Binning Analysis Research Articles

Genomic synergistic efficient carbon fixation and nitrogen removal induced by excessive inorganic carbon in the anammox-centered coupling system

Given the significance of HCO3- for autotrophic anammox bacteria (AnAOB), excessive HCO3- was always provided in anammox-related systems and engineering applications. However, its impact mechanism on anammox process at genome-level remains unknown. This study firstly established an anammox-centered coupling system that entails heterotrophic partial denitrification (PD) and hydrolytic acidification (A-PDHA) fed mainly with inorganic carbon (high HCO3- concentration and low C/N ratio). Metagenomic binning and metatranscriptomics analyses indicated that high HCO3- concentration enhanced expression of natural most efficient phosphoenolpyruvate (PEP) carboxylase within AnAOB, by up to 30.59 folds. This further induced AnAOB to achieve high-speed carbon-fixing reaction through cross-feeding of phosphate and PEP precursors with heterotrophs. Additionally, the enhanced activity of transporters and catalytic enzymes (up to 4949-fold) induced by low C/N ratio enabled heterotrophs to eliminate extracellular accumulated energy precursors mainly derived from carbon fixation products of AnAOB. This maintained high-speed carbon-fixing reaction within AnAOB and supplemented heterotrophs with organics. Moreover, assimilated energy precursors stimulated nitrogen metabolism enzymes, especially NO2- reductase (968.14 times), in heterotrophs. This established an energy-saving PD-A process mediated by interspecies NO shuttle. These variation resulted in efficient nitrogen removal (>95 %) and reduced external organic carbon demand (67 %) in A-PDHA system. This study unveils the great potential of an anammox-centered autotrophic-heterotrophic coupling system for achieving cost-effective nitrogen removal and enhancing carbon fixation under excessive HCO3- doses.

The occurrence of banana Fusarium wilt aggravates antibiotic resistance genes dissemination in soil

The spread of antibiotic resistance genes (ARGs) and subsequent soil-borne disease outbreaks are major threats to soil health and sustainable crop production. However, the relationship between occurrences of soil-borne diseases and the transmission of soil ARGs remains unclear. Here, soil ARGs, mobile genetic elements and microbial communities from co-located disease suppressive and conducive banana orchards were deciphered using metagenomics and metatranscriptomics approaches. In total, 23 ARG types, with 399 subtypes, were detected using a metagenomics approach, whereas 23 ARG types, with 452 subtypes, were discovered using a metatranscriptomics method. Furthermore, the metagenomics analysis revealed that the ARG total abundance levels were greater in rhizospheres (0.45 ARGs/16S rRNA on average) compared with bulk (0.32 ARGs/16S rRNA on average) soils. Interestingly, metatranscriptomics revealed that the total ARG abundances were greater in disease-conducive (8.85 ARGs/16S rRNA on average) soils than disease suppressive (1.45 ARGs/16S rRNA on average) soils. Mobile genetic elements showed the same trends as ARGs. Network and binning analyses indicated that Mycobacterium, Streptomyces, and Blastomonas are the main potential hosts of ARGs. Furthermore, Bacillus was significantly and negatively correlated with Fusarium (P < 0.05, r = −0.84) and hosts of ARGs (i.e., Mycobacterium, Streptomyces, and Blastomonas). By comparing metagenomic and metatranscriptomic analyses，this study demonstrated that metatranscriptomics may be more sensitive in indicating ARGs activities in soil. Our findings enable the more accurate assessment of the transmission risk of ARGs. The data provide a new perspective for recognizing soil health, in which soil-borne disease outbreaks appear to be associated with ARG spread, whereas beneficial microbe enrichment may mitigate wilt disease and ARG transmission.

A broadly protective antibody targeting glycoprotein Gn inhibits severe fever with thrombocytopenia syndrome virus infection

Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging bunyavirus that causes severe viral hemorrhagic fever and thrombocytopenia syndrome with a fatality rate of up to 30%. No licensed vaccines or therapeutics are currently available for humans. Here, we develop seven monoclonal antibodies (mAbs) against SFTSV surface glycoprotein Gn. Mechanistic studies show that three neutralizing mAbs (S2A5, S1G3, and S1H7) block multiple steps during SFTSV infection, including viral attachment and membrane fusion, whereas another neutralizing mAb (B1G11) primarily inhibits the viral attachment step. Epitope binning and X-ray crystallographic analyses reveal four distinct antigenic sites on Gn, three of which have not previously been reported, corresponding to domain I, domain II, and spanning domain I and domain II. One of the most potent neutralizing mAbs, S2A5, binds to a conserved epitope on Gn domain I and broadly neutralizes infection of six SFTSV strains corresponding to genotypes A to F. A single dose treatment of S2A5 affords both pre- and post-exposure protection of mice against lethal SFTSV challenge without apparent weight loss. Our results support the importance of glycoprotein Gn for eliciting a robust humoral response and pave a path for developing prophylactic and therapeutic antibodies against SFTSV infection.

Operational modal characterisation for long-term monitoring in offshore structures

In the effort to increase sustainability and help drive the energy sector to support oil and gas decarbonisation, the importance of identifying and characterising the current state of assets is becoming ever more crucial for operators, especially with regards to life extension and repurposing. Structural Health Monitoring (SHM) offers a promising and forward-thinking methodology for tracking asset integrity. In particular, Operational Modal Analysis (OMA) presents a proven, output only method for structure characterisation and modal tracking. However, Environmental and Operational Variations (EOV) can influence the modal properties of the structure making modal parameter estimation and tracking less reliable in the short- and long-term. This study employs an Automated Operational Modal Analysis (AOMA) methodology based on the combination of stochastic subspace identification and natural frequency histogram bin analysis for robust parameter extraction. The methodology is implemented in a complex of three bridge linked offshore platforms. Structural complexity, operational loading and significant modal couplings require sophisticated analysis. The preliminary results show discontinuity of the operational modes over a 6-month long monitoring period. The findings demonstrate the need of further analysis to understand the time-variant parameters which determine structural response across the asset lifetime.

Combined environmental pressure induces unique assembly patterns of micro-plastisphere biofilm microbial communities in constructed wetlands

The characteristics and dynamics of micro-plastisphere biofilm on the surface of microplastics (MPs) within artificial ecosystems, such as constructed wetlands (CWs), remain unclear, despite these ecosystems’ potential to serve as sinks for MPs. This study investigates the dynamic evolution of micro-plastisphere biofilm in CWs, utilizing simulated wastewater containing sulfamethoxazole and humic acid, through physicochemical characterization and metagenomic analysis. Two different types of commercial plastics, including non-degradable polyethylene and degradable polylactic acid, were shredded into MPs and studied. The findings reveal that the types, shape and incubation time of MPs, along with humic acid content in wastewater, affected the quantity and quality of biofilms, such as the biofilm composition, spatial structure and microbial communities. After just 15 days into incubation, numerous microbials were observed on MP samples, with increases in biofilms content and enhanced humification of extracellular polymeric substances over time. Additionally, microbial communities on polylactic acid MPs, or those incubated for longer time, exhibit higher diversity, connectivity and stability, along with reduced vulnerability. Conversely, biofilms on polyethylene MPs were thicker, with higher potential for greenhouse gas emission and increased risk of antibiotic resistance genes. The addition of humic acid demonstrated opposite effects on biofilms across environmental interfaces, possibly due to its dual potential to produce light-induced free radicals and serve as a carbon source. Binning analysis further uncovered a unique assembly pattern of nutrients cycle genes and antibiotic resistance genes, significantly correlated within micro-plastisphere microbial communities, under the combined stress of nutrition and sulfamethoxazole. These results emphasize the shaping of micro-plastisphere biofilm characteristics by unique environmental conditions in artificial ecosystems, and the need to understand how DOM and other pollutants covary with MP pollution.

Optimizing anaerobic digestion: Benefits of mild temperature transition from thermophilic to mesophilic conditions

Anaerobic digestion (AD) plays a significant role in renewable energy recovery. Upgrading AD from thermophilic (50–57 °C) to mesophilic (30–38 °C) conditions to enhance process stability and reduce energy input remains challenging due to the high sensitivity of thermophilic microbiomes to temperature fluctuations. Here we compare the effects of two decreasing-temperature modes from 55 to 35 °C on cell viability, microbial dynamics, and interspecies interactions. A sharp transition (ST) is a one-step transition by 20 °C d−1, while a mild transition (MT) is a stepwise transition by 1 °C d−1. We find a greater decrease in methane production with ST (88.8%) compared to MT (38.9%) during the transition period. ST mode overproduced reactive oxygen species by 1.6-fold, increased membrane permeability by 2.2-fold, and downregulated microbial energy metabolism by 25.1%, leading to increased apoptosis of anaerobes by 1.9-fold and release of intracellular substances by 2.9-fold, further constraining methanogenesis. The higher (1.6 vs. 1.1 copies per gyrA) metabolic activity of acetate-dependent methanogenesis implied more efficient methane production in a steady mesophilic, MT-mediated system. Metagenomic binning and network analyses indicated that ST induced dysbiosis in keystone species and greatly enhanced microbial functional redundancy, causing loss of microbial syntrophic interactions and redundant metabolic pathways. In contrast, the greater microbial interconnections (average degrees 44.9 vs. 22.1) in MT at a steady mesophilic state suggested that MT could better maintain necessary system functionality and stability through microbial syntrophy or specialized pathways. Adopting MT to transform thermophilic digesters into mesophilic digesters is feasible and could potentially enhance the further optimization and broader application of practical anaerobic engineering.

Lower extremity joint angle, moment, and coordination throughout a double limb drop vertical jump in individuals with anterior cruciate ligament reconstruction

ABSTRACT Individuals with anterior cruciate ligament reconstruction (ACLR) utilise different landing biomechanics between limbs, but previous analyses have not considered the continuous or simultaneous joint motion that occurs during landing and propulsion. The purpose of this study was to compare sagittal plane ankle/knee and knee/hip coordination patterns as well as ankle, knee, and hip angles and moments and vertical ground reaction force (vGRF) between the ACLR and uninjured limbs during landing and propulsion. Fifteen females and thirteen males performed a drop vertical jump from a 30 cm box placed half their height from force platforms. Coordination was compared using a modified vector coding technique and binning analysis. Kinematics and kinetics were time normalised for waveform analyses. Coordination was not different between limbs. The ACLR limb had smaller dorsiflexion angles from 11 to 16% of landing and 24 to 75% of landing and propulsion, knee flexion moments from 5 to 15% of landing, 20 to 31% of landing, and 35 to 91% of landing and propulsion, and vGRF from 92 to 94% of propulsion compared with the uninjured limb. The ACLR limb exhibited smaller dorsiflexion angles to potentially reduce the knee joint moment arm and mitigate the eccentric and concentric demands on the ACLR knee during landing and propulsion, respectively.

The Respective Effects of Vapor Pressure Deficit and Soil Moisture on Ecosystem Productivity in Southwest China

This study aims to examine the individual and combined effects of soil moisture (SM) and vapor pressure deficit (VPD) on ecosystem productivity in Southwest China. Utilizing the community land model (CLM) to simulate the regional soil moisture and vapor pressure deficit, we analyzed their impacts on ecosystem productivity through a data binning approach and employed sun-induced chlorophyll fluorescence yield (SIFyield) as a productivity indicator. Our findings highlight a significant coupling effect between SM and VPD, which diminishes with finer temporal data resolution. The data binning analysis indicates that VPD has a predominant influence on SIFyield across 70% of the study area, whereas SM is more influential in the remaining 30%. Notably, the correlation between SIFyield and SM, modulated by VPD, is stronger in forest and shrubland ecosystems, whereas in grasslands, the influence pattern is reversed, with VPD having a more significant impact. The study concludes that in Southwest China, ecosystem productivity is more significantly affected by VPD than by SM.

Abstract 1859: Diverse CD28-binding IgG and heavy chain-only antibodies for T-cell engager development

Abstract Engagement of the CD28 co-receptor by T-cell engager (TCE) molecules can enhance activation, proliferation, and anti-tumor activities, particularly in immunosuppressive tumor microenvironments. In this study, we present data on a diverse panel of CD28-binding IgG and heavy chain-only (HCAb) antibodies for T-cell co-stimulation. Our diverse panel of CD28-binding antibodies add co-stimulatory building blocks to our TCE repertoire. Using single B cell-screening, we identified fully human IgG and HCAb binders to human and non-human primate CD28 with a high degree of sequence diversity. We selected a subset of antibodies for expression and assessed binding to both human and cynomolgus CD28-expressing cells. These antibodies displayed a wide range of binding avidities in the sub-nanomolar to micromolar range, and epitope binning analysis identified seven epitope communities. Co-stimulatory activity for a subset of molecules was assessed in vitro. Antibodies displayed a wide range of crosslinked T-cell activation with the majority showing no activation independent of crosslinking. Data presented here describe a diverse set of CD28-binding antibodies ready for engineering into co-stimulatory TCEs. Combining these molecules with our TCE platform or other T-cell activating strategies will enable development of novel TCE modalities with co-stimulatory function for diverse tumor targets. Citation Format: Katherine Lam, Shirley Zhi, Lucas Kraft, Elena Vigano, Wei, Cristina Faralla, Esther Odekunle, Kelly Bullock, Erin Marshall, Melissa Cid, Grace Leung, Lindsay DeVorkin, Sherie Duncan. Diverse CD28-binding IgG and heavy chain-only antibodies for T-cell engager development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1859.

Analisis Pengaruh Variabel Nilai TIU, TWK, Dan TKP Terhadap Kelulusan SKD Pada Tes CPNS Menggunakan Analisa Bivariat Sederhana

This study aims to assess the impact of the General Intelligence Test (TIU), National Insight Test (TWK), and Personal Characteristics Test (TKP) on the success of the Basic Competency Selection (SKD) for Civil Servant Candidate (CPNS). Using data from participants in the Ministry of Law and Human Rights' SKD selection in 2023, we employed univariate analysis, simple bivariate analysis, and binning methods to comprehend variable relationships. Results reveal non-normal distributions for TIU, TWK, and TKP scores, highlighting the intricate nature of distribution in CPNS selection. While a positive correlation exists between variable values and total SKD score, binning analysis emphasizes TKP competitiveness over TIU and TWK scores. These findings offer practical insights for SKD participants to prepare effectively, with a focus on TIU, TWK, and TKP. Additionally, they contribute to transparency and effectiveness in the CPNS selection process. Further studies are recommended to explore additional factors, like age and gender, for the development of more holistic and accurate selection methods. This research supports enhancements in the adaptive and efficient CPNS SKD selection system.

Real-time breath analysis towards a healthy human breath profile.

The direct analysis of molecules contained within human breath has had significant implications for clinical and diagnostic applications in recent decades. However, attempts to compare one study to another or to reproduce previous work are hampered by: variability between sampling methodologies, human phenotypic variability, complex interactions between compounds within breath, and confounding signals from comorbidities. Towards this end, we have endeavored to create an averaged healthy human 'profile' against which follow-on studies might be compared. Through the use of direct secondary electrospray ionization combined with a high-resolution mass spectrometry and in-house bioinformatics pipeline, we seek to curate an average healthy human profile for breath and use this model to distinguish differences inter- and intra-day for human volunteers. Breath samples were significantly different in PERMANOVA analysis and ANOSIM analysis based on Time of Day, Participant ID, Date of Sample, Sex of Participant, and Age of Participant (p< 0.001). Optimal binning analysis identify strong associations between specific features and variables. These include 227 breath features identified as unique identifiers for 28 of the 31 participants. Four signals were identified to be strongly associated with female participants and one with male participants. A total of 37 signals were identified to be strongly associated with the time-of-day samples were taken. Threshold indicator taxa analysis indicated a shift in significant breath features across the age gradient of participants with peak disruption of breath metabolites occurring at around age 32. Forty-eight features were identified after filtering from which a healthy human breath profile for all participants was created.

Lower extremity and trunk sagittal plane coordination strategies and kinetic distribution during landing in males and females

ABSTRACT Force attenuation during landing requires coordinated motion of the ankle, knee, hip, and trunk, and strategies may differ between sexes. Sagittal plane coordination of the ankle/knee, knee/hip, and knee/trunk, and lower extremity and trunk kinematics and kinetics was compared throughout landing between 28 males and 28 females. Coordination was assessed with a modified vector coding technique and binning analysis. Total support moments (TSM), each joint’s percent contribution, and timing of the TSM were compared. Females landed with less isolated knee flexion in the ankle/knee, knee/hip, and knee/trunk couplings, but more simultaneous ankle/knee flexion, less simultaneous knee flexion/hip extension, and more simultaneous trunk/knee flexion. Females landed with larger plantarflexion angles from 0–16% and smaller trunk flexion angles from 0–78%. In females, absolute TSM were larger from 0–6% and smaller from 42–100%, and normalized TSM were larger from 0–8% and 26–42%. Females had greater ankle contribution to the TSM from 14–15% and 29–35%, smaller absolute peak TSM, and the peak TSM occurred earlier. Females compensated for less isolated knee flexion with greater simultaneous ankle/knee flexion early in landing and knee/trunk flexion later in landing. Coordination and TSM differences may influence force attenuation strategies and have implications for knee injury disparity between sexes.

Findings from the Longitudinal CINRG Becker Natural History Study.

Becker muscular dystrophy is an X-linked, genetic disorder causing progressive degeneration of skeletal and cardiac muscle, with a widely variable phenotype. A 3-year, longitudinal, prospective dataset contributed by patients with confirmed Becker muscular dystrophy was analyzed to characterize the natural history of this disorder. A better understanding of the natural history is crucial to rigorous therapeutic trials. A cohort of 83 patients with Becker muscular dystrophy (5-75 years at baseline) were followed for up to 3 years with annual assessments. Muscle and pulmonary function outcomes were analyzed herein. Age-stratified statistical analysis and modeling were conducted to analyze cross-sectional data, time-to-event data, and longitudinal data to characterize these clinical outcomes. Deletion mutations of dystrophin exons 45-47 or 45-48 were most common. Subgroup analysis showed greater pairwise association between motor outcomes at baseline than association between these outcomes and age. Stronger correlations between outcomes for adults than for those under 18 years were also observed. Using cross-sectional binning analysis, a ceiling effect was seen for North Star Ambulatory Assessment but not for other functional outcomes. Longitudinal analysis showed a decline in percentage predicted forced vital capacity over the life span. There was relative stability or improved median function for motor functional outcomes through childhood and adolescence and decreasing function with age thereafter. There is variable progression of outcomes resulting in significant heterogeneity of the clinical phenotype of Becker muscular dystrophy. Disease progression is largely manifest in adulthood. There are implications for clinical trial design revealed by this longitudinal analysis of a Becker natural history dataset.

Loss-Aware Histogram Binning and Principal Component Analysis for Customer Fleet Analytics

Loss-Aware Histogram Binning and Principal Component Analysis for Customer Fleet Analytics

Metabolic characteristics and the cross-feeding of Bacillus and Ca. Brocadia in an integrated partial denitrification-anammox reactor driven by glycerol

Integrated partial denitrification-anammox (PD/A) process was considered as a novel strategy for low ammonia wastewater treatment, but the potential roles of the functional bacteria were still unclear. In this study, metagenomic binning analysis coupling with metatranscriptomic analysis was used to reveal the metabolic patterns in a stable operating PD/A system driven by glycerol. The cross-feeding between Bacillus and Candidatus Brocadia, the two dominant functional bacteria that contributed 81.1 % of the total gene expression, was constructed. Bacillus exhibited high nitrite production potential in the assimilatory nitrate reduction pathway instead of partial denitrification. And Bacillus was the main glycerol utilizer capable of synthesizing intracellular glycogen and polyhydroxybutyrate, which was also the potential branched-chain amino acids and B-vitamins supplier. Candidatus Brocadia as an anammox bacteria surprisingly expressed the activity of 3-phosphate glycerol (obtained from Bacillus) degradation. This study provided a new understanding of the metabolic patterns and interactions in PD/A system.

Tire particles and its leachates: Impact on antibiotic resistance genes in coastal sediments

Tire particles (TPs), a significant group of microplastics, can be discharged into the coastal environments in various ways. However, our understanding of how TPs impact the antibiotic resistance and pathogenic risks of microorganisms in coastal sediments remains limited. In this study, we used metagenomics to investigate how TPs and their leachates could affect the prevalence of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and their potential risks to the living creatures such as soil invertebrates and microorganisms in the coastal sediments. We discovered that TP addition significantly increased the abundance and diversity of ARGs and VFGs in coastal sediments, with raw TPs displayed higher impacts than TP leachates and TPs after leaching on ARGs and VFGs. With increasing TP exposure concentrations, the co-occurrence frequency of ARGs and mobile genetic elements (MGEs) in the same contig also increased, suggesting that TPs could enhance the dispersal risk of ARGs. Our metagenome-based binning analysis further revealed that exposure to TPs increased the abundance of potentially pathogenic antibiotic-resistant bacteria (PARB). In addition, chemical additives of TP leachates (e.g., Zn and N-cyclohexylformamide) significantly affected the changes of ARGs in the pore water. In summary, our study provides novel insights into the adverse effects of TP pollutions on aggravating the dissemination and pathogenic risks of ARGs and PARB in the coastal environment.

Metagenomic binning analyses of swine manure composting reveal mechanism of nitrogen cycle amendment using kaolin

The efficient control of nitrogen loss in composting and the enhancement of product quality have become prominent concerns in current research. The positive role of varying concentrations kaolin in reducing nitrogen loss during composting was revealed using metagenomic binning combined with reverse transcription quantitative polymerase chain reaction. The results indicated that the addition of 0.5 % kaolin significantly (P < 0.05) up-regulated the expression of nosZ and nifH on day 35, while concurrently reducing norB abundance, resulting in a reduction of NH3 and N2O emissions by 61.4 % and 17.5 %, respectively. Notably, this study represents the first investigation into the co-occurrence of nitrogen functional genes and heavy metal resistance genes within metagenomic assembly genomes during composting. Emerging evidence indicates that kaolin effectively impedes the binding of Cu/Zn to nirK and nosZ gene reductases through passivation. This study offers a novel approach to enhance compost quality and waste material utilization.

Longitudinal Quantification of Sub‐Regional Hippocampal Amyloid‐Beta Burden in Ex‐Vivo slices from the AppNL‐G‐F Mouse Model of Alzheimer’s Disease

AbstractBackgroundAmyloid‐beta (Aβ) pathology is suggested to precede the onset of clinical Alzheimer’s disease symptoms by up to two decades. The humanised AppNL‐G‐F knock‐in model of amyloidopathy has accelerated pathogenesis and can be used to study AD progression. Here we used it to quantify the temporal and spatial characteristics of Aβ plaque accumulation as they first appear in the hippocampus, and as pathology continues to develop.MethodAppNL‐G‐F knock‐in mice and wild‐type mice at 1, 3, 6, and 9 months of age were transcardially perfused with PBS followed by 4% paraformaldehyde (PFA), followed by preparation of coronal slices for immunohistochemistry analysis. Samples were stained with anti‐Aβ antibody (6E10) together with a neuronal marker, NeuN, and DAPI. Images were taken of sub‐hippocampal regions (CA1, CA3, DG), in left/right hemispheres, and ventral/dorsal segments using a confocal microscope (Leica SP8). Summation of intensity across Z‐stacks in Fiji was used to quantify Aβ plaques in regions of interest.ResultWe found age to be a statistically significant factor on determining area density, with hippocampal deposition observed by 3 months. Bin analysis showed a near‐exponential reduction in plaque number with increasing plaque size, increasing with age. Regionally, there was an increase in plaque density in CA3, with non‐linear regression analysis indicating area density for CA3 is most strongly correlated with age. Within the CA1 region, the densest plaque formation was in the pyramidal cell layer. Further analysis at the aged 9‐month time point suggested a differential pathology across the axial plane and greater left‐hemispheric lateralisation.ConclusionThis data provides further evidence for the protracted timeline to which AppNL‐G‐F knock‐in mice recapitulate key AD neuropathologies including insoluble amyloidosis beginning before 3 months in the hippocampus. It also indicates potentially novel differential sub‐regional Aβ accumulation patterns, axial variations, and hemispheric asymmetries, offering mechanistic insights for plaque localisation and differential susceptibility to Aβ. This could aid advancement of Αβ‐targeting therapies.

Microbial community dynamics and metagenomics reveal the potential role of unconventional functional microorganisms in nitrogen and phosphorus removal biofilm system

The conventional functional microorganisms for nitrogen and phosphorus removal, such as Nitrosomonas, Nitrobacter, Nitrospira and Candidatus Accumulibacter, were hotspots in past research. However, the role of diverse unconventional functional microorganisms was neglected. In this study, a biofilm system was developed to explore the potential role of unconventional functional microorganisms in nutrients removal. According to the results of microbial community dynamics and metagenomics, complete ammonia oxidizing (comammox) bacteria was 20 times more abundant than ammonia-oxidizing bacteria (AOB) at day 121 and its abundance of amoA gene was almost the same as AOB. Although Nitrospira dominated the nitrite-oxidizing bacteria (NOB), diverse unconventional nxrB-containing microorganisms, particularly Chloroflexi, also significantly contributed to the nitrite oxidation. Binning analysis showed that Myxococcota-affiliated Haliangium had the necessary genes owns by phosphorus-accumulating organisms (PAO) and was likely to be the primary PAO since its abundance (6.38 %) was much higher than other conventional PAO (0.70 %). Comparing metagenome-assembled genomes of comammox bacteria with AOB and ammonia-oxidizing archaea (AOA), it possessed potential metabolic versatility in hydrogen and phosphorus, which may be the primary reason for the positive effect of the alternating anaerobic and aerobic conditions on the enrichment of comammox bacteria. Collectively, our findings broaden the understanding on the microbial mechanism of nitrogen and phosphorus removal in biofilm system.

Discovery of neutralizing SARS-CoV-2 antibodies enriched in a unique antigen specific B cell cluster.

Despite development of effective SARS-CoV-2 vaccines, a sub-group of vaccine non-responders depends on therapeutic antibodies or small-molecule drugs in cases of severe disease. However, perpetual viral evolution has required continuous efficacy monitoring as well as exploration of new therapeutic antibodies, to circumvent resistance mutations arising in the viral population. We performed SARS-CoV-2-specific B cell sorting and subsequent single-cell sequencing on material from 15 SARS-CoV-2 convalescent participants. Through screening of 455 monoclonal antibodies for SARS-CoV-2 variant binding and virus neutralization, we identified a cluster of activated B cells highly enriched for SARS-CoV-2 neutralizing antibodies. Epitope binning and Cryo-EM structure analysis identified the majority of neutralizing antibodies having epitopes overlapping with the ACE2 receptor binding motif (class 1 binders). Extensive functional antibody characterization identified two potent neutralizing antibodies, one retaining SARS-CoV-1 neutralizing capability, while both bind major common variants of concern and display prophylactic efficacy in vivo. The transcriptomic signature of activated B cells harboring broadly binding neutralizing antibodies with therapeutic potential identified here, may be a guide in future efforts of rapid therapeutic antibody discovery.