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Qiu, Y.

Publications and source records attributed to Qiu, Y..

At least 109 records · Page 6Linked to original sources
bioRxiv2024

Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity

Chemical modifications in mRNAs, such as pseudouridine (psi), can control gene expression. Yet, we know little about how they are regulated, especially in neurons. We applied nanopore direct RNA sequencing to investigate psi dynamics in SH-SY5Y cells in response to two perturbations that model a natural and unnatural cellular state: retinoic-acid-mediated differentiation (healthy) and exposure to the neurotoxicant, lead (unhealthy). We discovered that the expression of some psi writers change significantly in response to physiological conditions. We also found that globally, lead-treated cells have more psi sites but lower relative occupancy than untreated cells and differentiated cells. Interestingly, examples of highly plastic sites were accompanied by constant expression for psi writers, suggesting trans-regulation. Many positions were static throughout all three cellular states, suggestive of a "housekeeping" function. This study enables investigations into mechanisms that control psi modifications in neurons and its possible protective effects in response to cellular stress.

systems biology↗
bioRxiv2024

Genome-wide association study elucidates the genetic architecture of manganese tolerance in Brassica napus

Brassica napus (canola) is a significant contributor to the worlds oil production and is cultivated across continents, yet acidic soils with Al3+ and Mn2+ toxicities limit its production. The genetic determinants underlying acidic soil tolerance in canola are unknown and require to be uncovered for canola breeding and production. Here, through comprehensive phenotyping, whole genome resequencing, and genome-wide association analysis, we identified three QTLs for tolerance to Mn2+ toxicity on chromosomes A09, C03, and C09. Allelism tests between four tolerance sources confirmed that at least one locus on A09 controls Mn2+ tolerance in B. napus. Integrated analysis of genomic and expression QTL and Mn2+ tolerance data reveals that BnMTP8.A09, in conjunction with BnMATE.C03, BnMTP8.C04 and BnMTP8.C08, play a central role in conferring Mn2+ tolerance in B. napus. Gene expression analysis revealed a high correlation (R2 = 0.74) between Mn2+ tolerance and the BnMTP8.A09 expression. Yeast complementation assays show that BnMTP8.A09 can complement manganese-hypersensitive yeast mutant strain PMR1{Delta} and restore Mn2+ tolerance to wild-type levels. Inductively coupled plasma mass spectrometry revealed that Mn2+ tolerant accessions accumulate less Mn in the shoots compared to Mn2+ sensitives, suggesting that the BnMTP8.A09 transporter likely sequesters Mn2+ into the tonoplast. Taken together, our research unveils the genetic architecture of Mn2+ tolerance and identifies BnMTP8.A09 as a major gene imparting tolerance to Mn2+ toxicity in B. napus.

plant biology↗
bioRxiv2024

Have AI-Generated Texts from LLM Infiltrated the Realm of Scientific Writing? A Large-Scale Analysis of Preprint Platforms

Since the release of ChatGPT in 2022, AI-generated texts have inevitably permeated various types of writing, sparking debates about the quality and quantity of content produced by such large language models (LLM). This study investigates a critical question: Have AI-generated texts from LLM infiltrated the realm of scientific writing, and if so, to what extent and in what setting? By analyzing a dataset comprised of preprint manuscripts uploaded to arXiv, bioRxiv, and medRxiv over the past two years, we confirmed and quantified the widespread influence of AI-generated texts in scientific publications using the latest LLM-text detection technique, the Binoculars LLM-detector. Further analyses with this tool reveal that: (1) the AI influence correlates with the trend of ChatGPT web searches; (2) it is widespread across many scientific domains but exhibits distinct impacts within them (highest: computer science, engineering sciences); (3) the influence varies with authors who have different language speaking backgrounds and geographic regions according to the location of their affiliations (Italy, China, etc.); (4) AI-generated texts are used in various content types in manuscripts (most significant: hypothesis formulation, conclusion summarization); (5) AI usage has a positive influence on papers impact, measured by its citation numbers. Based on these findings, suggestions about the advantages and regulation of AI-augmented scientific writing are discussed.

scientific communication and education↗
bioRxiv2024

Optimized CART Cell Therapy for Metastatic Aggressive Thyroid Cancer

Most thyroid cancer deaths are attributed to a subset of poorly differentiated, metastatic tumors. To improve treatment options for aggressive thyroid cancers, we developed a novel thyroid-stimulating hormone receptor (TSHR)-targeted chimeric antigen receptor T (CART) cell therapy, which demonstrated antigen-specific activation and antitumor efficacy against TSHR+ cell lines in vitro and in vivo. However, de-differentiated thyroid cancers downregulate TSHR. We therefore developed a potent treatment strategy by combining our novel TSHR-CART cells with mitogen-activated protein kinase (MAPK) inhibitors, which redifferentiate thyroid tumors and upregulate TSHR expression. In patient-derived anaplastic thyroid cancer xenografts, combination therapy of TSHR-CART cells and MAPK inhibitors led to increased TSHR expression on the tumor tissue and significantly enhanced antitumor efficacy and prolonged survival compared to TSHR-CART monotherapy. Based on our data, we are launching a phase I clinical trial for TSHR-CART cell therapy alone or in combination with MAPK inhibitors in patients with metastatic thyroid cancers. STATEMENT OF SIGNIFICANCEPoor target selection and antigen escape limit CART cell efficacy in solid tumors. We developed TSHR-CART cells to treat differentiated thyroid cancers but observed TSHR downregulation in dedifferentiated thyroid cancers. We found that MAPK inhibitors restored TSHR expression and sensitized these cancers to TSHR-CART cell therapy.

immunology↗
bioRxiv2024

The GC-content at the 5'ends of human protein-coding genes is undergoing mutational decay

In vertebrates, most protein-coding genes have a peak of GC-content near their 5 transcriptional start site (TSS). This feature promotes both the efficient nuclear export and translation of mRNAs. Despite the importance of GC-content for RNA metabolism, its general features, origin, and maintenance remain mysterious. We investigated the evolutionary forces shaping GC-content at the transcriptional start site (TSS) of genes through both comparative genomic analysis of nucleotide substitution rates between different species and by examining human de novo mutations. Our data suggests that GC-peaks at TSSs were present in the last vertebrate common ancestor and are largely dictated by recombination patterns. We observe that in primates and rodents, where recombination is directed away from TSSs by PRDM9, GC-content at protein-coding gene TSSs is currently undergoing mutational decay. In canids, which lack PRDM9 and perform recombination at TSSs, GC-content at protein-coding gene TSSs is increasing. These patterns extend into the open reading frame affecting protein-coding regions, and we show that changes in GC-content due to recombination affect synonymous codon position choices at the start of the open reading frame. Our results indicate that although high GC-content in protein-coding genes may be shaped by selective pressures to enhance expression, the dynamics of GC-content in mammals are largely shaped by patterns of recombination.

genomics↗
bioRxiv2024

Double-stranded RNA induces retinal pigment epithelium cell degeneration and inflammation

RIG-I signaling has been previously implicated as a driver of inflammation to the retinal pigment epithelium (RPE) during age-related macular degeneration (AMD). Double-stranded RNA (dsRNA) is known to initiate RIG-I signaling and lead to a type I interferon response. We show through shRNA knockdown that RIG-I is essential for initiating an interferon response in iPS-RPE in response to both synthetic dsRNA-mimetic 3p-hpRNA and the double-stranded retrotransposable element Alu. Analysis of human tissue from patients suffering from AMD show accumulation of dsRNA, peaking at the geographic atrophy (GA) stage. Using a new murine model of 3p-hpRNA subretinal challenge to RPE cells, we confirmed that accumulation of dsRNA initiates a type I interferon response, as well as RPE and photoreceptor degeneration. Although RPE response to synthetic dsRNA was acute, extensive leukocyte migration was observed. The results from this study verify the importance of RIG-I signaling in regulating inflammation in the subretinal space and implicates dsRNA accumulation as a driver of AMD pathogenesis.

cell biology↗
bioRxiv2024

Contractile to extensile transitions and mechanical adaptability enabled by activity in cytoskeletal structures

Cytoskeletal network architecture is crucial in determining emergent morphology and dynamics, particularly in processes like stress fiber nucleation, where cells respond to mechanical cues. However, a clear understanding of the connection between architecture, dynamics, and mechanical response remains lacking. In this study, we investigate how self-assembled cytoskeletal structures respond to external mechanical perturbations, focusing on filament and crosslinker mixtures in two dimensions. Using agent-based models complemented by coarse-grained thermodynamic analysis, we reveal how molecular motor activity enables cytoskeletal structures to robustly adapt to changing mechanical conditions. Our simulations demonstrate that under tensile forces, self-assembled active asters transform into bundle-like structures, reminiscent of de novo stress fiber formation in living cells, while pre-existing active bundles elongate further in a reproducible and regulated manner. In contrast, passive assemblies exhibit no such qualitative morphological reorganization, highlighting the critical role of activity in mechanical adaptation. We derive a simple relation approximating active stress as a function of average relative motor alignment, a measure of mesoscopic architecture, which allows us to predict changes in stress characteristics in response to mechanical perturbations with or without morphological reorganization. Our results demonstrate how mesoscopic architecture and motor activity work in tandem to enable robust morphological and mechanical adaptation in cytoskeletal structures, providing insight into cellular mechanosensing and stress fiber formation.

biophysics↗
bioRxiv2024

Increased regional P2X7R expression detected by GSK1482160 PET in a tauopathy mouse model

Neuroinflammation plays an important role in Alzheimers disease and primary tauopathies. The aim of the current study was to map [18F]GSK1482160 for imaging of purinergic P2X7R in Alzheimers disease and primary tauopathy mouse models. MicroPET was performed using [18F]GSK1482160 in widely used mouse models of Alzheimers disease (APP/PS1, 5xFAD and 3xTg), 4-repeat tauopathy (rTg4510) mice and age-matched wild-type mice. Increased uptake of [18F]GSK1482160 was observed in the cortex and basal forebrain of 7-month-old rTg4510 mice compared to age-matched wild-type mice and compared to 3-month-old rTg4510 mice. Nonparametric Spearmans rank analysis revealed a positive correlation between tau [18F]APN-1607 uptake and [18F]GSK1482160 in the hippocampus of rTg4510 mice. No significant differences in the uptake of [18F]GSK1482160 were observed between wild-type mice and APP/PS1 mice (5, 10 months), 5xFAD mice (3, 7 months) or 3xTg mice (10 months). Immunofluorescence staining further indicated the distribution of P2X7Rs in the brains of 7-month-old rTg4510 mice with accumulation of tau inclusion compared to wild-type mice. These findings provide in vivo imaging evidence for increased P2X7R in the brains of tauopathy model mice.

neuroscience↗
bioRxiv2024

Multi-omic characterization of allele-specific regulatory variation in hybrid pigs

Genetic variation in the regulation of gene expression contributes substantially to phenotypic variation. Understanding how variation in DNA sequences and epigentic modifications leads to gene expression variation remains a challenging task. In hybrid animals where cellular environments are homogeneous, differences between the expression of paternal and maternal alleles must be due to cis sequence or epigenic differences. Therefore, hybrid mapping is a powerful approach to efficiently identify and characterize genes under regulation through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we performed a comprehensive multi-omic characterization of regulatory variation across brain, liver, muscle, and placenta in four developmental stages. We produced one of the largest multi-omic datasets to date in pigs, including 16 whole genome sequenced genomes, 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We developed a novel read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We showed that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identified 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. By integrating methylation, chromatin accessibility, and gene expression data, many of these allele specific expression can be explained by allele specific methylation and/or chromatin accessibility. This study provides one of the most comprehensive characterizations of regulatory variation across multiple tissues and developmental stages in pigs and offers new opportunity of genetic improvement for this important food animal species.

developmental biology↗
bioRxiv2023

Inhibition of MMP 2 protects the endothelial glycocalyx and improves diastolic function in diabetic cardiomyopathy

The coronary microvascular endothelial glycocalyx (EGlx) is a vital regulator of vascular permeability and EGlx damage contributes to the development of diabetic cardiomyopathy. Matrix metalloproteinases 2 and 9 (MMP2/9) have been identified as key enzymes in the degradation of EGlx components, notably syndecan 4 (SDC4), and are upregulated in diabetes. We tested the hypothesis that inhibition of MMP2/9 can protect the EGlx and improve diastolic function in diabetic cardiomyopathy. Type 1 diabetes was induced in FVB mice by streptozotocin (STZ) injections. Mice were treated with daily injections of the MMP2/9 inhibitor, SB-3CT, for 2 weeks from 7 weeks post STZ. Echocardiography was utilised to assess heart function and lectin staining for the measurement of EGlx depth. Immunolabelling of heart sections for albumin provided an indication of albumin extravasation. A mechanism of EGlx shedding was investigated in vitro in human coronary microvascular endothelial cells treated with TNF- and SB-3CT. Diabetic mice developed diastolic dysfunction from 6 weeks post STZ. MMP2/9 inhibition reversed diastolic dysfunction, EGlx thinning and albumin extravasation in diabetic animals. In vitro, TNF- caused an increase in MMP9 activity and SDC4 shedding from human coronary microvascular endothelial cells. Treatment with SB-3CT reduced MMP9 activity and prevented SDC4 shedding. Knockdown of MMP9 expression prevented TNF- induced SDC4 shedding. This study demonstrates MMP2/9 inhibition as a strategy to protect the EGlx and improve diastolic function in diabetic cardiomyopathy. Our findings suggest new avenues for therapeutic interventions in cardiovascular complications associated with diabetes. Statements and DeclarationsO_ST_ABSCompeting interestsC_ST_ABSThe authors have no competing interests to declare that are relevant to the content of this article.

physiology↗
bioRxiv2023

Small molecule inhibitor binds to NLRP3 and prevents inflammasome activation

Despite recent advances in the mechanism of oxidized DNA activating NLRP3, the molecular mechanism and consequence of oxidized DNA associating with NLRP3 remains unknown. Cytosolic NLRP3 binds oxidized DNA which has been released from the mitochondria, which subsequently triggers inflammasome activation. Human glycosylase (hOGG1) repairs oxidized DNA damage which inhibits inflammasome activation. The fold of NLRP3 pyrin domain contains amino acids and a protein fold similar to hOGG1. Amino acids that enable hOGG1 to bind and cleave oxidized DNA are conserved in NLRP3. We found NLRP3 could bind and cleave oxidized guanine within mitochondrial DNA. The binding of oxidized DNA to NLRP3 was prevented by small molecule drugs which also inhibit hOGG1. These same drugs also inhibited inflammasome activation. Elucidating this mechanism will enable design of drug memetics that treat inflammasome pathologies, illustrated herein by NLRP3 pyrin domain inhibitors which suppressed interleukin-1{beta} (IL-1{beta}) production in macrophages. One-Sentence SummaryNLRP3 cleaves oxidized DNA and small molecule drug binding inhibits inflammasome activation.

immunology↗
bioRxiv2023

NS2B-D55E and NS2B-E65D Variations are Responsible for Differences in NS2B-NS3 Protease Activities Between Japanese Encephalitis Virus Genotype I and III in Fluorogenic Peptide Model

Japanese Encephalitis Virus (JEV) NS2B-NS3 is a protein complex composed of NS3 proteases and a NS2B cofactor. The N-terminal protease domain (180 residues) of NS3 (NS3(pro)) interacts directly with a central 40-amino acid hydrophilic domain of NS2B (NS2B(H)) to form an active serine protease. In this study, the recombinant NS2B(H)-NS3(pro) proteases were prepared in E. coli and used to compare the enzymatic activity between genotype I (GI) and III (GIII) NS2B-NS3 proteases. The GI NS2B(H)-NS3(pro) was able to cleave the sites at internal C, NS2A/NS2B, NS2B/NS3 and NS3/NS4A junctions that were identical to the sites proteolytically processed by GIII NS2B(H)-NS3(pro). Analysis of the enzymatic activity of recombinant NS2B(H)-NS3(pro) proteases using a model of fluorogenic peptide substrate revealed that the proteolytical processing activity of GIII NS2B(H)-NS3(pro) was significantly higher than that of GI NS2B(H)-NS3(pro). There were eight amino acid variations between GI and GIII NS2B(H)-NS3(pro), which may be responsible for the difference in enzymatic activities between GI and GIII proteases. Therefore, recombinant mutants were generated by exchanging NS2B(H) and NS3(pro) domains between GI and GIII NS2B(H)-NS3(pro) and subjected to protease activity analysis. Substitution of NS2B(H) significantly altered the protease activities, as compared to the parental NS2B(H)-NS3(pro), suggesting that NS2B(H) played an essential role in regulation of NS3(pro) protease activity. To further identify the amino acids responsible for the difference in protease activities, multiple substitution mutants including the individual and combined mutations at the variant residue 55 and 65 of NS2B(H) were generated and subjected to protease activity analysis. Replacement of NS2B-55 and NS2B-65 of GI to GIII significantly increased the enzymatic activity of GI NS2B(H)-NS3(pro) protease, whereas mutation of NS2B-55 and NS2B-65 of GIII to GI remarkably reduced the enzymatic activity of GIII NS2B(H)-NS3(pro) protease. Overall, these data demonstrated that NS2B-55 and NS2B-65 variations in hydrophilic domain of NS2B co-contributed to the difference in NS2B(H)-NS3(pro) protease activities between GI and GIII. These observations gain an insight into the role of NS2B in regulation of NS3 protease activities, which is useful for understanding the replication of JEV GI and GIII viruses.

microbiology↗
bioRxiv2023

FITM2 deficiency results in ER lipid accumulation, ER stress, reduced apolipoprotein B lipidation, and VLDL triglyceride secretion in vitro and in mouse liver

Structured AbstractO_ST_ABSObjectivesC_ST_ABSTriglyceride (TG) association with apolipoprotein B100 (apoB100) serves to form very low density lipoproteins (VLDL) in the liver. The repertoire of factors that facilitate this association is incompletely defined. FITM2, an integral endoplasmic reticulum (ER) protein, was originally discovered as a factor participating in cytoplasmic lipid droplets (LDs) in tissues that do not form VLDL. We hypothesized that in the liver, in addition to promoting cytosolic LD formation, FITM2 would also transfer TG from its site of synthesis in the ER membrane to nascent VLDL particles within the ER lumen. MethodsExperiments were conducted using a rat hepatic cell line (McArdle-RH7777, or McA cells), an established model of mammalian lipoprotein metabolism, and mice. FITM2 expression was reduced using siRNA in cells and by liver specific cre-recombinase mediated deletion of the Fitm2 gene in mice. Effects of FITM2 deficiency on VLDL assembly and secretion in vitro and in vivo were measured by multiple methods, including density gradient ultracentrifugation, chromatography, mass spectrometry, simulated Raman spectroscopy (SRS) microscopy, sub-cellular fractionation, immunoprecipitation, immunofluorescence, and electron microscopy. Main findings1) FITM2-deficient hepatic cells in vitro and in vivo secrete TG-depleted VLDL particles, but the number of particles is unchanged compared to controls; 2) FITM2 deficiency in mice on a high fat diet (HFD) results in decreased plasma TG levels. The number of apoB100-containing lipoproteins remains similar, but shift from VLDL to LDL density; 3) Both in vitro and in vivo, when TG synthesis is stimulated and FITM2 is deficient, TG accumulates in the ER, and despite its availability this pool is unable to fully lipidate apoB100 particles; 4) FITM2 deficiency disrupts ER morphology and results in ER stress. Principal conclusionsThe results suggest that FITM2 contributes to VLDL lipidation, especially when newly synthesized hepatic TG is in abundance. In addition to its fundamental importance in VLDL assembly, the results also suggest that under dysmetabolic conditions, FITM2 may be a limiting factor that ultimately contributes to non-alcoholic fatty liver disease (NAFLD) and steatohepatitis (NASH).

biochemistry↗
bioRxiv2023

eSVD-DE: Cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings

BackgroundSingle-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of methods to investigate differentially expressed (DE) genes among such datasets with numerous individuals. While numerous methods exist to find DE genes for scRNA data from limited individuals, differential-expression testing for large cohorts of case and control individuals using scRNA data poses unique challenges due to substantial effects of human variation, i.e., individual-level confounding covariates that are difficult to account for in the presence of sparsely-observed genes. ResultsWe develop the eSVD-DE, a matrix factorization that pools information across genes and removes confounding covariate effects, followed by a novel two-sample test in mean expression between case and control individuals. In general, differential testing after dimension reduction yields an inflation of Type-1 errors. However, we overcome this by testing for differences between the case and control individuals posterior mean distributions via a hierarchical model. In previously published datasets of various biological systems, eSVD-DE has more accuracy and power compared to other DE methods typically repurposed for analyzing cohort-wide differential expression. ConclusionseSVD-DE proposes a novel and powerful way to test for DE genes among cohorts after performing a dimension reduction. Accurate identification of differential expression on the individual level, instead of the cell level, is important for linking scRNA-seq studies to our understanding of the human population.

genomics↗
bioRxiv2023

Improving Hi-C contact matrices using genome graphs

Three-dimensional chromosome structure plays an important role in fundamental genomic functions. Hi-C, a high-throughput, sequencing-based technique, has drastically expanded our comprehension of 3D chromosome structures. The first step of Hi-C analysis pipeline involves mapping sequencing reads from Hi-C to linear reference genomes. However, the linear reference genome does not incorporate genetic variation information, which can lead to incorrect read alignments, especially when analyzing samples with substantial genomic differences from the reference such as cancer samples. Using genome graphs as the reference facilitates more accurate mapping of reads, however, new algorithms are required for inferring linear genomes from Hi-C reads mapped on genome graphs and constructing corresponding Hi-C contact matrices, which is a prerequisite for the subsequent steps of the Hi-C analysis such as identifying topologically associated domains and calling chromatin loops. We introduce the problem of genome sequence inference from Hi-C data mediated by genome graphs. We formalize this problem, show the hardness of solving this problem, and introduce a novel heuristic algorithm specifically tailored to this problem. We provide a theoretical analysis to evaluate the efficacy of our algorithm. Finally, our empirical experiments indicate that the linear genomes inferred from our method lead to the creation of improved Hi-C contact matrices. These enhanced matrices show a reduction in erroneous patterns caused by structural variations and are more effective in accurately capturing the structures of topologically associated domains.

genomics↗
bioRxiv2023

Virome analysis provides new insights into the pathogenesis mechanism and treatment of SLE disease

Systemic lupus erythematosus (SLE) is a multi-system autoimmune disease. Many viruses have been reported to be associated with SLE, but the diversity of the virome in SLE and the mechanisms underlying the interactions between viral infection and SLE are still unclear. This study identified ten human virus species from 826 RNA-Seq samples of human blood from 688 SLE patients and 138 healthy controls. SLE patients were found to have higher positive rates of viruses than healthy controls, although the virus abundances were low and comparable in both SLE patients and healthy controls. Analysis of the antiviral interferon-stimulated genes (ISGs) in samples showed higher ISG expression levels in virus-positive samples compared to virus-negative samples, which confirmed viral infections in virus-positive samples. Further analysis of differential expression genes between virus-positive and negative SLE patients showed that several genes that were up-regulated in SLE patients were further up-regulated after viral infections, and they were mainly enriched in immune response-related biological processes, suggesting an excess immune response in SLE patients after viral infections. Finally, three marker genes of the SLE severity, namely STAT1, STAT5A, and STAT5B, showed higher expression levels in virus-positive SLE patients compared to those in virus-negative SLE patients, suggesting that viral infections may aggravate the SLE disease. Overall, the study deepens our understanding of the association between viruses and SLE and provides new insights into prevention and control of the disease.

bioinformatics↗
bioRxiv2023

Climate warming suppresses soil abundant fungal taxa and reduces soil carbon efflux in a semi-arid grassland

The abundance, diversity and activity of soil microorganisms critically control the fate of recent plant carbon (C) inputs as well as protecting soil organic C, regulating C-climate feedbacks. However, the effects of climate change drivers such as warming and precipitation change on soil microbial communities and C dynamics remain poorly understood. Utilizing a long-term field warming and precipitation manipulation in a semi-arid grassland on the Loess Plateau and a complementary incubation experiment, here we show that warming and rainfall reduction differentially affect the abundance and composition of bacteria and fungi, and soil C efflux. Warming significantly reduced the abundance of fungi but not bacteria, increasing the relative dominance of bacteria in the soil microbial community. In particular, warming shifted the community composition of abundant fungi in favor of oligotrophic Capnodiales and Hypocreales over potential saprotroph Archaeorhizomycetales. In contrast, precipitation reduction increased soil microbial biomass, but did not significantly affect either the abundance or diversity of bacteria. Furthermore, soil abundant, not rare, fungal community composition was significantly correlated with soil CO2 efflux. Our findings suggest that alterations in the fungal community composition, in response to changes in soil C and moisture, dominate the microbial responses to climate change and thus control soil C dynamics in semi-arid grasslands. Impact statementSemi-arid grasslands play a critical role in global carbon (C) cycle and potential feedbacks to climate change. Understanding the responses of soil microorganisms to warming and rainfall change is key to evaluating and predicting semi-arid grassland soil C dynamics under future climate change scenarios. Our study showed that warming induced a shift in the abundant fungal community, favoring oligotrophic fungi (i.e., Capnodiales and Hypocreales) over the potential saprotrophic Archaeorhizomycetales, and reduced C efflux. These findings advance our understanding of soil microbial and C responses to climate change drivers and may help predict and possibly manage soil C sequestration in semi-arid grasslands.

ecology↗