Biology subjects

Dai, Z.

Publications and source records attributed to Dai, Z..

At least 109 records · Page 6Linked to original sources

bioRxiv2021

Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria.

Loss of basic utilities, such as drinking water and electricity distribution, were sustained for months in the aftermath of Hurricane Marias (HM) landfall in Puerto Rico (PR) in September 2017. The goal of this study was to assess if there was deterioration in biological quality of drinking water due to these disruptions. This study characterized the microbial composition of drinking water following HM across nine drinking water systems (DWSs) in PR and utilized an extended temporal sampling campaign to determine if changes in the drinking water microbiome were indicative of HM associated disturbance followed by recovery. In addition to monitoring water chemistry, the samples were subjected to culture independent targeted and non-targeted microbial analysis including quantitative PCR (qPCR) and genome-resolved metagenomics. The qPCR results showed that residual disinfectant was the major driver of bacterial concentrations in tap water with marked decrease in concentrations from early to late sampling timepoints. While Mycobacterium avium and Pseudomonas aeruginosa were not detected in any sampling locations and timepoints, genetic material from Leptospira and Legionella pneumophila were transiently detected in a few sampling locations. The majority of metagenome assembled genomes (MAGs) recovered from these samples were not associated with pathogens and were consistent with bacterial community members routinely detected in DWSs. Further, whole metagenome-level comparisons between drinking water samples collected in this study with samples from other full-scale DWS indicated no significant deviation from expected community membership of the drinking water microbiome. Overall, our results suggest that disruptions due to HM did not result in significant and sustained deterioration of biological quality of drinking water at our study sites. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/442998v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@100c1e9org.highwire.dtl.DTLVardef@bae402org.highwire.dtl.DTLVardef@1cf41bborg.highwire.dtl.DTLVardef@1e46105_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Loss of Endothelial HIF-Prolyl hydroxylase 2 (PHD2) Induces Cardiac Hypertrophy and Fibrosis

BackgroundCardiac hypertrophy and fibrosis are common adaptive responses to injury and stress, eventually leading to heart failure. Hypoxia signaling is important to the (patho)physiological process of cardiac remodeling. However, the role of endothelial Prolyl-4 hydroxylase 2 (PHD2)/hypoxia inducible factors (HIFs) signaling in the pathogenesis of heart failure remains elusive. Methods and ResultsMice with Tie2-Cre-mediated deletion of Egln1 (encoding PHD2) (Egln1Tie2Cre) exhibited left ventricular (LV) hypertrophy evident by increased thickness of anterior and posterior wall and LV mass, as well as cardiac fibrosis. Tamoxifen-induced endothelial Egln1 deletion in adult mice also induced LV hypertrophy and fibrosis. Additionally, we observed a marked decrease of PHD2 expression in heart tissues and cardiovascular endothelial cells from patients with cardiomyopathy. Moreover, genetic ablation of Hif2a but not Hif1a in Egln1Tie2Cre mice normalized cardiac size and function. RNA sequencing analysis also demonstrated HIF-2 as a critical mediator of signaling related to cardiac hypertrophy and fibrosis. Pharmacological inhibition of HIF-2 attenuated cardiac hypertrophy and fibrosis in Egln1Tie2Cre mice. ConclusionsThe present studies define for the first time an unexpected role of endothelial PHD2 deficiency in inducing cardiac hypertrophy and fibrosis in a HIF-2 dependent manner. PHD2 was markedly decreased in cardiovascular endothelial cells in patients with cardiomyopathy. Thus, targeting PHD2/HIF-2 signaling may represent a novel therapeutic approach for the treatment of pathological cardiac hypertrophy and failure.

physiology↗

bioRxiv2021

Aberrant Temporal-spatial Patterns to Sad expressions in Major Depressive Disorders via Hidden Markov Model

BackgroundThe pathological mechanisms of Major depressive disorders (MDD) is associated with over-expressing of negative emotions, and the overall temporal-spatial patterns underlying over-representation in depression still remained to be revealed to date. We hypothesized that the aberrant spatio-temporal attributes of the process of sad expressions relate to MDD and help to detect depression severity. MethodsWe enrolled a total of 96 subjects including 47 MDDs and 49 healthy controls (HCs), and recorded their Magnetoencephalography data under a sad expressions recognition task. A hidden Markov model (HMM) was applied to separate the whole neural activity into several brain states, then to characterize the dynamics. To find the disrupted spatial-temporal features, power estimations and fractional occupancy of each state were contrasted between MDDs and HCs. ResultsThree states were found over the period of emotional stimuli processing procedure. The visual state was mainly distributed in early stage (0 - 270ms) and the limbic state in middle and later stage (270ms - 600ms) of the task, while the fronto-parietal state remained a steady proportion across the whole period. MDDs activated statistically more in limbic system during limbic state (p = 0.0045) and less in frontoparietal control network during fronto-parietal state (p = 5.38*10-5) relative to HCs. Hamilton-Depression-Rating Scale scores was significantly correlated with the predicted severity value using the state descriptors (p = 0.0062, r = 0.3933). DiscussionAs human brain exhibited varied activation patterns under the negative stimuli, MDDs expressed disrupted temporal-spatial activated patterns across varied stages involving the primary visual perception and emotional contents processing compared to HCs, indicting disordered regulation of brain functions. Furthermore, descriptors built by HMM could be potential biomarkers for identifying the severity of depression disorders.

neuroscience↗

bioRxiv2020

Extracting and Interpreting the Effects of Higher Order Sequence Features on Peptide MHC Binding

Understanding the factors contributing to peptide MHC (pMHC) affinity is critical for the study of immune responses and the development of novel therapeutics. Developments in yeast display platforms have enabled the collection of pMHC binding data for vast libraries of peptides. However, methods for interpreting this data are still at an early stage. In this work we propose an approach for extracting peptide sequence features that affect pMHC binding from such datasets. In the process we develop the theoretical framework for fitting and interpreting these features. We demonstrate that these features accurately capture the kinetics underlying pMHC binding, and can be used to predict pMHC binding well enough to rival the current state of the art. We then analyze the extracted factors and show that they correlate with our current structural understanding of MHC molecules. Finally, we discuss the implication these factors have on the complexity of peptide engineering.

immunology↗

bioRxiv2020

Blocking of EGFR Signaling is a Latent Strategy for the Improvement of Prognosis of HPV Induced Cancer

Human papillomavirus (HPV) is a dsDNA virus and its high-risk subtypes increase cancer risks. Yet, the mechanism of HPV infection and pathogenesis still remain unclear. Therefore, understanding the molecular mechanisms, and the pathogenesis of HPV are crucial in the prevention of HPV related cancers. In this study, we analyzed cervix squamous cell carcinoma (CESC) and head and neck carcinoma (HNSC) combined data to investigate various HPV induced cancer common feature. We showed that epidermal growth factor receptor (EGFR) was downregulated in HPV positive (HPV+) cancer, and that HPV+ cancer patients exhibited better prognosis than HPV negative (HPV-) cancer patients. Our study also showed that TP53 mutation rate is lower in HPV+ cancer than in HPV- cancer and that TP53 can be modulated by HPV E7 protein. However, there was no significant difference in the expression of wildtype TP53 in both groups. Subsequently, we constructed HPV-human interaction network and found that EGFR is a critical factor. From the network, we also noticed that EGFR is regulated by HPV E7 protein and hsa-miR-944. Moreover, while phosphorylated EGFR is associated with a worse prognosis, EGFR total express level is not significantly correlated with prognosis. This indicates that EGFR activation will induce a worse outcome in HPV+ cancer patients. Further enrichment analysis showed that EGFR downstream pathway and cancer relative pathway are diversely activated in HPV+ cancer and HPV- cancer. In summary, HPV E7 protein downregulates EGFR that downregulates phosphorylated EGFR and inhibit EGFR related pathways which in turn and consequently induce better prognosis. ImportanceAlthough HPV infection has been studied in various cancer types, there are only limited studies that have focused on the common effect of HPV related cancer. Consequently, this study focused on CESC and HNSC, two cancer types with high HPV infection proportion in cohort, thereby, intending to dig out the common effects and mechanisms of HPV+ cancers. Unlike some virus-human interaction prediction studies, the P-HIPSter database provides virus-human protein interaction based on protein structure prediction. Through this data, our interaction network was able to uncover previously unnoticed protein interactions. Our finding revealed that HPV infection caused various gene expression differences, and a great amount of which interact with EGFR, a cancer related gene. Therefore, since EGFR is associated with HPV+ cancer patients survival, some FDA proved EGFR inhibitors would be potential anti-HPV drugs.

microbiology↗

bioRxiv2020

Transcription factor-target relationships complicated by knockout analysis

Knockout analysis is a common tool to reveal transcription factor (TF) functions. However, such a reverse genetic analysis based on observed phenotype changes in mutant cell may lead to a misunderstanding of TF wild-type functions. Here, a model was proposed, in which the knockout-observed TF-target regulatory relationships might only occur in mutant cell, and they do not reflect TF normal functions in wild-type cell. Actually, the knockout of one TF might release another TF which is the protein-protein interaction partner of the deleted TF. The free TF could bind its new target genes and cause their significant expression changes. These seemingly TF knockout affected genes are thus not directly regulated by the deleted TF, but are gain-of-regulated genes of the latter TF in mutant cell. Based on this model, multiple sources of genome-wide data were used to identify 20 such TF pairs, and one pair was validated using other independent data. TF wild-type regulatory genes are not associated with their gain-of-regulated genes. My findings revealed TF-target relationships complicated by TF knockout analysis.

genetics↗

bioRxiv2020

Machine learning optimization of peptides for presentation by class II MHCs

T cells play a critical role in normal immune responses to pathogens and cancer and can be targeted to MHC-presented antigens via interventions such as peptide vaccines. Here, we present a machine learning method to optimize the presentation of peptides by class II MHCs by modifying the peptides anchor residues. Our method first learns a model of peptide affinity for a class II MHC using an ensemble of deep residual networks, and then uses the model to propose anchor residue changes to improve peptide affinity. We use a high throughput yeast display assay to show that anchor residue optimization successfully improved peptide binding.

immunology↗

bioRxiv2020

Fire effect and its legacy modulate soil bacterial and fungal communities in Chinese boreal forests along a chronosequence

Wildfire has increasingly profound and pervasive consequences for forest ecosystems via directly altering soil physicochemical properties and modulating microbial community. In this study, we examined the changes in soil properties and microbial community at different periods after highly severe wildfire events (44 plots, 113 samples) in the Chinese Great Khingan Mountains. We also separated charcoals from burnt soils to establish the relationship between soil microbes and the microbes colonized on the charcoal. Wildfire significantly altered bacterial and fungal community structures across a 29-year chronosequence. The network analysis revealed that from 17 years after fire, the complexity and connectivity of bacterial and fungal communities were significantly increased. Differential abundance analysis suggested that bacterial and fungal OTUs were enriched or depleted only during 0-4 years after fire. In addition, soil factors, including soil pH, total C and N, soil water content, and dissolved C and N, are key determinants of soil bacterial and fungal communities from 17 years after fire. The fire-derived charcoals provided a new and unusual niche for microbial colonization and charcoal microbes had a significantly different community structure from the burnt soil microbes. Our data suggest that soil bacterial and fungal communities changed dramatically during the recovery from fire events in terms of the abundance and co-occurrence networks in the boreal forest ecosystems. ImportancePervious research has reported fire altered soil microbial community composition and function during short-term succession in boreal forests. However, the long-term effect of fire and fire-derived charcoals which are regarded as fire legacy effect on soil bacterial and fungal communities composition and structure have not previously been shown. Understanding how soil microbes particularly the keystone taxa and determinative soil factors, respond to fire and its legacy matter charcoal, is critical for predicting how future fire influences soil nutrient transformations and biological processes. We accessed time chronosequence to examine the effect of fire history on soil microbial abundance and co-occurrence network. These findings suggest that soil microbes can be reshaped by fire and its legacy effect of fire-derived charcoal even in the long periods after fire and provide further insights into fire and its legacy effect.

ecology↗

bioRxiv2020

Polarized endosome dynamics engage cytosolic Par-3 and dynein during asymmetric division

Asymmetric cell division (ACD), which produces two daughters with different fates, is fundamental for generating cellular diversity. In the developing embryos of both invertebrates and vertebrates, asymmetrically dividing progenitors generate daughter cells with differential activity of Notch signaling1-7, a key regulator of cell fate decisions8,9. The cell polarity regulator Par-3 is critical for establishing this Notch asymmetry1,4,6, but the underlying mechanisms are not understood. Here, employing in vivo time-lapse imaging in the developing zebrafish forebrain during the mitotic cycle of radial glia, the principal vertebrate neural stem cells10,11, we show that during ACD, endosomes containing the Notch ligand Delta D (Dld) undergo convergent movement toward the cleavage plane, followed by preferential segregation into the posterior (and subsequently basal) Notchhi daughter. This asymmetric segregation requires the activity of Par-3 and the dynein motor complex. Employing label-retention expansion microscopy, we further detect Par-3 in the cytosol in association with the dynein light intermediate chain 1 (DLIC1) on Dld endosomes, suggesting a direct involvement of Par-3 in dynein-mediated polarized transport of Notch signaling endosomes. Our data reveal an unanticipated mechanism by which Par-3 regulates cell fate decision by directly polarizing Notch signaling components during ACD.

cell biology↗

bioRxiv2020

Cellular Stress Signaling Activates Type-I IFN Response Through FOXO3-regulated Lamin Posttranslational Modification

Neural stem/progenitor cells (NSPCs) persist over the lifespan while encountering constant challenges from age or injury related brain environmental changes, including elevated oxidative stress. A time-dependent stress response that regulates the dynamic balance between quiescence and differentiation is thus essential to preserve NSPC long-term regenerative potential. Here we report that acutely elevated cellular oxidative stress in NSPCs suppresses neurogenic differentiation through induction of FOXO3-mediated cGAS/STING and type I interferon (IFN-I) responses. We show that oxidative stress activates FOXO3 promoting upregulation of its transcriptional target glycine-N-methyltransferase (GNMT) and thus depletion of s-adenosylmethionine (SAM), a key co-substrate involved in methyl group transfer reactions. Mechanistically, we demonstrate that reduced intracellular SAM availability disrupts carboxymethylation and maturation of nuclear lamin, which trigger cytosolic release of chromatin fragments and subsequent activation of the cGAS/STING/IFN-I cascade. Together, our findings suggest the FOXO3-GNMT/SAM-lamin-cGAS/STING-IFN-I signaling cascade as a critical stress response program that preserves its long-term regenerative potential.

cell biology↗

bioRxiv2020

Generation and Validation of Versatile Inducible CRISPRi Embryonic Stem Cell and Mouse Models

CRISPR-Cas9 has been widely used far beyond genome editing. Fusions of deactivated Cas9 (dCas9) to transcription effectors enable interrogation of the epigenome and controlling of gene expression. However the large transgene size of dCas9-fusion hinders its applications especially in somatic tissues. Here, we develop a robust CRISPR interference (CRISPRi) system by transgenic expression of doxycycline (Dox) inducible dCas9-KRAB in mouse embryonic stem cells (iKRAB ESC). After introduction of specific gRNAs, the induced dCas9-KRAB efficiently maintains gene inactivation, though it exerts modest effects on active gene expression. Proper timing of Dox addition during cell differentiation or reprogramming allows us to study or screen spatiotemporally activated promoters or enhancers and thereby the gene functions. Furthermore, taking the ESC for blastocyst injection, we generate an iKRAB knockin (KI) mouse model that enables shut-down of gene expression and loss-of-function studies ex vivo and in vivo by a simple transduction of gRNAs. Thus, our inducible CRISPRi ESC line and KI mouse provide versatile and convenient platforms for functional interrogation and high-throughput screens of specific genes and potential regulatory elements in the setting of development or diseases.

genetics↗

bioRxiv2020

A novel full-reduced HMGB1 and kartogenin-containing bio-active scaffold for meniscus regeneration

A novel bio-active scaffold for enhancing wounded meniscus healing has been developed by combination of High mobility group box 1 protein (HMGB1) and kartogenin (KGN) with alginate gel. The properties of the bio-active scaffold were also investigated using an in vitro cell culture model and in vivo rat wounded meniscus healing model. This HMGB1-KGN-containing bioactive scaffold released HMGB1 and KGN into wound area and kept high concentrations of HMGB1 and KGN in the system for more than two weeks. This HMGB1-KGN-containing bioactive scaffold also activated rat bone marrow stem cells (BMSCs) from G0 to GAlert stage and promoted cell proliferation as evidenced by 5-bromo-2-deoxyuridine (BrdU) incorporation testing. Our results also demonstrated that the HMGB1-KGN-containing bioactive scaffold induced cell migration in vitro and recruited the cells to wound area to promote wounded rat meniscus healing in vivo.

bioengineering↗

bioRxiv2020

Neuron-glia Integrity: Functional Assessment, Molecular Underpinnings, and Implication for Higher Brain Functions

We developed a theory of neuron-glia integrity to underline the fact that neurons and glia cells work together in the central nervous system. Here we substantiated this theory and exemplified the implication of intact neuron-glia integrity for higher brain functions. An animal model of maternal separation with early weaning (MSEW) was applied to neonatal rats to mimic early life neglect and abuse in humans. Behavioral performance of rats was evaluated at adulthood, followed by functional assessments of neuron-glia integrity in living rats, and the demonstration of molecular underpinnings of impaired neuron-glia integrity in MSEW rats. MSEW rats showed higher levels of anxiety and explorative activity, higher glutamate level, but lower GABA level in PFC and hippocampus. MSEW procedure down-regulated protein levels of GLT-1 and ATP-, but up-regulated GAD65 and GS, while had no effects on GLAST and PAG. Moreover, it reduced the fractional anisotropy values in various brain regions, in addition to increasing NAA levels. Concurrently, MSEW led to hypomyelination in PFC as evidenced by relevant cellular and molecular changes.

neuroscience↗

bioRxiv2019

Differences in berry primary and secondary metabolisms identified by transcriptomic and metabolic profiling of two table grape color somatic variants

Anthocyanins are flavonoids responsible for the color of berries in skin-pigmented grapevine (Vitis vinifera L.). Due to the widely adopted vegetative propagation of this species, somatic mutations occurring in meristematic cell layers can be fixed and passed into the rest of the plant when cloned. In this study we focused on the transcriptomic and metabolic differences between two color somatic variants. Using microscopic, metabolic and mRNA profiling analyses we compared the table grape cultivar (cv.) Red Globe (RG, with purplish berry skin) and cv. Chimenti Globe (CG, with a contrasting reddish berry skin color). As expected, significant differences were found in the composition of flavonoids and other phenylpropanoids, but also in their upstream precursors shikimate and phenylalanine. Among primary metabolites, sugar phosphates related with sucrose biosynthesis were less accumulated in cv. CG. The red-skinned cv. CG only contained di-hydroxylated anthocyanins (i.e. peonidin and cyanidin) while the tri-hydroxylated derivatives malvidin, delphinidin and petunidin were absent, in correlation to the reddish cv. CG skin coloration. Transcriptomic analysis showed alteration in flavonoid metabolism and terpenoid pathways and in primary metabolism such as sugar content. Eleven flavonoid 35-hydroxylase gene copies were down-regulated in cv. CG. This family of cytochrome P450 oxidoreductases are key in the biosynthesis of tri-hydroxylated anthocyanins. Many transcription factors appeared down-regulated in cv. CG in correlation to the metabolic and transcriptomic changes observed. The use of molecular markers and its confirmation with our RNA-seq data showed the exclusive presence of the null MYBA2 white allele (i.e. homozygous in both L1 and L2 layers) in the two somatic variants. Therefore, the differences in MYBA1 expression seem sufficient for the skin pigmentation differences and the changes in MYBA target gene expression in cv. Chimenti Globe.

plant biology↗

bioRxiv2019

Quantitative analysis of the physiological contributions of glucose to the TCA cycle

ABSTRACTThe carbon source for catabolism in vivo is a fundamental question in metabolic physiology. Limited by data and rigorous mathematical analysis, controversy exists over the nutritional sources for carbon in the tricarboxylic acid (TCA) cycle under physiological settings. Using isotope-labeling data in vivo across several experimental conditions, we construct multiple models of central carbon metabolism and develop methods based on metabolic flux analysis (MFA) to solve for the preferences of glucose, lactate, and other nutrients used in the TCA cycle across many tissues. We show that in nearly all circumstances, glucose contributes more than lactate as a nutrient source for the TCA cycle. This conclusion is verified in different animal strains from different studies, different administrations of 13C glucose, and is extended to multiple tissue types. Thus, this quantitative analysis of organismal metabolism defines the relative contributions of nutrient fluxes in physiology, provides a resource for analysis of in vivo isotope tracing data, and concludes that glucose is the major nutrient used for catabolism in mammals.Competing Interest StatementThe authors have declared no competing interest.View Full Text

systems biology↗

bioRxiv2019

Disinfection exhibits systematic impacts on the drinking water microbiome.

Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without the use of a disinfectant. The impact of these contrasting approaches on the drinking water microbiome is not systematically understood. We utilized genome-resolved metagenomics to compare the structure, metabolic traits, and population genomes of drinking water microbiomes across multiple full-scale drinking water systems utilizing these two-distinct microbial growth control strategies. Microbial communities cluster together at the structural- and functional potential-level based on the presence or absence of a disinfectant residual. Disinfectant residual concentrations alone explained 17 and 6.5% of the variance in structure and functional potential of the drinking water microbiome, respectively, despite including samples from multiple drinking water systems with variable source waters and source water communities, treatment strategies, and chemical compositions. The drinking water microbiome is structurally and functionally less diverse and less variable across disinfected systems as compared to non-disinfected systems. While bacteria were the most abundant domain, archaea and eukaryota were more abundant in non-disinfected and disinfected systems, respectively. Community-level differences in functional potential were driven by enrichment of genes associated with carbon and nitrogen fixation in non-disinfected systems and {gamma}-aminobutyrate metabolism in disinfected systems which may be associated with the recycling of amino acids. Metagenome-assembled genome-level analyses for a subset of phylogenetically related microorganisms suggests that disinfection may select for microorganisms capable of using fatty acids, presumably from microbial decay products, via the glyoxylate cycle. Overall, we find that disinfection exhibits systematic and consistent selective pressures on the drinking water microbiome and may select for microorganisms able to utilize microbial decay products originating from disinfection inactivated microorganisms.

microbiology↗

bioRxiv2019

Identification of a Central Neural Circuit that Regulates Anxiety-induced Bone Loss

The homeostasis of bone metabolism is finely regulated by the central nervous system and recent studies have suggested that mood disorders, such as anxiety, are closely related to bone metabolic abnormalities; however, our understanding of central neural circuits regulating bone metabolism is still largely limited. In this study, we first demonstrate that confined isolation of human participants under normal gravity resulted in decreased bone density and elevated anxiety levels. We then used an established mouse model to dissect the neural circuitry regulating anxiety-induced bone loss. Combining electrophysiological, optogenetic and chemogenetic approaches, we demonstrate that GABAergic neural circuitry in ventromedial hypothalamus (VMH) modulates anxiety-induced bone loss; importantly, the GABAergic input in VMHdm arose from a specific group of somatostatin neurons in the bed nucleus of the stria terminalis (BNST), which is both indispensable for anxiety-induced bone loss and able to trigger bone loss in the absence of stressors. VGLUT2 neurons in Nucleus tractus solitaries (NTS) and peripheral sympathetic system were employed by this BNST-VMH neural circuit to regulate anxiety-induced bone loss. Overall, we uncovered new GABAergic neural circuitry from the forebrain to hypothalamus, used in the regulation of anxiety-induced bone loss, and revealed a population of somatostatin neurons in BNST not previously implicated in bone mass regulation. These findings thus identify the underlying central neural mechanism of psychiatric disorders, such as anxiety, that influences bone metabolism at the circuit level.\n\nOne Sentence SummaryIdentification of a new GABAergic neural circuit from forebrain to hypothalamus used for regulation of anxiety-induced bone loss.

neuroscience↗

bioRxiv2019

Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems.

The discovery of the complete ammonia oxidizing (comammox) bacteria overturns the traditional two-organism nitrification paradigm which largely underpins the design and operation of nitrogen removal during wastewater treatment. Quantifying the abundance, diversity, and activity of comammox bacteria in wastewater treatment systems is important for ensuring a clear understanding of the nitrogen biotransformations responsible for ammonia removal. To this end, we conducted a yearlong survey of 14 full-scale nitrogen removal systems including mainstream conventional and simultaneous nitrification-denitrification and side-stream partial nitrification-anammox systems with varying process configurations. Metagenomics and genome-resolved metagenomics identified comammox bacteria in mainstream conventional and simultaneous nitrification-denitrification systems, with no evidence for their presence in side-stream partial nitrification-anammox systems. Further, comammox bacterial diversity was restricted to clade A and these clade A comammox bacteria were detected in systems with long solids retention times (>10 days) and/or in the attached growth phase. Using a newly designed qPCR assay targeting the amoB gene of clade A comammox bacteria in combination with quantitation of other canonical nitrifiers, we show that long solids retention time is the key process parameter associated with the prevalence and abundance of comammox bacteria. The increase in comammox bacterial abundance was not associated with concomitant decrease in the abundance of canonical nitrifiers; however, systems with comammox bacteria showed significantly better and temporally stable ammonia removal compared to systems where they were not detected. Finally, in contrast to recent studies, we do not find any significant association of comammox bacterial prevalence and abundance with dissolved oxygen concentrations in this study.\n\nHighlightsO_LIClade A comammox bacteria were detected in wastewater nitrogen removal systems.\nC_LIO_LINew qPCR assay targeting the amoB gene of clade A comammox bacteria was developed.\nC_LIO_LIComammox bacteria are prevalent in mainstream conventional and simultaneous nitrification-denitrification systems with long solids retention times (>10 days).\nC_LIO_LIComammox bacteria were not detected in sidestream partial nitrification-anammox systems included in this study.\nC_LI\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC=\"FIGDIR/small/696351v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@3228c9org.highwire.dtl.DTLVardef@113dfb8org.highwire.dtl.DTLVardef@1c4adaforg.highwire.dtl.DTLVardef@166f997_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACT\n\nC_FIG

microbiology↗