances, which favorably improved the system stability. Illumina sequencing demonstrated that HBS reactor possessed high microbial abundance and diversity and was enriched with plenty of nitrifying and denitrifying bacteria, which synergistically intensified the whole biological nitrogen removal process in this system. The study presented the feasibility and adaptability of HBS for energy-efficient rural wastewater treatment.

Effect of tire wear particle accumulation on nitrogen removal and greenhouse gases abatement in bioretention systems: Soil characteristics, microbial community, and functional genes

Tire wear particles (TWPs), as predominant microplastics (MPs) in road runoff, can be captured and retained by bioretention systems (BRS). This study aimed to investigate the effect of TWPs accumulation on nitrogen processes, focusing on soil characteristics, microbial community, and functional genes. Two groups of lab-scale bioretention columns containing TWPs (0 and 100 mg g-1) were established. The removal efficiencies of NH4+-N and TN in BRS significantly decreased by 7.60%-24.79% and 1.98%-11.09%, respectively, during the 101 days of TWPs exposure. Interestingly, the emission fluxes of N2O and CO2 were significantly decreased, while the emission flux of CH4 was substantially increased. Furthermore, prolonged TWPs exposure significantly influenced the contents of soil organic matter (increased by 27.07%) and NH4+-N (decreased by 42.15%) in the planting layer. TWPs exposure also significantly increased dehydrogenase activity and substrate-induced respiration rate, thereby promoting microbial metabolism. Microbial sequencing results revealed that TWPs decreased the relative abundance of nitrifying bacteria (Nitrospira and Nitrosomonas) and denitrifying bacteria (Dechloromonas and Thauera), reducing the nitrification rate by 42.24%. PICRUSt2 analysis further indicated that TWPs changed the relative abundance of functional genes related to nitrogen and enzyme-coding genes.

The impact of benzoic acid and lactic acid on the treatment efficiency and microbial community in the sulfur autotrophic denitrification process

Nitrate poses a potential threat to aquatic ecosystems. This study focuses on the sulfur autotrophic denitrification mechanism in the process of water culture wastewater treatment, which has been successfully applied to the degradation of nitrogen in water culture farm effluents. However, the coexistence of organic acids in the treatment process is a common environmental challenge, significantly affecting the activity of denitrifying bacteria. This paper aims to explore the effects of adding benzoic acid and lactic acid on denitrification performance, organic acid removal rate, and microbial population abundance in sulfur autotrophic denitrification systems under optimal operating conditions, sulfur deficiency, and high hydraulic load. In experiments with 50 mg·L-1 of benzoic acid or lactic acid alone, the results show that benzoic acid and lactic acid have a stimulating effect on denitrification activity, with the stimulating effect significantly greater than the inhibitory effect. Under optimal operating conditions, the average denitrification rate of the system remained above 99%; under S/N = 1.5 conditions, the average denitrification rate increased from 88.34% to 91.93% and 85.91%; under HRT = 6 h conditions, the average denitrification rate increased from 75.25% to 97.79% and 96.58%. In addition, the addition of organic acids led to a decrease in microbial population abundance. At the phylum level, Proteobacteria has always been the dominant bacterial genus, and its relative abundance significantly increased after the addition of benzoic acid, from 40.2% to 61.5% and 62.4%. At the genus level, Thiobacillus, Sulfurimonas, Chryseobacterium, and Thermomonas maintained high population abundances under different conditions. PRACTITIONER POINTS: Employing autotrophic denitrification process for treating high-nitrate wastewater. Utilizing organic acids as external carbon sources. Denitrifying bacteria demonstrate high utilization efficiency towards organic acids. Organic acids promote denitrification more than they inhibit it. The promotion is manifested in the enhancement of activity and microbial abundance.

New insights into functional divergence and adaptive evolution of uncultured bacteria in anammox community by complete genome-centric analysis

Anaerobic ammonium-oxidation (anammox) bacteria play a crucial role in global nitrogen cycling and wastewater nitrogen removal, but they share symbiotic relationships with various other microorganisms. Functional divergence and adaptive evolution of uncultured bacteria in anammox community remain underexplored. Although shotgun metagenomics based on short reads has been widely used in anammox research, metagenome-assembled genomes (MAGs) are often discontinuous and highly contaminated, which limits in-depth analyses of anammox communities. Here, for the first time, we performed Pacific Biosciences high-fidelity (HiFi) long-read sequencing on the anammox granule sludge sample from a lab-scale bioreactor, and obtained 30 accurate and complete metagenome-assembled genomes (cMAGs). These cMAGs were obtained by selecting high-quality circular contigs from initial assemblies of long reads generated by HiFi sequencing, eliminating the need for Illumina short reads, binning, and reassembly. One new anammox species affiliated with Candidatus Jettenia and three species affiliated with novel families were found in this anammox community. cMAG-centric analysis revealed functional divergence in general and nitrogen metabolism among the anammox community members, and they might adopt a cross-feeding strategy in organic matter, cofactors, and vitamins. Furthermore, we identified 63 mobile genetic elements (MGEs) and 50 putative horizontal gene transfer (HGT) events within these cMAGs. The results suggest that HGT events and MGEs related to phage and integration or excision, particularly transposons containing tnpA in anammox bacteria, might play important roles in the adaptive evolution of this anammox community. The cMAGs generated in the present study could be used to establish of a comprehensive database for anammox bacteria and associated microorganisms. These findings highlight the advantages of HiFi sequencing for the studies of complex mixed cultures and advance the understanding of anammox communities.

Enhancement of electron transfer via magnetite in nitrite-dependent anaerobic methane oxidation system

Nitrite-dependent anaerobic methane oxidation (n-DAMO) is a novel denitrification process that simultaneously further removes and utilizes methane from anaerobic effluent from wastewater treatment plants. However, the metabolic activity of n-DAMO bacteria is relative low for practical application. In this study, conductive magnetite was added into lab-scale sequencing batch reactor inoculated with n-DAMO bacteria to study the influence on n-DAMO process. With magnetite amendment, the nitrogen removal rate could reach 34.9 mg N·L-1d-1, nearly 2.5 times more than that of control group. Magnetite significantly facilitated the interspecies electron transfer and built electrically connected community with high capacitance. Enzymatic activities of electron transport chain were significantly elevated. Functional gene expression and enzyme activities associated with nitrogen and methane metabolism had been highly up-regulated. These results not only propose a useful strategy in n-DAMO application but also provide insights into the stimulating mechanism of magnetite in n-DAMO process.

Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures

Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.

Removal of sulfamethoxazole and Cu, Cd compound pollution by arbuscular mycorrhizal fungi enhanced vertical flow constructed wetlands

The combined pollution of antibiotics and heavy metals (HMs) has a serious impact on the water ecological environment. Previous researches mainly focused on the removal of antibiotics or HMs as single pollutants, with limited investigation into the treatment efficiencies and underlying mechanisms associated with their co-occurring pollution. In this study, 16 micro vertical flow constructed wetlands (MVFCWs) were constructed to treat composite wastewater consisting of sulfamethoxazole (SMX), copper (Cu) and cadmium (Cd), involving two different inoculation treatments (arbuscular mycorrhizal fungi (AMF) inoculated and uninoculated) and eight kinds of pollutant exposure (Control Check (CK), SMX, Cu, Cd, SMX + Cu, SMX + Cd, Cu + Cd, SMX + Cu + Cd). The findings of this study demonstrated that the inoculation of AMF in MVFCWs resulted in removal efficiencies of SMX, Cu, and Cd ranging from 18.70% to 80.52%, 75.18% to 96.61%, and 40.50% to 89.23%, respectively. Cu and CuCd promoted the degradation of SMX in the early stage and inhibited the degradation of SMX in the later stage. Cd did not demonstrate a comparable promotive impact on SMX degradation, and its addition hindered Cu removal. However, comparatively, the presence of Cu exerted a more pronounced inhibitory effect on Cd removal. Furthermore, the addition of Cu augmented the abundances of Proteobacteria, Bacteroidetes (at the phylum level) and Rhodobacter, Lacunisphaera and Flavobacterium (at the genus level), and Cu exposure showed a substantially stronger influence on the microbial community than that of Cd and SMX. AMF might confer protection to plants against HMs and antibiotics by enriching Nakamurella and Lacunisphaera. These findings proved that AMF-C. indica MVFCW was a promising system, and the inoculation of AMF effectively enhanced the simultaneous removal of compound pollution.

Exploratory study on the metabolic similarity of denitrifying carbon sources

Mixed carbon sources have been developed for denitrification to eliminate the "carbon dependency" problem of single carbon. The metabolic correlation between different carbon sources is significant as guidance for the development of novel mixed carbon sources. In this study, to explore the metabolic similarity of denitrifying carbon sources, we selected alcohols (methanol, ethanol, and glycerol) and saccharide carbon sources (glucose, sucrose, and starch). Batch denitrification experiments revealed that methanol-acclimated sludge improved the denitrification rate of both methanol (14.42 mg-N/gMLVSS*h) and ethanol (9.65 mg-N/gMLVSS*h), whereas ethanol-acclimated sludge improved the denitrification rate of both methanol (7.80 mg-N/gMLVSS*h) and ethanol (22.23 mg-N/gMLVSS*h). In addition, the glucose-acclimated sludge and sucrose-acclimated sludge possibly improved the denitrification rate of glucose and sucrose, and the glycerol-acclimated sludge improved the denitrification rate of volatile fatty acids (VFAs), alcohols, and saccharide carbon sources. Functional gene analysis revealed that methanol, ethanol, and glycerol exhibited active alcohol oxidation and glyoxylate metabolism, and glycerol, glucose, and sucrose exhibited active glycolysis metabolism. This indicated that the similarity in the denitrification metabolism of these carbon sources was based on functional gene similarity, and glycerol-acclimated sludge exhibited the most diverse metabolism, which ensured its good denitrification effect with other carbon sources.

Competitive enrichment of comammox Nitrospira in floccular sludge

The discovery of complete ammonium oxidation (comammox) has subverted the traditional perception of two-step nitrification, which plays a key role in achieving biological nitrogen removal from wastewater. Floccular sludge-based treatment technologies are being applied at the majority of wastewater treatment plants in service where detection of various abundances and activities of comammox bacteria have been reported. However, limited efforts have been made to enrich and subsequently characterize comammox bacteria in floccular sludge. To this end, a lab-scale sequencing batch reactor (SBR) in the step-feeding mode was applied in this work to enrich comammox bacteria through controlling appropriate operational conditions (dissolved oxygen of 0.5 ± 0.1 g-O2/m3, influent ammonium of 40 g-N/m3 and uncontrolled longer sludge retention time). After 215-d operation, comammox bacteria gradually gained competitive advantages over counterparts in the SBR with a stable nitrification efficiency of 92.2 ± 2.2 %: the relative abundance of Nitrospira reached 42.9 ± 1.3 %, which was 13 times higher than that of Nitrosomonas, and the amoA gene level of comammox bacteria increased to 7.7 ± 2.1 × 106 copies/g-biomass, nearly 50 times higher than that of conventional ammonium-oxidizing bacteria. The enrichment of comammox bacteria, especially Clade A Candidatus Nitrospira nitrosa, in the floccular sludge led to (i) apparent affinity constants for ammonium and oxygen of 3.296 ± 0.989 g-N/m3 and 0.110 ± 0.004 g-O2/m3, respectively, and (ii) significantly low N2O and NO production, with emission factors being 0.136 ± 0.026 % and 0.023 ± 0.013 %, respectively.

Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea

In aquatic ecosystems, zooplankton-associated bacteria potentially have a great impact on the structure of ecosystems and trophic networks by providing various metabolic pathways and altering the ecological niche of host species. To understand the composition and drivers of zooplankton gut microbiota, we investigated the associated microbial communities of four zooplankton genera from different seasons in the Baltic Sea using the 16S rRNA gene. Among the 143 ASVs (amplified sequence variants) observed belonging to heterotrophic bacteria, 28 ASVs were shared across all zooplankton hosts over the season, and these shared core ASVs represented more than 25% and up to 60% of relative abundance in zooplankton hosts but were present at low relative abundance in the filtered water. Zooplankton host identity had stronger effects on bacterial composition than seasonal variation, with the composition of gut bacterial communities showing host-specific clustering patterns. Although bacterial compositions and dominating core bacteria were different between zooplankton hosts, higher gut bacteria diversity and more bacteria contributing to the temporal variation were found in Temora and Pseudocalanus, compared to Acartia and Synchaeta. Diet diatom and filamentous cyanobacteria negatively correlated with gut bacteria diversity, but the difference in diet composition did not explain the dissimilarity of gut bacteria composition, suggesting a general effect of diet on the inner conditions in the zooplankton gut. Synchaeta maintained high stability of gut bacterial communities with unexpectedly low bacteria-bacteria interactions as compared to the copepods, indicating host-specific regulation traits. Our results suggest that the patterns of gut bacteria dynamics are host-specific and the variability of gut bacteria is not only related to host taxonomy but also related to host behavior and life history traits.

Quantitative effect of adding percentages of anammox granules on the start-up process and microbial community analysis

The anaerobic ammonium oxidation (anammox) process is challenging due to its long start-up duration and high demand for mature anammox seed sludge. However, adding a small amount of anammox sludge to the inoculum can be a reasonable solution. This study investigated the effect of adding percentage of anammox granules (0, 1, 2, 4, and 8%) in the seed sludge on the anammox start-up process. The anammox process was achieved in all five reactors after 55, 6, 5, 3 and 0 days. Increasing the adding percentage effectively shortened the duration of lag phase and cell lysis, but had little effect on the final nitrogen removal performance, except for 4% adding percentage. Families of Brocadiaceae, Burkholderiaceae, Ignavibacteriaceae, SJA-28, and Rhodocyclaceae were dominant, with a core microbiota of eight operational taxonomic unites (OTUs), and Candidatus Brocadia fulgida became the dominant anammox species. Seven synergistic members with anammox bacteria were identified by correlation network analysis. Major potential functional groups involved in C and N cycle were also observed by FAPROTAX. Together with the qPCR and sequencing results, it was suggested that more than 2% of adding percentages would result in a short lag phase, rapid growth rate in elevation stage, high final performances, and anammox bacteria abundance comparable to that in the anammox seed sludge. This crucial finding indicated the feasibility of economical and rapid start-up of the anammox process with a minimum amount of anammox seed sludge.

Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique

The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.

Enhanced nitrogen and phosphorus removal by a novel ecological floating bed integrated with three-dimensional biofilm electrode system

The ecological floating bed (EFB) has been used extensively for the purification of eutrophication water. However, the traditional EFB (T-EFB) often exhibits a decline in nitrogen and phosphorus removal because of the limited adsorption capacity of fillers and inadequate electron donors. In the present study, a series of electrolysis-ecological floating beds (EC-EFBs) were constructed to investigate the decontamination performance of conventional pollutants. EC-EFB outperformed T-EFB in terms of nitrogen and phosphorus removal. Its removal efficiency of total nitrogen and total phosphorus was 20.51-32.95% and 45.06-96.20%, which were higher than that in T-EFB.. Moreover, the plants in EC-EFB demonstrated higher metabolic activity than those in T-EFB. Under the electrolysis condition of 0.51 mA/cm2 for 24 h, the malondialdehyde content and superoxide dismutase activity in EC-EFB were 6.08 nmol/g and 22.61 U/g, which were significantly lower compared to T-EFB (38.65 nmol/g and 26.13 U/g). And the soluble protein content of plant leaves increased from 3.31 mg/g to 5.72 mg/g in EC-EFB. Microbial analysis revealed that electrolysis could significantly change the microbial community and facilitate the proliferation of nitrogen-functional microbes, such as Thermomonas, Hydrogenophaga, Deinococcus, and Zoogloea. It is important to highlight that the hydrogen evolution reaction at the cathode area facilitated phosphorus removal in EC-EFB, thereby inhibiting phosphorus leaching. This study provides a promising and innovative technology for the purification of eutrophic water.

Combination of sequencing batch reactor activated sludge process with sludge lysis using thermophilic bacterial community for minimizing excess sludge

Sludge reduction is a major challenge in biological wastewater treatment. Hydrolytic enzymes secreted by thermophilic bacteria can lyse sludge and thus achieve sludge reduction, and the indigenous thermophilic community in sludge can lyse sludge more effectively. In this study, the feasibility of combining a sludge lysis reactor based on thermophilic bacteria community (LTBC reactor, 75 °C) with a conventional sequencing batch activated sludge reactor (SBR) for sludge reduction (i.e., LTBC-SBR process) was systematically investigated first time. The effect of lysed sludge returning to the biochemical tank on pollutant removal efficiency, sludge flocculation, sludge settling, and microbial community and function of the LTBC-SBR process was studied. In the LTBC1-SBR process, a sludge growth rate of 0.71 g TSS/day was observed when the lysed sludge reflux ratio (LRR) was 1, and the sludge generation was reduced by 81.5% compared to the conventional SBR reactor. In the LTBC1-SBR process, the removal efficiencies of chemical oxygen demand and total nitrogen were 94.0% and 80.5%, respectively. There was no significant difference in the sludge volume index from the SBR to the LTBC1-SBR stage, however, the effluent suspended solids concentration increased from 35.2 ± 2.1 mg/L to 80.1 ± 5.3 mg/L. This was attributed to the reflux of sludge lysate. In addition, the changes in extracellular polymers content and composition resulted in poor sludge flocculation performance. Heterotrophic bacteria associated with Actinobacteria and Patescibacteria enriched in LTBC1-SBR with relative abundance of 28.51 ± 1.25% and 20.01 ± 1.21%, respectively, which decomposed the macromolecules in the refluxed lysed sludge and contributed to the sludge reduction. Furthermore, due to the inhibition of nitrite-oxidizing bacteria, the nitrite concentration in the effluent of the LTBC1-SBR system reached 4.7 ± 1.1 mg/L, and part of the denitrification process was achieved by short-cut nitrification and simultaneous denitrification. These results indicate that in-situ sludge reduction technology based on lyse sludge lysing by thermophilic community has considerable potential to be widely used in wastewater treatment.

Response of nitrite accumulation, sludge characteristic and microbial transition to carbon source during the partial denitrification (PD) process

Partial denitrification (PD, nitrate (NO3--N) → nitrite (NO2--N)) as a novel pathway for NO2--N production has been widely concerned, but the specific conditions for highly efficient and stable nitrite maintenance are not yet fully understood. In this study, the effects of carbon sources (acetate, R1; propionate, R2; glucose, R3) on NO2--N accumulation was discussed without seeding PD sludge and the mechanism analysis related to sludge characteristic and microbial evolution were elucidated. The optimal NO2--N, nitrate-to-nitrite transformation ratio (NTR) and nitrite removal efficiency (NRE) reached up to 32.10 mg/L, 98.01 %, and 86.95 % in R1. However, due to the complex metabolic pathway of glucose, the peak time of NO2--N production delayed from 30 min to 60 min. The sludge particle size decreased from 154.2 μm (R1), 130.8 μm (R2) to 112.6 μm (R3) with the increasing extracellular polymeric substances (EPS) from 80.75-85.44 mg/gVSS, 82.68-92.75 mg/gVSS to 106.31-110.25 mg/gVSS, where the ratio of proteins/polysaccharides (PN/PS) was proved to be closely associated with NO2--N generation. For the microbial evolution, Saccharimonadales (70.42 %) dominated the glucose system, while Bacillus (7.42-21.63 %) and Terrimonas (4.24-5.71 %) were the main contributors for NO2--N accumulation in the acetate and propionate systems. The achievement of PD showed many advantages of lower carbon demand, minimal sludge production, lesser greenhouse gas emission and prominent nutrient removal, offering an economically and technically attractive alternative for NO3--N containing wastewater treatment.

Metabolic implications for predatory and parasitic bacterial lineages in activated sludge wastewater treatment systems

Deciphering unclear microbial interactions is key to improving biological wastewater treatment processes. Microbial predation and parasitism in wastewater treatment ecosystems are unexplored survival strategies that have long been known and have recently attracted attention because these interspecies interactions may contribute to the reduction of excess sludge. Here, microbial community profiling of 600 activated sludge samples taken from six industrial and one municipal wastewater treatment processes (WWTPs) was conducted. To identify the shared lineages in the WWTPs, the shared microbial constituents were defined as the family level taxa that had ≥ 0.1% average relative abundance and detected in all processes. The microbial community analysis assigned 106 families as the shared microbial constituents in the WWTPs. Correlation analysis showed that 98 of the 106 shared families were significantly correlated with total carbon (TC) and/or total nitrogen (TN) concentrations, suggesting that they may contribute to wastewater remediation. Most possible predatory or parasitic bacteria belonging to the phyla Bdellovibrionota, Myxococcota, and Candidatus Patescibacteria were found to be the shared families and negatively correlated with TC/TN; thus, they were frequently present in the WWTPs and could be involved in the removal of carbon/nitrogen derived from cell components. Shotgun metagenome-resolved metabolic reconstructions indicated that gene homologs associated with predation or parasitism are conserved in the Bdellovibrionota, Myxococcota, and Ca. Patescibacteria genomes (e.g., host interaction (hit) locus, Tad-like secretion complexes, and type IV pilus assembly proteins). This study provides insights into the complex microbial interactions potentially linked to the reduction of excess sludge biomass in these processes.

Influence of soil nutrients on the presence and distribution of CPR bacteria in a long-term crop rotation experiment

Bacteria affiliated with the Candidate Phyla Radiation (CPR) are a hyper-diverse group of ultra-small bacteria with versatile yet sparse metabolisms. However, most insights into this group come from a surprisingly small number of environments, and recovery of CPR bacteria from soils has been hindered due to their extremely low abundance within complex microbial assemblages. In this study we enriched soil samples from 14 different soil fertility treatments for ultra-small (<0.45 μm) bacteria in order to study rare soil CPR. 42 samples were sequenced, enabling the reconstruction of 27 quality CPR metagenome-assembled genomes (MAGs) further classified as Parcubacteria/Paceibacteria, Saccharibacteria/Saccharimonadia and ABY1, in addition to representative genomes from Gemmatimonadetes, Dependentiae and Chlamydae phyla. These genomes were fully annotated and used to reconstruct the CPR community across all 14 plots. Additionally, for five of these plots, the entire microbiota was reconstructed using 16S amplification, showing that specific soil CPR may form symbiotic relationships with a varied and circumstantial range of hosts. Cullars CPR had a prevalence of enzymes predicted to degrade plant-derived carbohydrates, which suggests they have a role in plant biomass degradation. Parcubacteria appear to be more apt at microfauna necromass degradation. Cullars Saccharibacteria and a Parcubacteria group were shown to carry a possible aerotolerance mechanism coupled with potential for aerobic respiration, which appear to be a unique adaptation to the oxic soil environment. Reconstruction of CPR communities across treatment plots showed that they were not impacted by changes in nutrient levels or microbiota composition, being only impacted by extreme conditions, causing some CPR to dominate the community. These findings corroborate the understanding that soil-dwelling CPR bacteria have a very broad symbiont range and have metabolic capabilities associated to soil environments which allows them to scavenge resources and form resilient communities. The contributions of these microbial dark matter species to soil ecology and plant interactions will be of significant interest in future studies.

Ball-milled magnetic sludge biochar enables fast aerobic granulation in anoxic/oxic process for the treatment of coal chemical wastewater

Coal chemical wastewater (CCW) containing toxic and hazardous matters requires to be treated prior to discharge. Promoting the in-situ formation of magnetic aerobic granular sludge (mAGS) in continuous flow reactor process has a great potential for CCW remediation. However, long granulation time and low stability limit the application of AGS technology. In this study, Fe₃O₄/sludge biochar (Fe₃O₄/SC) with biochar matrix derived from coal chemical sludge were applied to facilitate the aerobic granulation in two-stage continuous flow reactors, containing separated anoxic and oxic reaction units (abbreviated as A/O process). The performance of A/O process was evaluated at various hydraulic retention times (HRTs) (42 h, 27 h, and 15 h). Magnetic Fe₃O₄/SC with porous structures, high specific surface area (BET = 96.69 m²/g), and abundant functional groups was successfully prepared by ball-milled method. Adding magnetic Fe₃O₄/SC to A/O process could promote aerobic granulation (85 days) and the removal of chemical oxygen demand (COD), ammonia nitrogen (NH₄⁺-N)_, and total nitrogen (TN) from CCW at all tested HRTs. Since the formed mAGS had high biomass, good settling ability, and high electrochemical activities, mAGS-based A/O process had high tolerance to the decrease of HRT from 42 h to 15 h for CCW treatment. The optimized HRT for A/O process was 27 h, at which Fe₃O₄/SC addition can result in the increase of COD, NH₄⁺-N and TN removal efficiencies by 2.5 %, 4.7 % and 10.5 %, respectively. Based on 16S rRNA genes sequencing, the relative abundances of genus Nitrosomonas, Hyphomicrobium/Hydrogenophaga and Gaiella in mAGS accounting for nitrification, denitrification as well as COD removal were increased during aerobic granulation. Overall, this study proved that adding Fe₃O₄/SC to A/O process was effective for facilitating aerobic granulation and CCW treatment.

Effects of reducing, stabilizing, and antibiotic agents on "Candidatus Kuenenia stuttgartiensis"

Anaerobic ammon ium oxidizing (anammox) bacteria oxidize ammonium and reduce nitrite, producing N₂, and could play a major role in energy-optimized wastewater treatment. However, sensitivity to various environmental conditions and slow growth currently hinder their wide application. Here, we attempted to determine online the effect of environmental stresses on anammox bacteria by using an overnight batch activity test with whole cells, in which anammox activity was calculated by quantifying N₂ production via headspace-pressure monitoring. A planktonic mixed culture dominated by "Candidatus Kuenenia stuttgartiensis" strain CSTR1 was cultivated in a 30-L semi-continuous stirring tank reactor. In overnight resting-cell anammox activity tests, oxygen caused strong inhibition of anammox activity, which was reversed by sodium sulfite (30 µM). The tested antibiotics sulfamethoxazole, kanamycin, and ciprofloxacin elicited their effect on a dose-dependent manner; however, strain CSTR1 was highly resistant to sulfamethoxazole. Anammox activity was improved by activated carbon and Fe₂O₃. Protein expression analysis from resting cells after anammox activity stimulation revealed that NapC/NirT family cytochrome c (KsCSTR_12840), hydrazine synthase, hydrazine dehydrogenase, hydroxylamine oxidase, and nitrate:nitrite oxidoreductase were upregulated, while a putative hydroxylamine oxidoreductase HAO (KsCSTR_49490) was downregulated. These findings contribute to the growing knowledge on anammox bacteria physiology, eventually leading to the control of anammox bacteria growth and activity in real-world application. KEY POINTS: • Sulfite additions can reverse oxygen inhibition of the anammox process • Anammox activity was improved by activated carbon and ferric oxide • Sulfamethoxazole marginally affected anammox activity.

High-throughput sequencing as a tool for monitoring prokaryote communities in a wastewater treatment plant

In this study, the DNA metabarcoding technique was used to explore the prokaryote diversity and community structure in wastewater collected in spring and winter 2020-2021 as well as the efficiency of the treatment in a wastewater treatment plant (WWTP) in Ría de Vigo (NW Spain). The samplings included raw wastewater from the inlet stream (M1), the discharge water after the disinfection treatment (M3) and mussels used as bioindicators of possible contamination of the marine environment. Significant differences were discovered in the microbiome of each type of sample (M1, M3 and mussels), with 92 %, 45 % and 44 % of exclusive OTUs found in mussel, M3 and M1 samples respectively. Seasonal differences were also detected in wastewater samples, with which abiotic parameters (temperature, pH) could be strongly involved. Bacteria present in raw wastewater (M1) were associated with the human gut microbiome, and therefore, potential pathogens that could be circulating in the population in specific periods were detected (e.g., Arcobacter sp. and Clostridium sp.). A considerable decrease in putative pathogenic organisms from the M1 to M3 wastewater fractions and the scarce presence in mussels (<0.5 % total reads) confirmed the effectiveness of pathogen removal in the wastewater treatment plant. Our results showed the potential of the DNA metabarcoding technique for monitoring studies and confirmed its application in wastewater-based epidemiology (WBE) and environmental contamination studies. Although this technique cannot determine if the infective pathogens are present, it can characterize the microbial communities and the putative pathogens that are circulating through the population (microbiome of M1) and also confirm the efficacy of depuration treatment, which can directly affect the aquaculture sector and even human and veterinary health.

Comparison of the characteristics of gut microbiota response to lead in Bufo gargarizans tadpole at different developmental stages

In amphibians, lead (Pb) exposure could alter the composition and structure of gut microbiota, but changes involving microbiota of several successive phases following Pb exposure have been less studied. In the present study, we compared the effects of Pb exposure on morphological parameters and gut microbiota of Bufo gargarizans at Gosner stage (Gs) 33, Gs36, and Gs42. Our results showed that total length (TL), snout-vent length (SVL), and body wet weight (TW) of B. gargarizans at Gs33, as well as TL and SVL at Gs42, were significantly increased after Pb exposure. In addition, high-throughput sequencing analysis indicated that gut microbiota has distinct responses to Pb exposure at different developmental stages. The diversity of gut microbiota was significantly reduced under Pb exposure at Gs33, while it was significantly increased at Gs42. In terms of community composition, Spirochaetota, Armatimonadota, and Patescibacteria appeared in the control groups at Gs42, but not after Pb treatment. Furthermore, functional prediction indicated that the relative abundance of metabolism pathway was significantly decreased at Gs33 and Gs36, and significantly increased at Gs42. Our results fill an important knowledge gap and provide comparative information on the gut microbiota of tadpoles at different developmental stages following Pb exposure.

Enhanced nitrogen removal in mainstream deammonification systems at ambient temperature by novel modified carriers and differentiation of microbial community transformation

Zeolite-modified polyurethane (ZP) carriers and zeolite/tourmaline-modified polyurethane (ZTP) carriers were proposed to enhance mainstream deammonification. The system with ZTP carriers was rapidly established in 28 days with a nitrogen removal rate (NRR) of 0.150 kg N·(m³·d)^-1. Moreover, the facilitative effect of tourmaline was suggested by the highest humic acid peak intensity and more balanced potential activity. Besides, SEM-EDS analysis revealed carrier characteristic improvement was achieved in both novel carriers while maintaining an excellent spatial structure. Moreover, the microbial analysis suggested that both modified carriers support the substrate supply to anaerobic ammonium oxidizing bacteria (AnAOB) by enhancing dissimilatory nitrate reduction to ammonium and partial denitrification under nitrate accumulation conditions. Nevertheless, the ZTP system had a greater advantage over maintaining the original AnAOB (Candidatus Jettenia) and ammonium oxidizing bacteria (Nitrosomonas) abundance. Overall, this study provides ZTP carriers with great potential for facilitating the establishment of mainstream deammonification at full-scale WWTPs.

Development of microbial communities in biofilm and activated sludge in a hybrid reactor

Microorganisms play a key role in biological wastewater treatment. The form in which biomass develops determines the efficiency and mechanisms of organic compound conversion, due to different conditions in various microbial structures. However, the results of studies comparing the microbial communities in biofilm and activated sludge have often conflicted. Therefore, this study compared the composition and development of the bacterial communities in biofilm and activated sludge in a hybrid reactor, employing 16S rRNA sequencing. Statistical analysis of the sequencing data included the identification of taxa characteristic to the biofilm and activated sludge, alpha and beta diversity analysis, and network analysis. These analyses indicated that the biofilm bacterial community was richer and more diverse than the activated sludge community. The mean numbers of OTU were 1614 in the biofilm and 993 in the activated sludge, and the mean values of the Chao1 (1735 vs. 1105) and Shannon (5.3 vs. 4.3) biodiversity indices were significantly higher for the biofilm. The biofilm was a better environment for development of nitrifiers (e.g., Nitrosomonas, Nitrospira) and phosphorus accumulating organisms (Candidatus Accumulibacter). Bacteria in the biofilm co-occurrence network had more connections (based on Spearman's rank correlation coefficient) with each other, indicating that they interact more than those in the activated sludge.

Metagenomic insights into the symbiotic relationship in anammox consortia at reduced temperature

Anammox as a promising biological nitrogen removal technology has attracted much attention. However, cold temperature would limit its wide application and little is known about the microbial interactions between anammox bacteria (AnAOB) and heterotrophic bacteria at cold temperature. Here, we observed reduced temperature (25-15 °C) promoted the secretion of EPS and thus stimulated bigger size of granular sludge in a laboratory-scale anammox reactor. We further combined co-occurrence network analysis and genome-centered metagenomics to explore the potential interactions between AnAOB and heterotrophic bacteria. Network analysis suggested 22 out of 25 positively related species were reported as definite heterotrophic bacteria in subnetwork of AnAOB. Genome-centered metagenomics analysis yielded 23 metagenomic assembly genomes (MAGs), and we found that Acidobacteriota-affiliated bacteria could biosynthesize most polysaccharides (PS) precursors and contain the most glycosyltransferases and transporters to facilitate exopolysaccharides biosynthesis, together with partial PS precursors produced by AnAOB. AMX1 as the only anammox genome could synthesize most amino acids and cross feed with some heterotrophs to affect the extracellular protein function. Additionally, Bacteroidota, Planctomycetota, Chloroflexota, and Proteobacteria could contribute folate and molybdopterin cofactor for AMX1 to benefit their activity and growth. Superphylum Patescibacteria could survive by cross-feeding with AnAOB and heterotrophic organisms about organic compounds (Glyceraldehyde-3P and lactate). These cross-feedings maintained the stability of anammox reactor performance and emphasize the importance of heterotrophs in anammox system at reduced temperature.

Research of cervical microbiota alterations with human papillomavirus infection status and women age in Sanmenxia area of China

Background

Human papillomavirus (HPV) infection is the leading cause of cervical cancer. More and more studies discovered that cervical microbiota (CM) composition correlated with HPV infection and the development of cervical cancer. However, more studies need to be implemented to clarify the complex interaction between microbiota and the mechanism of disease development, especially in a specific area of China.

Materials and methods

In this study, 16S rDNA sequencing was applied on 276 Thin-prep Cytologic Test (TCT) samples of patients from the Sanmenxia area. Systematical analysis of the microbiota structure, diversity, group, and functional differences between different HPV infection groups and age groups, and co-occurrence relationships of the microbiota was carried out.

Results

The major microbiota compositions of all patients include Lactobacillus iners, Escherichia coli, Enterococcus faecalis, and Atopobium vaginae at species level, and Staphylococcus, Lactobacillus, Gardnerella, Bosea, Streptococcus, and Sneathia in genus level. Microbiota diversity was found significantly different between HPV-positive (Chao1 index: 98.8869, p < 0.01), unique-268 infected (infections with one of the HPV genotype 52, 56, or 58, 107.3885, p < 0.01), multi-268 infected (infections with two or more of HPV genotype 52, 56, and 58, 97.5337, p = 0.1012), other1 (94.9619, p < 0.05) groups and HPV-negative group (83.5299). Women older than 60 years old have higher microbiota diversity (108.8851, p < 0.01, n = 255) than younger women (87.0171, n = 21). The abundance of Gardnerella and Atopobium vaginae was significantly higher in the HPV-positive group than in the HPV-negative group, while Burkholderiaceae and Mycoplasma were more abundant in the unique-268 group compared to the negative group. Gamma-proteobacteria and Pseudomonas were found more abundant in older than 60 patients than younger groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) analysis revealed the effects on metabolism by microbiota that the metabolism of cells, proteins, and genetic information-related pathways significantly differed between HPV-negative and positive groups. In contrast, lipid metabolism, signal transduction, and cell cycle metabolism pathway significantly differed between multi-268 and negative groups.

Conclusion

The HPV infection status and age of women were related to CM’s diversity and function pathways. The complex CM co-occurrent relationships and their mechanism in disease development need to be further investigated.

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

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

Nitrite accumulation, denitrification kinetic and microbial evolution in the partial denitrification process: The combined effects of carbon source and nitrate concentration

The combined effects of carbon source (HAc, HPr, Glu, Glu + HAc) and nitrate concentration (40, 80 mg/L labeling as R₄₀, R₈₀) on partial denitrification (PD) were discussed at C/N ratio of 2.5 (COD = 100, 200 mg/L). The optimal NO₂^--N and NTR reached to 67.03 mg/L, 99.14% in HAc-R₈₀ system, and denitrification kinetics revealed the same conclusion, corresponding to higher COD utilization rate (CUR: 58.46 mgCOD/(gVSS·h)), nitrate reduction rate (N_aRR: 29.94 mgN/(gVSS·h)) and nitrite accumulation rate (N_iAR: 29.68 mgN/(gVSS·h)). The preference order was HAc > HPr > Glu + HAc > Glu in both R₄₀ and R₈₀ systems due to different metabolic pathways, however, the NO₂^--N accumulation and kinetic parameters of R₈₀ group were dramatically higher than those in R₄₀ for the same carbon source. The R₈₀ group facilitated more concentrated biodiversity (607-808 OTUs) with Terrimonas and norank_f_Saprospiraceae responsible for high NO₂^--N accumulation in HAc and HPr served systems, while norank_f_norank_o_Saccharimonadales and OLB13 dominated the Glu containing systems.

Enhanced anaerobic reduction of nitrobenzene at high salinity by betaine acting as osmoprotectant and regulator of metabolism

Anaerobic technology is extensively applied in the treatment of industrial organic wastewater, but high salinity always triggers microbial cell dehydration, causing the failure of the anaerobic process. In this work, betaine, one kind of compatible solutes which could balance the osmotic pressure of anaerobic biomass, was exogenously added for enhancing the anaerobic reduction of nitrobenzene (NB) at high salinity. Only 100 mg L^-1 betaine dosing could significantly promote the removal efficiency of NB within 35 h at 9% salinity (36.92 ± 4.02% without betaine and 72.94 ± 6.57% with betaine). The relieving effects on salt stress could be observed in the promotion of more extracellular polymeric substances (EPS) secretion with betaine addition. Additionally, the oxidation-reduction potential (ORP), as well as the electron transfer system (ETS) value, was increased with betaine addition, which was reflected in the improvement of system removal efficiency and enzyme activity. Microbial community analysis demonstrated that Bacillus and Clostridiisalibacter which were positively correlated with the stability of the anaerobic process were enriched with betaine addition at high salinity. Metagenomic analysis speculated that the encoding genes for salt tolerance (kdpB/oadA/betA/opuD/epsP/epsH) and NB degradation (nfsA/wrbA/ccdA/menC) obtained higher relative abundance with betaine addition under high salt environment, which might be the key to improving salt tolerance of anaerobic biomass. The long-term assessment demonstrated that exogenous addition betaine played an important role in maintaining the stability of the anaerobic system, which would be a potential strategy to achieve a high-efficiency anaerobic process under high salinity conditions.

Metabolic Potential of the Superphylum Patescibacteria Reconstructed from Activated Sludge Samples from a Municipal Wastewater Treatment Plant

Patescibacteria are widely distributed in various environments and often detected in activated sludge. However, limited information is currently available on their phylogeny, morphology, and ecophysiological role in activated sludge or interactions with other microorganisms. In the present study, we identified microorganisms that interacted with Patescibacteria in activated sludge via a correlation ana-lysis using the 16S rRNA gene, and predicted the metabolic potential of Patescibacteria using a metagenomic ana-lysis. The metagenome-assembled genomes of Patescibacteria consisted of three Saccharimonadia, three Parcubacteria, and one Gracilibacteria, and showed a strong positive correlation of relative abundance with Chitinophagales. Metabolic predictions from ten recovered patescibacterial and five Chitinophagales metagenome-assembled genomes supported mutualistic interactions between a member of Saccharimonadia and Chitinophagales via N-acetylglucosamine, between a member of Parcubacteria and Chitinophagales via nitrogen compounds related to denitrification, and between Gracilibacteria and Chitinophagales via phospholipids in activated sludge. The present results indicate that various interactions between Patescibacteria and Chitinophagales are important for the survival of Patescibacteria in activated sludge ecosystems.

Integrated thermal hydrolysis pretreated anaerobic digestion centrate and municipal wastewater treatment via partial nitritation/anammox process: A promising approach to alleviate inhibitory effects and enhance nitrogen removal

Two-stage Partial nitritation/Anammox (PN/A) was firstly performed for recalcitrant organics (RO)-rich thermal hydrolysis pretreated anaerobic digestion (THP-AD) centrate treatment with municipal wastewater (MW) as co-substrate. Results indicated the inhibitory effects of RO was alleviated and high nitrate issue in PN/A effluent was addressed by cotreatment strategy. Stable PN with nitrite accumulation ratio of 95% and N removal efficiency of 97.1% were well maintained at MW of 80%. Nevertheless, nitrate accumulation and anammox activity loss were observed with lowering MW proportion owing to the weakened denitrification activity and aggravated inhibitory effect. Microbial analysis revealed Nitrosomonas was the major ammonium oxidizing bacteria and the ideal PN performance was due to the effective out-selection of nitrite oxidizing bacteria. Candidatus Kuenenia was identified as the primary bacteria for nitrogen removal (82.7%), and the controlled abundance of heterotrophic denitrifiers in anammox system ensured the enhanced nitrogen removal regardless of high COD loading from THP-AD centrate.

Characterization of Microbial Communities in Wastewater Treatment Plants Containing Heavy Metals Located in Chemical Industrial Zones

Water pollution caused by heavy metals (HMs) poses a serious risk to human health and the environment and can increase the risk of diabetes, cancer, and hypertension in particular. In this study, two full-scale wastewater treatment plants (WWTPs) in industrial zones in southern China were selected to analyze the microbial community structure, diversity, similarity, and differentiation in the anoxic/oxic (AO) and anoxic/oxic membrane bioreactor (AO-MBR) units under the stress of HMs. High-throughput sequencing showed that microbial diversity and abundance were higher in the AO process than in the AO-MBR process. In the two WWTPs, the common dominant phyla were Proteobacteria and Bacteroidetes, while the common dominant genera were Gemmatimonadaceae, Anaerolineaceae, Saprospiraceae, and Terrimonas. Manganese (Mn) and zinc (Zn) positively correlated with Saccharimonadales, Nakamurella, Micrococcales, and Microtrichales, whereas copper (Cu) and iron (Fe) positively correlated with Longilinea and Ferruginibacter. Additionally, the relative abundances of Chloroflexi, Patescibacteria, and Firmicutes differed significantly (p < 0.05) between the two processes. These results may provide comprehensive outlooks on the characterization of microbial communities in WWTPs, which could also help to reduce the potential environmental risks of the effluent from WWTPs located in industrial zones.

The intrinsic relevance of nitrogen removal pathway to varying nitrate loading rate in a polycaprolactone-supported denitrification system

Up to date, the intrinsic association of nitrate loading rate (NLR) with treatment performance of solid-phase denitrification (SPD) systems is still ambiguous. To address this issue, three continuous up-flow bioreactors were configured. They were packed with polycaprolactone (PCL) under a filling ratio of 30%, 60% or 90% and were operated under a varying NLR of 0.34 ± 0.01-3.99 ± 0.12 gN/(L·d). Results showed that the denitrification efficiency was high (RE > 96%) and stable except the case with the highest NLR, which was mainly attributed to the lack of available carbon sources. At the phylum or genus level, most of the detected dominant bacterial taxa were either associated with organics degradation or nitrogen metabolism. The difference in bacterial community structure among the three stages was mainly caused by NLR rather than the filling ratio. Moreover, as the NLR got higher, the Bray-Curtis distance between samples from the same stage became shorter. By the results of gene or enzyme prediction performed in PICRUSt2, the main nitrogen metabolism pathways in these reactors were denitrification, dissimilatory nitrate reduction to ammonium (DNRA), assimilatory nitrate reduction to ammonium (ANRA) and nitrogen fixation. Moreover, aerobic and anaerobic nitrate dissimilation coexisted in the systems with the latter playing a dominant role. Finally, denitrification and DNRA occurred under both high and low NLR conditions while nitrogen fixation and ANRA preferred to occur under low NLR environments. These findings might help guide practical applications.

Carbon metabolism and adaptation of hyperalkaliphilic microbes in serpentinizing spring of Manleluag, the Philippines

Reduced substrates produced by the serpentinization reaction under hydration of olivine may have fuelled biological processes on early Earth. To understand the adaptive strategies and carbon metabolism of the microbes in the serpentinizing ecosystems, we reconstructed 18 draft genomes representing dominant species of Omnitrophicaeota, Gammaproteobacteria and Methanobacteria from the Manleluag serpentinizing spring in Zambales, Philippines (hyperalkaline and rich in methane and hydrogen). Phylogenomics revealed that two genomes were affiliated with a candidate phylum NPL-UPA2 and the references of all our genomes were derived from ground waters, hot springs and the deep biosphere. C1 metabolism appears to be widespread as most of the genomes code for methanogenesis, CO oxidation and CO₂ fixation. However, likely due to the low CO₂ concentration and election acceptors, the biomass in the spring was extremely low (<10³  cell/ml). Various Na⁺ and K⁺ transporters and Na⁺ -driving ATPases appear to be encoded by these genomes, suggesting that nutrient acquisition, bioenergetics and normal cytoplasmic pH were dependent on Na⁺ and K⁺ pumps. Our results advance our understanding of the metabolic potentials and bioenergetics of serpentinizing springs and provide a framework of the ecology of early Earth.

The feasibility and mechanism of redox-active biochar for promoting anammox performance

Redox-active biochar has been regarded as an effective additive to promote heterotrophic denitrification, yet little is known about the feasibility of adding biochar for promoting anammox performance. In this study, we investigated the effects of different biochar doses (3-14 g/L; 1.5-7.1 g/g VSS) on anammox performance. Results showed that, in a short term (40 days), biochar could enhance anammox nitrogen removal rate (NRR) and nitrogen removal efficiency (NRE) by 0-18.0% and 0.2%-11.6%, respectively; this enhancement effect increased at 3-10 g biochar/L assays and reached a plateau at 10-14 g biochar/L assays. The optimal biochar dosage was identified to be 10 g/L (5.1 g/g VSS), with the NRR and NRE being 5.6%-18.0% and 4.0%-11.6% higher than those of the control, respectively. The highest specific anammox activity was simultaneously obtained at 10 g biochar/L assay, being 51% higher than that of the control. It revealed that biochar promoted the secretion of extracellular polymeric substances (increased by 30%-40% compared with that of the control) and increased the ratio of extracellular proteins to polysaccharides as well, directly enhancing the extracellular electron transfer capacity (ETC) of anammox biomass. The increased ETC of anammox biomass would further accelerate the metabolic activities of anammox bacteria, and promote the relative abundance of anammox bacteria, i.e., Ca. Brocadia was enriched by 5.8-12.6 folds than that of the control. These results demonstrate that biochar is feasible to enhance anammox activity and nitrogen removal performance, facilitating to a fast startup and enhanced nitrogen removal of anammox system.

New Insight Into the Interspecies Shift of Anammox Bacteria Ca. "Brocadia" and Ca. "Jettenia" in Reactors Fed With Formate and Folate

The sensitivity of anaerobic ammonium-oxidizing (anammox) bacteria to environmental fluctuations is a frequent cause of reactor malfunctions. It was hypothesized that the addition of formate and folate would have a stimulating effect on anammox bacteria, which in turn would lead to the stability of the anammox process under conditions of a sharp increase in ammonium load, i.e., it helps overcome a stress factor. The effect of formate and folate was investigated using a setup consisting of three parallel sequencing batch reactors equipped with a carrier. Two runs of the reactors were performed. The composition of the microbial community was studied by the 16S rRNA gene profiling and metagenomic analysis. Among anammox bacteria, Ca. "Brocadia" spp. dominated during the first run. A stimulatory effect of folate on the daily nitrogen removal rate (dN) was identified. The addition of formate led to progress in dissimilatory nitrate reduction and stimulated the growth of Ca. "Jettenia" spp. The spatial separation of two anammox species was observed in the formate reactor: Ca. "Brocadia" occupied the carrier and Ca. "Jettenia"-the walls of the reactors. Biomass storage at low temperature without feeding led to an interspecies shift in anammox bacteria in favor of Ca. "Jettenia." During the second run, a domination of Ca. "Jettenia" spp. was recorded along with a stimulating effect of formate, and there was no effect of folate on dN. A comparative genome analysis revealed the patterns suggesting different strategies used by Ca. "Brocadia" and Ca. "Jettenia" spp. to cope with environmental changes.

Wastewater Treatment: Current and Future Techniques

Recently, national and international effluent standards have become more stringent, posing a significant challenge in the water treatment industry. Accordingly, treatment techniques with minimal energy consumption and maximal performance are urgently required for wastewater and water treatments. This topic was investigated from both technical and environmental perspectives to improve water and wastewater treatment techniques and enhance the quality of water bodies. This Special Issue (SI) has attracted investigations by researchers worldwide, including those from Australia, the United States, Finland, Turkey, South Africa, Oman, China, Japan, Malaysia, and Pakistan. In this SI, research and review articles propose and discuss efficient water and wastewater treatment techniques. We hope that the readers of Water can learn about new aspects of wastewater treatment using physicochemical, biological, and hybrid techniques. Finally, we hope that this SI will contribute to the United Nations’ Sustainable Development Goal 6, which is to ensure a secure water supply globally through cost-efficient technologies.

Insights into the fouling layer of flat-sheet membrane and its development in an integrated oxidation ditch-membrane bioreactor

This work revealed the characteristics of fouling layer on the flat-sheet membranes and its development in an integrated oxidation-ditch membrane bioreactor. During the operation period (130 days), the reactor performed very well in removing pollutants. As the operation proceeded, membrane fouling occurred on the flat-sheet membranes and trans-membrane pressure showed a cyclical variation. The experimental results showed that the process of membrane fouling appeared successively in two different structures: biofilm (BF) and sludge fouling (SF). The substances causing membrane fouling were mainly organic foulants and a small amount of inorganic metal compounds, especially the protein-like and fulvic acid-like substances in loosely bound extracellular polymeric substances (LB-EPS). The analysis of microbial communities revealed that SF and BF had very different microbial properties. Although most membrane foulants could be removed by physical and chemical cleaning methods, the protein-like and fulvic acid-like substances in BF were contribute much to causing irreversible membrane fouling.

Diversity of <i>Candidatus</i> Patescibacteria in Activated Sludge Revealed by a Size-‍Fractionation Approach

Uncultivated members of Candidatus Patescibacteria are commonly found in activated sludge treating sewage and are widely distributed in wastewater treatment plants in different regions and countries. However, the phylogenetic diversity of Ca. Patescibacteria is difficult to examine because of their low relative abundance in the environment. Since Ca. Patescibacteria members have small cell sizes, we herein collected small microorganisms from activated sludge using a filtration-based size-fractionation approach (i.e., 0.45–0.22‍ ‍μm and 0.22–0.1‍ ‍μm fractions). Fractionated samples were characterized using 16S rRNA gene amplicon and shotgun metagenomic sequence ana­lyses. The amplicon ana­lysis revealed that the relative abundance of Ca. Patescibacteria increased to 73.5% and 52.5% in the 0.45–0.22‍ ‍μm and 0.22–0.1‍ ‍μm fraction samples, respectively, from 5.8% in the unfractionated sample. The members recovered from the two size-fractionated samples included Ca. Saccharimonadia, Ca. Gracilibacteria, Ca. Paceibacteria, Ca. Microgenomatia, class-level uncultured lineage ABY1, Ca. Berkelbacteria, WS6 (Ca. Dojkabacteria), and WWE3, with Ca. Saccharimonadia being predominant in both fraction samples. The number of operational taxonomic units belonging to Ca. Patescibacteria was approximately 6-fold higher in the size-fractionated samples than in the unfractionated sample. The shotgun metagenomic ana­lysis of the 0.45–0.22‍ ‍μm fractioned sample enabled the reconstruction of 24 high-quality patescibacterial bins. The bins obtained were classified into diverse clades at the family and genus levels, some of which were rarely detected in previous activated sludge studies. Collectively, the present results suggest that the overall diversity of Ca. Patescibacteria inhabiting activated sludge is higher than previously expected.

Effects of alkalinity addition with different strategies on CANON process: Start-up, performance, and microbial community

The effects of alkalinity addition with different strategies on the start-up, performance, and microbial community of completely autotrophic nitrogen removal over nitrite (CANON) were investigated over 450 days. In phase I, the alkalinity was increased gradually from 300 to 2,000 mg/L to obtain the optimal range. In phase II, the reactor was restarted to verify the appropriate alkalinity value of 1,600 mg/L. The fact that it only took 90 days (phase I: 170 days) to complete the start-up of CANON in phase II demonstrated that an alkalinity value of 1,600 mg/L was suitable when the influent NH₄ ⁺ -N concentration was 200 mg/L (alkalinity/NH₄ ⁺ -N = 8:1). The slope (k = 2.00) of NH₄ ⁺ -N concentration decrease in phase II during the start-up process was significantly higher than that in phase I (k = 1.50). High removal efficiencies of NH₄ ⁺ -N (98%) and TN (80%) were attained in both phases. Specific anaerobic ammonium oxidation (anammox) activity tests showed that the anammox activity of the two phases reached 3.31 and 5.31 mg TN/(g VSS·h), respectively. High-throughput sequencing analysis revealed that appropriate alkalinity could promote the enrichment of Candidatus Brocadia, C. Jettenia, and C. Kuenenia (total abundance of 31.96%) while effectively inhibiting Nitrospira (abundance of less than 0.50%). PRACTITIONER POINTS: An alkalinity/NH₄ ⁺ -N ratio of 8 promoted the rapid start-up and stable performance of CANON. NH₄ ⁺ -N and TN removal efficiencies of 98% and 80%, respectively, were obtained. High alkalinity promoted the enrichment of Candidatus Brocadia, Candidatus Jettenia, Candidatus Kuenenia and inhibited Nitrospira.

Biosolid-Amended Soil Enhances Defense Responses in Tomato Based on Metagenomic Profile and Expression of Pathogenesis-Related Genes

Biosolid application is an effective strategy, alternative to synthetic chemicals, for enhancing plant growth and performance and improving soil properties. In previous research, biosolid application has shown promising results with respect to tomato resistance against Fusarium oxysporum f. sp. radicis-lycopersici (Forl). Herein, we aimed at elucidating the effect of biosolid application on the plant-microbiome response mechanisms for tomato resistance against Forl at a molecular level. More specifically, plant-microbiome interactions in the presence of biosolid application and the biocontrol mechanism against Forl in tomato were investigated. We examined whether biosolids application in vitro could act as an inhibitor of growth and sporulation of Forl. The effect of biosolid application on the biocontrol of Forl was investigated based on the enhanced plant resistance, measured as expression of pathogen-response genes, and pathogen suppression in the context of soil microbiome diversity, abundance, and predicted functions. The expression of the pathogen-response genes was variably induced in tomato plants in different time points between 12 and 72 h post inoculation in the biosolid-enriched treatments, in the presence or absence of pathogens, indicating activation of defense responses in the plant. This further suggests that biosolid application resulted in a successful priming of tomato plants inducing resistance mechanisms against Forl. Our results have also demonstrated that biosolid application alters microbial diversity and the predicted soil functioning, along with the relative abundance of specific phyla and classes, as a proxy for disease suppression. Overall, the use of biosolid as a sustainable soil amendment had positive effects not only on plant health and protection, but also on growth of non-pathogenic antagonistic microorganisms against Forl in the tomato rhizosphere and thus, on plant-soil microbiome interactions, toward biocontrol of Forl.

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.