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

Enhancing biofilm formation with powder carriers for efficient nitrogen and phosphorus removal

This study assesses the improvement in nitrogen and phosphorus removal from wastewater achieved through the integration of zeolite and attapulgite carrier materials into the activated sludge (AS) process. It was found that the addition of these materials significantly enhanced the processing performance of the reactor. Specifically, the use of zeolite and attapulgite powders increased sludge particle sizes to averages of 231.56 μm and 219.62 μm, respectively. This facilitated micro-granule formation, substantially improving the settling characteristics of the sludge and boosting the activity and proliferation of essential microbes. Illumina MiSeq sequencing demonstrated significant accumulations of DGAOs (Candidatus_Competibacter) and DPAOs (Candidatus_Accumulibacter). Furthermore, these carriers augmented the protein content in extracellular polymers, enhancing the hydrophobicity of the sludge and promoting aggregation. Comparative analysis based on the extended Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory indicated a preferential adhesion affinity of sludge for zeolite compared to attapulgite, attributed primarily to Lewis acid-base and electric double-layer interactions. These findings underscore zeolite's enhanced efficacy in biomass fixation and suggest significant potential for the technological advancement of wastewater treatment plants.

Unique episymbiotic relationship between Candidatus Patescibacteria and Zoogloea in activated sludge flocs at a municipal wastewater treatment plant

Candidatus Patescibacteria, also known as candidate phyla radiation (CPR), including the class-level uncultured clade JAEDAM01 (formerly a subclass of Gracilibacteria/GN02/BD1-5), are ubiquitous in activated sludge. However, their characteristics and relationships with other organisms are largely unknown. They are believed to be episymbiotic, endosymbiotic or predatory. Despite our understanding of their limited metabolic capacity, their precise roles remain elusive due to the difficulty in cultivating and identifying them. In previous research, we successfully recovered high-quality metagenome-assembled genomes (MAGs), including a member of JAEDAM01 from activated sludge flocs. In this study, we designed new probes to visualize the targeted JAEDAM01-associated MAG HHAS10 and identified its host using fluorescence in situ hybridization (FISH). The FISH observations revealed that JAEDAM01 HHAS10-like cells were located within dense clusters of Zoogloea, and the fluorescence brightness of zoogloeal cells decreased in the vicinity of the CPR cells. The Zoogloea MAGs possessed genes related to extracellular polymeric substance biosynthesis, floc formation and nutrient removal, including a polyhydroxyalkanoate (PHA) accumulation pathway. The JAEDAM01 MAG HHAS10 possessed genes associated with type IV pili, competence protein EC and PHA degradation, suggesting a Zoogloea-dependent lifestyle in activated sludge flocs. These findings indicate a new symbiotic relationship between JAEDAM01 and Zoogloea.

Impact of operating conditions on N2O accumulation in Nitrate-DAMO system: Kinetics and microbiological analysis

Nitrate-dependent anaerobic methane oxidation (Nitrate-DAMO) is a novel and sustainable process that removes both nitrogen and methane. Previously, the metabolic pathway of Nitrate-DAMO has been intensively studied with some results. However, the production and consumption of nitrous oxide (N2O) in the Nitrate-DAMO system were widely disregarded. In this study, a Nitrate-DAMO system was used to investigate the effect of operational parameters (C/N ratio, pH, and temperature) on N2O accumulation, and the optimal operating conditions were determined (C/N = 3, pH = 6.5, and temperature = 20 °C). In this study, an enzyme kinetic model was used to fit the nitrate nitrogen degradation and the nitrous oxide production and elimination under different operating conditions. The thermodynamic model of N2O production and elimination in the system also has been constructed. Multiple linear regression analysis found that pH was the most important factor influencing N2O accumulation. The Metagenomics sequencing results showed that alkaline pH promoted the abundance of Nor genes and denitrifying bacteria, which were significantly and positively correlated with N2O emissions. And alkaline pH also promoted the production of Mdo genes related to the N2O-driven AOM reaction, indicating that part of the N2O was consumed by denitrifying bacteria and the other part was consumed by the N2O-driven AOM reaction. These findings reveal the mechanism of N2O production and consumption in DAMO systems and provide a theoretical basis for reducing N2O production and greenhouse gas emissions in actual operation.

From small water bodies to lakes: Exploring the diversity of freshwater bacteria in an Alpine Biosphere Reserve

Small water bodies, although supporting high biodiversity, are often understudied in the Alpine region. In this work, we characterized the planktic and benthic bacterial communities, as well as the water chemistry, of a wide physiographic range of 19 freshwater bodies within an Alpine Biosphere Reserve, including ponds, pasture ponds, peat bogs, shallow lakes, and lakes. We collected both water and surface sediment samples, followed by metabarcoding analysis based on the V3-V4 regions of the 16S rRNA gene. We investigated the changes in biodiversity and the distribution of unique and shared amplicon sequence variants (ASVs) between water (11,829 ASVs) and surface sediment (19,145 ASVs) habitats, as well as across different freshwater typologies. The majority of ASVs (78 %) were unique to a single sample, highlighting the variability and uniqueness of bacterial communities in such freshwater bodies. Most freshwater environments showed higher α-diversity in sediment samples (median, 1469 ASVs) compared to water (468 ASVs). We found that water and sediment habitats harboured unique bacterial communities with significant differences in their taxonomic compositions. Benthic bacteria were associated with several biogeochemical and degradative processes occurring in the sediments, with no notable differences among freshwater typologies and with phylogenetically and ecologically similar species. Conversely, planktic communities showed greater heterogeneity: small water bodies and peat bogs were characterized by higher relative abundances of Patescibacteria (up to 33 %), while lakes and shallow lakes were dominated by Actinobacteriota (up to 36 %). Cyanobacteria (426 ASVs) were generally distributed at low abundances in both water and sediment habitats. Overall, our results provided essential insights into the bacterial ecology of understudied environments such as ponds and pasture ponds and highlighted the importance of further exploring their rich pelagic and benthic bacterial biodiversity.

Diverse sources of fecal contamination in macroalgae wrack-affected environment adjacent to river outflow along the Baltic Sea coast

We investigated the dynamics of feces-associated microorganisms in areas with wrack accumulation in the southeastern part of the Baltic Sea. Our study covered single-day (2021 ) and multi-day (2022) observations during the recreational season. We collected water, sand, and wrack samples and assessed the abundance of fecal indicator bacteria (FIB), as well metagenomic analysis was conducted to monitor changes in microbial composition. Based on metagenomic data we identified taxa associated with feces, sewage, and ruminant sources. Human-related fecal pollution based on genetic markers correlated with the presence of Lachnospiraceae, Prevotellaceae and Rickenellacea abundance. Higher abundance and diversity of feces-associated and ruminant-associated taxa and the presence of enteric pathogens were observed when wrack accumulated near the river outflow in 2021, suggesting a potential link with fecal pollution from the river. As a preventive measure, it is recommended to remove the wrack to reduce the risk of exposure to potential enteric pathogens if it is accumulated next to the river outflow.

Seasonal and anthropogenic influences on bacterioplankton communities: ecological impacts in the coastal waters of Qinhuangdao, Northern China

Marine bacterioplankton play a crucial role in the cycling of carbon, nitrogen, and phosphorus in coastal waters. And the impact of environmental factors on bacterial community structure and ecological functions is a dynamic ongoing process. To systematically assess the relationship between environmental changes and bacterioplankton communities, this study delved into the spatiotemporal distribution and predicted metabolic characteristics of bacterioplankton communities at two estuarine beaches in Northern China. Coastal water samples were collected regularly in spring, summer, and autumn, and were analyzed in combination with environmental parameters and bacterioplankton community. Results indicated significant seasonal variations in bacterioplankton communities as Bacteroidetes and Actinobacteria were enriched in spring, Cyanobacteria proliferated in summer. While Pseudomonadota and microorganisms associated with organic matter decomposition prevailed in autumn, closely linked to seasonal variation of temperature, light and nutrients such as nitrogen and phosphorus. Particularly in summer, increased tourism activities and riverine inputs significantly raised nutrient levels, promoting the proliferation of specific photosynthetic microorganisms, potentially linked to the occurrence of phytoplankton blooms. Spearman correlation analysis further revealed significant correlations between bacterioplankton communities and environmental factors such as salinity, chlorophyll a, and total dissolved phosphorus (TDP). Additionally, the metabolic features of the spring bacterioplankton community were primarily characterized by enhanced activities in the prokaryotic carbon fixation pathways, reflecting rapid adaptation to increased light and temperature, as well as significant contributions to primary productivity. In summer, the bacterial communities were involved in enhanced glycolysis and biosynthetic pathways, reflecting high energy metabolism and responses to increased light and biomass. In autumn, microorganisms adapted to the accelerated decomposition of organic matter and the seasonal changes in environmental conditions through enhanced amino acid metabolism and material cycling pathways. These findings demonstrate that seasonal changes and human activities significantly influence the structure and function of bacterioplankton communities by altering nutrient dynamics and physical environmental conditions. This study provides important scientific insights into the marine biological responses under global change.

From metagenomes to metabolism: Systematically assessing the metabolic flux feasibilities for "Candidatus Accumulibacter" species during anaerobic substrate uptake

With the rapid growing availability of metagenome assembled genomes (MAGs) and associated metabolic models, the identification of metabolic potential in individual community members has become possible. However, the field still lacks an unbiassed systematic evaluation of the generated metagenomic information to uncover not only metabolic potential, but also feasibilities of these models under specific environmental conditions. In this study, we present a systematic analysis of the metabolic potential in species of "Candidatus Accumulibacter", a group of polyphosphate-accumulating organisms (PAOs). We constructed a metabolic model of the central carbon metabolism and compared the metabolic potential among available MAGs for "Ca. Accumulibacter" species. By combining Elementary Flux Modes Analysis (EFMA) with max-min driving force (MDF) optimization, we obtained all possible flux distributions of the metabolic network and calculated their individual thermodynamic feasibility. Our findings reveal significant variations in the metabolic potential among "Ca. Accumulibacter" MAGs, particularly in the presence of anaplerotic reactions. EFMA revealed 700 unique flux distributions in the complete metabolic model that enable the anaerobic uptake of acetate and its conversion into polyhydroxyalkanoates (PHAs), a well-known phenotype of "Ca. Accumulibacter". However, thermodynamic constraints narrowed down this solution space to 146 models that were stoichiometrically and thermodynamically feasible (MDF > 0 kJ/mol), of which only 8 were strongly feasible (MDF > 7 kJ/mol). Notably, several novel flux distributions for the metabolic model were identified, suggesting putative, yet unreported, functions within the PAO communities. Overall, this work provides valuable insights into the metabolic variability among "Ca. Accumulibacter" species and redefines the anaerobic metabolic potential in the context of phosphate removal. More generally, the integrated workflow presented in this paper can be applied to any metabolic model obtained from a MAG generated from microbial communities to objectively narrow the expected phenotypes from community members.

Gut microbial ecology and exposome of a healthy Pakistani cohort

BACKGROUND

Pakistan is a multi-ethnic society where there is a disparity between dietary habits, genetic composition, and environmental exposures. The microbial ecology of healthy Pakistani gut in the context of anthropometric, sociodemographic, and dietary patterns holds interest by virtue of it being one of the most populous countries, and also being a Lower Middle Income Country (LMIC).

METHODS

16S rRNA profiling of healthy gut microbiome of normo-weight healthy Pakistani individuals from different regions of residence is performed with additional meta-data collected through filled questionnaires. The current health status is then linked to dietary patterns through [Formula: see text] test of independence and Generalized Linear Latent Variable Model (GLLVM) where distribution of individual microbes is regressed against all recorded sources of variability. To identify the core microbiome signature, a dynamic approach is used that considers into account species occupancy as well as consistency across assumed grouping of samples including organization by gender and province of residence. Fitting neutral modeling then revealed core microbiome that is selected by the environment.

RESULTS

A strong determinant of disparity is by province of residence. It is also established that the male microbiome is better adapted to the local niche than the female microbiome, and that there is microbial taxonomic and functional diversity in different ethnicities, dietary patterns and lifestyle habits. Some microbial genera, such as, Megamonas, Porphyromonas, Haemophilus, Klebsiella and Finegoldia showed significant associations with consumption of pickle, fresh fruits, rice, and cheese. Our analyses suggest current health status being associated with the diet, sleeping patterns, employment status, and the medical history.

CONCLUSIONS

This study provides a snapshot of the healthy core Pakistani gut microbiome by focusing on the most populous provinces and ethnic groups residing in predominantly urban areas. The study serves a reference dataset for exploring variations in disease status and designing personalized dietary and lifestyle interventions to promote gut health, particularly in LMICs settings.

Removal of intI1, ARGs, and SARS-CoV-2 and changes in bacterial communities in four sewage treatment facilities

Currently, discharge regulations for wastewater treatment plants (WWTPs) are based on conventional parameters, but more is needed to ensure safe water reuse. In particular, emerging pollutants, as antimicrobials and antibiotic resistance genes (ARGs), are not considered. This research focuses on the fate of emerging biological contaminants during wastewater treatment in Mexico City. intI1 and the ARGs cphA-02, OXA-10 and sul1 were analyzed by qPCR; pathogenic bacteria species were characterized by high throughput sequencing of complete 16S rRNA gene, and fragments of SARS-CoV-2 were quantified by RT-qPCR. Conventional parameters (chemical oxygen demand and coliform bacteria) were also determined. Two sampling campaigns (rainy and dry seasons) were carried out in four municipal WWTPs in Mexico City, representing five biological treatment processes: conventional activated sludge, extended aeration activated sludge, membrane bioreactor, direct anaerobic digestion, and constructed wetland, followed by ultraviolet light or chlorine disinfection. In most cases, gene fragments of SARS-CoV-2 were eliminated below the detection limit of RT-qPCR. The abundance of intI1 positively correlated with the sul1, OXA-10, and cphA-02 abundances; intI1 and the ARGs here studied were partially removed in the WWTPs, and in most cases, the number of copies per second discarded in the sludge were higher those in the effluent. The treatment processes decreased the abundance of dominant bacterial groups in the raw wastewater, while enriching bacterial groups in the effluent and the biological sludge, with possible pollutant removal capabilities. Bacterial communities in the raw wastewater showed the predominance of the genus Arcobacter (from 62.4 to 86.0 %) containing potentially pathogenic species. Additionally, DNA of some species persisted after the treatment processes: A. johnsonii, A. junii, A. caviae, A. hydrophila, A. veronii, A. butzleri, A. cryaerophilus, Chryseobacterium indologenes, Hafnia paralvei, M. osloensis, Pseudomonas putida and Vibrio cholerae, which deserves special attention in future regulation for safe water reuse.

Response of denitrification microbiome to the nitrogen flux in three Gorges reservoir (TGR) sediments during two seasonal water fluctuation events

Three Gorges Reservoir (TGR) water fluctuation creates high water level (HWL) and low water level (LWL) condition in TGR aquatic ecosystem. HWL fluies significant nutrients, mainly introducing carbon and nitrogen into the ecosystem. The nitrogen input is a concern for water quality management of TGR since the possible eutrophication caused by nitrogen spike. Sediment denitrification is widely recognized as the dominant nitrogen removal process in freshwater ecosystem. Therefore, the response of TGR sediments microbiome to the input nitrogen flucatution is crucial for both nitrogen balance and the eutrophication status of the ecosystem. Using high throughout sequencing of 16S rRNA gene and the predicted denitrification enzyme, and qualitative PCR of denitrification functional genes, we investigated how TGR sediments denitrification microbiome respond to the input nitrogen flux during two seasonal water fluctuation events. Concomitant to expected input carbon and nitrogen, we observed distinct microbial community structure and denitrification microbiota in HWL and LWL, and also in seasonal sampling events. Sediments pH, total nitrogen and nitrate were the significant impact factors in shaping the microbial community structure. Important denitrification microbiota (e.g., Saprospiraceae, Gemmatimonadaceae, Pseudomonas) are the main taxa of the microbial community and also showed water level and seasonal variation. The relative abundance of denitrification enzyme (nar, nir, nor, nos) and function genes (nirS, nirK, nosZ) were higher in LWL than HWL. Denitrification enzyme were significantly (p < 0.05) correlated with the nitrate concentration. In addition, the relative abundance of denitrification enzyme and function genes increased during the transition from 2014 HWL to 2015 LWL. Results suggested that TGR sediments denitrification is nitrate concentration dependent. The denitrification microbiome is initially inhibited due to high nitrate input, then they developed denitrification ability in response to high nitrate concentration.

Influence of C/N ratio and ammonia on nitrogen removal and N2O emissions from one-stage partial denitrification coupled with anammox

The development of low carbon treatment processes is an important issue worldwide. Partial denitrification coupled with anammox (PD/A) is a novel strategy to remove nitrogen and reduce N2O emissions. The influence of C/N ratio and NH4+ concentration on nitrogen removal and N2O emissions was investigated in batch reactors filled with PD/A coupled sludge. A C/N ratio of 2.1 was effective for nitrogen removal and N2O reduction; higher ammonia concentration might make anammox more active and indirectly reduce N2O emissions. Long-term operation further confirmed that a C/N ratio of 2.1 resulted in a minimum effluent N2O concentration (mean value of 0.94 μmol L-1); as the influent NH4+ concentration decreased to 50 mg L-1 (NH4+-N/NO3--N: 1), the nitrogen removal rate increased to 82.41%. Microbial analysis showed that anammox bacteria (Candidatus Jettenia and Ca. Brocadia) were enriched in the PD/A system and Ca. Brocadia gradually dominated the anammox community, with the relative abundance increasing from 1.69% to 18.44% between days 97 and 141. Finally, functional gene analysis indicated that the abundance of nirS/K and hao involved in partial denitrification and anammox, respectively, increased during long-term operation of the reactor; this change benefitted nitrogen metabolism in anammox, which could indirectly reduce N2O emissions.

The enrichment of more functional microbes induced by the increasing hydraulic retention time accounts for the increment of autotrophic denitrification performance

With pyrite (FeS2) and polycaprolactone (PCL) as electron donors, three denitrification systems, namely FeS2-based autotrophic denitrification (PAD) system, PCL-supported heterotrophic denitrification (PHD) system and split-mixotrophic denitrification (PPMD) system, were constructed and operated under varying hydraulic retention times (HRT, 1-48 h). Compared with PAD or PHD, the PPMD system could achieve higher removals of NO3--N and PO43--P, and the effluent SO42- concentration was greatly reduced to 7.28 mg/L. Similarly, the abundance of the dominant genera involved in the PAD (Thiobacillus, Sulfurimonas, and Ferritrophicum, etc.) or PHD (Syntrophomonas, Desulfomicrobium, and Desulfovibrio, etc.) process all increased in the PPMD system. Gene prediction completed by PICRUSt2 showed that the abundance of the functional genes involved in denitrification and sulfur oxidation all increased with the increase of HRT. This also accounted for the increased contribution of autotrophic denitrification to total nitrogen removal in the PPMD system. In addition, the analysis of metabolic pathways disclosed the specific conversion mechanisms of nitrogen and sulfur inside the reactor.

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.

Novel Cross-domain Symbiosis between Candidatus Patescibacteria and Hydrogenotrophic Methanogenic Archaea Methanospirillum Discovered in a Methanogenic Ecosystem

To identify novel cross-domain symbiosis between Candidatus Patescibacteria and Archaea, we performed fluorescence in situ hybridization (FISH) on enrichment cultures derived from methanogenic bioreactor sludge with the newly designed 32-520-1066 probe targeting the family-level uncultured clade 32-520/UBA5633 lineage in the class Ca. Paceibacteria. All FISH-detectable 32-520/UBA5633 cells were attached to Methanospirillum, indicating high host specificity. Transmission electron microscopy observations revealed 32-520/UBA5633-like cells that were specifically adherent to the plug structure of Methanospirillum-like rod-shaped cells. The metagenome-assembled genomes of 32-520/UBA5633 encoded unique gene clusters comprising pilin signal peptides and type IV pilins. These results provide novel insights into unseen symbiosis between Ca. Patescibacteria and Archaea.