Biology subjects

Dong, X.

Publications and source records attributed to Dong, X..

At least 235 records · Page 13Linked to original sources

bioRxiv2022

Type 17 Follicular Helper T (Tfh17) Cells are Superior for Memory Maintenance

A defining feature of successful vaccination is the ability to induce long-lived antigen- specific memory cells. Follicular helper T (Tfh) cells specialize in providing help to B cells in mounting protective humoral immunity in infection and after vaccination. Memory Tfh cells that retain the CXCR5 expression can confer protection through enhancing humoral response upon antigen re-exposure but how they are maintained is poorly understood. CXCR5+ memory Tfh cells in human blood are divided into Tfh1, Tfh2 and Tfh17 cells by the expression of chemokine receptors CXCR3 and CCR6 associated with Th1 and Th17 respectively. Here, we developed a new method to induce Tfh1, Tfh2 and Tfh17-like (iTfh1, iTfh2 and iTfh17) cells in vitro. Although all three iTfh subsets efficiently support antibody responses in recipient mice with immediate immunization, iTfh17 cells are superior to iTfh1 and iTfh2 cells in supporting antibody response to a later immunization after extended resting in vivo to mimic memory maintenance. Notably, the counterpart human Tfh17 cells are selectively enriched in CCR7+ central memory Tfh (TfhCM) with survival and proliferative advantages. Furthermore, the analysis of multiple human cohorts that received different vaccines for HBV, influenza virus, tetanus toxin or measles revealed that vaccine-specific Tfh17 cells outcompete Tfh1 or Tfh2 cells for the persistence in memory phase. Therefore, the complementary mouse and human results showing the advantage of Tfh17 cells in maintenance and memory function supports the notion that Tfh17-induced immunization might be preferable in vaccine development to confer long-term protection.

immunology↗

bioRxiv2022

Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures

The current lack of benchmark datasets with inbuilt ground-truth makes it challenging to compare the performance of existing long-read isoform detection and differential expression analysis workflows. Here, we present a benchmark experiment using two human lung adenocarcinoma cell lines that were each profiled in triplicate together with synthetic, spliced, spike-in RNAs ("sequins"). Samples were deeply sequenced on both Illumina short-read and Oxford Nanopore Technologies long-read platforms. Alongside the ground-truth available via the sequins, we created in silico mixture samples to allow performance assessment in the absence of true positives or true negatives. Our results show that, StringTie2 and bambu outperformed other tools from the 6 isoform detection tools tested, DESeq2, edgeR and limma-voom were best amongst the 5 differential transcript expression tools tested and there was no clear front-runner for performing differential transcript usage analysis between the 5 tools compared, which suggests further methods development is needed for this application.

bioinformatics↗

bioRxiv2022

Losartan controls immune checkpoint blocker-induced edema and improves survival in glioblastoma

Immune checkpoint blockers (ICBs) have failed in all Phase III glioblastoma trials. Here, we found that ICBs induce cerebral edema in some patients and mice with glioblastoma. Through single-cell RNA sequencing, intravital imaging, and T cell blocking studies in mice, we demonstrated that this edema results from an inflammatory response following anti-PD1 antibody treatment that disrupts the blood-tumor-barrier. Used in lieu of immunosuppressive corticosteroids, the angiotensin receptor blocker losartan prevented this ICB-induced edema and reprogrammed the tumor microenvironment, curing 20% of mice which increased to 40% in combination with standard of care treatment. Using a bihemispheric tumor model, we identified a "hot" tumor immune signature prior to losartan+anti-PD1 therapy that predicted long-term survival. Our findings provide the rationale and associated biomarkers to test losartan with ICBs in glioblastoma patients. One-Sentence SummaryLosartan prevents immunotherapy-associated edema and enhances the outcome of immunotherapy in glioblastoma.

cancer biology↗

bioRxiv2022

MrgprA3-expressing pruriceptors drive pruritogen-induced alloknesis through mechanosensitive Piezo2 channel

Although touch and itch are coded by distinct neuronal populations, light touch also provokes itch in the presence of exogenous pruritogens, resulting in a phenomenon called alloknesis. However, the cellular and molecular mechanisms underlying the initiation of pruritogen-induced mechanical itch sensitization are poorly understood. Here we show that intradermal injections of histamine or chloroquine (CQ) provoke alloknesis through activation of TRPV1- and MrgprA3- expressing prurioceptors, and functional ablation of these neurons reverses pruritogen-induced alloknesis. Moreover, genetic ablation of mechanosensitive Piezo2 channel function from MrgprA3-expressing prurioceptors also dampens pruritogen-induced alloknesis. Mechanistically, histamine and CQ sensitize Piezo2 channel function through activation of the PLC-PKC{delta} signaling. Collectively, our data uncovered a TRPV1+/MrgprA3+ prurioceptor-Piezo2 signaling axis in the initiation of pruritogen-induced mechanical itch sensitization in the skin.

neuroscience↗

bioRxiv2022

S373P Mutation of Spike Protein in SARS-CoV-2 Stabilizes Omicron

A cluster of several newly occurring mutations on Omicron are found at the {beta}-core region of spike proteins receptor-binding domain (RBD), where mutation rarely happened before. Notably, the binding of SARS-CoV-2 to human receptor ACE2 via RBD happens in a dynamic airway environment, where mechanical force caused by coughing or sneezing occurs and applies to the proteins. Thus, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of RBDs and found that the mechanical stability of Omicron RBD increased by ~20% compared with the wild-type. Molecular dynamics simulations revealed that Omicron RBD showed more hydrogen bonds in the {beta}-core region due to the closing of the -helical motif caused primarily by mutation S373P, which was further confirmed experimentally. Moreover, the binding ability of Omicron to ACE2 is promoted with a stabilized RBD. This work reveals the effect of the highly conserved mutation S373P which is present in most Omicron subvariants, including BA.1-5, BQ. 1, XBB, and CH.1.1.

biophysics↗

bioRxiv2022

A novel inovirus reprograms metabolism and motility of marine Alteromonas

Members from the Inoviridae family with striking features are widespread, highly diverse and ecologically pervasive across multiple hosts and environments; however, very small amount of inoviruses have been isolated and studied. Here, a filamentous phage infecting Alteromonas abrolhosensis, designated {phi}AFP1, was isolated from the South China Sea and represented as a novel genus of Inoviridae. {phi}AFP1 consisted of a single-stranded DNA genome (5986 bp), encoding eight putative ORFs. Comparative analyses revealed {phi}AFP1 could be regarded as genetic mosaics, which especially came from Ralstonia and Stenotrophomonas phages. The temporal transcriptome analysis of A. abrolhosensis to {phi}AFP1 infection reveals that 7.78% of the host genes were differentially expressed. The genes involved in translation processes, ribosome pathways and degradation of multiple amino acid pathways at plateau period were upregulated, while host material catabolic and bacterial motility-related genes were downregulated, indicating that {phi}AFP1 might hijack the energy of the host for the synthesis of phage proteins. {phi}AFP1 exerted the step-by-step control on host genes through the appropriate level of the utilizing host resources, affirming a new non-standard regulatory strategy of viral temperately control over the host transcriptional profile. Our study provides novel information for a better understanding of filamentous phage characteristics and phage-host interactions.

microbiology↗

bioRxiv2022

Inferring CTCF insulators and anchored loops across human tissues and cell types

CCCTC-binding factor (CTCF) is a transcription regulator which is involved in many cellular processes. How CTCF recognizes DNA sequence to exert chromosome barrier or enhancer blocking effects remains to be fully interrogated. Despite many computational tools were developed to predict CTCF-mediated loops qualitatively or quantitatively, few could specially evaluate the regulatory potential of DNA sequence at CTCF binding sites (CBSs) and how it affects chromatin loop formation. Here, we developed a deep learning model, DeepAnchor, to precisely characterize the binding patterns for different types of CBSs. By incorporating base-wise genomic/epigenomic features, we revealed distinct chromatin and sequence features for CTCF-mediated insulation and looping at a high resolution, such as two sequence motifs flanking the core CTCF motif at loop-associated CBSs. Besides, we leveraged the predicted anchor score to optimize the loop extrusion model and achieved the best performance in predicting CTCF-anchored loops. We established a compendium of context-specific CTCF-anchored loops across 52 human tissue/cell types and found that genomic disruption of CTCF-anchored loops may represent a general causal mechanism of disease pathogenesis. These computational models, together with the established resource, could facilitate the mechanistic research on how the CTCF-mediated cis-regulatory elements (CREs) shapes context-specific gene regulation in cell development and disease progression.

bioinformatics↗

bioRxiv2022

SARS-CoV-2 minor variant genomes at the start of the pandemic contained markers of VoCs

SARS-CoV-2 emerged through limited zoonotic spillovers and was predicted to have constrained sequence diversity. The dominant consensus and minor variant genomes were determined from the earliest samples associated with the Huanan market and the start of the pandemic. The sequence data confirmed that the dominant consensus genomes shared very close homology. However, there were minor variant genomes present in each sample, which encompassed synonymous and non-synonymous changes. Fusion sequences characteristic of defective RNAs were identified that could be linked between patients. Several substitutions (but not deletions) associated with much later variants of concern (VoCs) were already present as minor variant genomes. This suggests it may be possible to predict futures variants at the start of a pandemic by examining where variability in sequence occurs.

microbiology↗

bioRxiv2022

Preferential cross-linking of the stereospecific complex over the encounter complexes by DOPA2, a faster cross-linker than DSS

Transient protein-protein interactions are fundamental aspects of many biochemical reactions, but they are technically challenging to study. Chemical cross-linking of proteins coupled with mass spectrometry (CXMS) analysis is a powerful tool to facilitate the analysis of transient interactions. Central to this technology are chemical cross-linkers. Here, using two transient heterodimeric complexes--EIN/HPr with a KD of 7 M and EIIAGlc/EIIBGlc with a KD of 25 M--as model systems, we compared the effects of two amine-specific homo-bifunctional cross-linkers of different cross-linking speeds. Protein cross-linking by DOPA2, a di-ortho-phthalaldehyde cross-linker, is 60-120 times faster than that by DSS, an N-hydroxysuccinimide ester cross-linker. We analyzed the differences in the number of cross-links identified that reflected the stereospecific complex (SC), the final lowest-energy conformational state, and that of cross-links that reflected the encounter complexes (ECs), an ensemble of short-lived intermediate conformations mediated by nonspecific electrostatic interactions. We found that the faster DOPA2 cross-linking favored the SC whereas the slower DSS cross-linking favored the ECs. We propose a mechanistic model for this intriguing observation. This study suggests that it is feasible to probe the dynamics of protein-protein interaction using cross-linkers of different cross-linking speeds.

biochemistry↗

bioRxiv2022

The majority of microorganisms in gas hydrate bearing subseafloor sediments ferment macromolecules

BackgroundGas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Sedimentary organic matter and upward methane fluids represent two important sources of carbon and energy for deep biosphere. However, which metabolism dominates the deep subseafloor of gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas-hydrate rich sediments up to 49 meters below seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions, and performed metagenomic and metatranscriptomic analyses to characterize microbial diversity and their role in carbon mineralization. ResultsComparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones clearly distinguish from those below the SMI. Chloroflexota, are most abundant above the SMI, whereas Caldatribacteriota dominate below the SMI. Verrucomicrobiota, Bathyarchaeia and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest roles in fermentation of macromolecule. By contrast, sulfate reducers and methanogens, organisms that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs of the ANME-1 group thrived in or slightly below the current sulfate methane interface. Rare members from Heimdallarchaeia were identified to encode the potential for anaerobic oxidation of short-chain hydrocarbons. ConclusionsThese findings indicate that fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes.

microbiology↗

bioRxiv2022

VPS9D1-AS1 overexpression amplifies intratumoral TGF-β signaling and promotes tumor cell escape from CD8+ T cell killing in colorectal cancer

Efficacy of immunotherapy is limited in patients with colorectal cancer (CRC) because high expression of tumor-derived transforming growth factor (TGF)-{beta} pathway molecules and interferon (IFN)-stimulated genes (ISGs) promotes tumor immune evasion. Here, we identified a long noncoding RNA (lncRNA), VPS9D1-AS1, which was located in ribosomes and amplified TGF-{beta} signaling and ISG expression. We show that high expression of VPS9D1-AS1 was negatively associated with T lymphocyte infiltration in two independent cohorts of CRC. VPS9D1-AS1 served as a scaffolding lncRNA by binding with ribosome protein S3 (RPS3) and a competing endogenous RNA (ceRNA) to sponge miR-22-5p/514a-3p to increase the translation of TGF-{beta}, TGFBR1, and SMAD1/5/9. VPS9D1-AS1 knockout downregulated OAS1, an ISG gene, which further reduced IFNAR1 levels in tumor cells. Conversely, tumor cells overexpressing VPS9D1-AS1 were resistant to CD8+ T cell killing and lowered IFNAR1 expression in CD8+ T cells. In a conditional overexpression mouse model, VPS9D1-AS1 enhanced tumorigenesis and suppressed the infiltration of CD8+ T cells. Treating tumor-bearing mice with antisense oligonucleotide drugs targeting VPS9D1-AS1 significantly suppressed tumor growth. Our findings indicate that the tumor-derived VPS9D1-AS1/TGF-{beta}/ISG signaling cascade promotes tumor growth and enhances immune evasion and may thus serve as a potential therapeutic target for CRC.

cancer biology↗

bioRxiv2022

A Bispecific Antibody Targeting RBD and S2 Potently Neutralizes SARS-CoV-2 Omicron and Other Variants of Concern

Emerging severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants, especially the Omicron variant, have impaired the efficacy of existing vaccines and most therapeutic antibodies, highlighting the need for additional antibody-based tools that can efficiently neutralize emerging SARS-CoV-2 variants. The use of a "single" agent to simultaneously target multiple distinct epitopes on the spike is desirable to overcome the neutralizing escape of SARS-CoV-2 variants. Herein, we generated a human-derived IgG-like bispecific antibody (bsAb), Bi-Nab35B5-47D10, which successfully retained the specificity and simultaneously bound to the two distinct epitopes on RBD and S2. Bi-Nab35B5-47D10 showed improved spike binding breadth among wild-type (WT) SARS-CoV-2, variants of concern (VOCs) and variants being monitored (VBMs) compared with its parental mAbs. Furthermore, pseudotyped virus neutralization demonstrated that Bi-Nab35B5-47D10 can efficiently neutralize VBMs including Alpha (B.1.1.7), Beta (B.1.351) and Kappa (B.1.617.1) and VOCs including Delta (B.1.617.2), Omicron BA.1 and Omicron BA.2. Crucially, Bi-Nab35B5-47D10 substantially improved neutralizing activity against Omicron BA.1 (IC50= 27.3 ng/mL) and Omicron BA.2 (IC50= 121.1 ng/mL) compared with their parental mAbs. Therefore, Bi-Nab35B5-47D10 represents a potential effective countermeasure against SARS-CoV-2 Omicron and other variants of concern. ImportanceThe new highly contagious SARS-CoV-2 Omicron variant caused substantial breakthrough infections and has become the dominant strain in countries across the world. Omicron variants usually bear high mutations in the spike protein and exhibit considerable escape of most potent neutralization monoclonal antibodies and reduced efficacy of current COVID-19 vaccines. The development of neutralizing antibodies with potent efficacy against the Omicron variant is still an urgent priority. Here, we generated a bsAb, Bi-Nab35B5-47D10, that simultaneously targets SARS-CoV-2 RBD and S2 and improved neutralizing potency and breadth against SARS-CoV-2 WT and the tested variants compared with their parental antibodies. Notably, Bi-Nab35B5-47D10 has more potent neutralizing activity against the VOC Omicron pseudotyped virus. Therefore, Bi-Nab35B5-47D10 is a feasible and potentially effective strategy to treat and prevent COVID-19.

immunology↗

bioRxiv2022

Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

Deep sea cold seep sediments host abundant and diverse bacterial and archaeal populations that significantly influence biogeochemical cycles. While numerous studies have revealed the community structure and functional capabilities of cold seep microbiomes, little is known about their genetic heterogeneity within species. Here, we examined intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 4.3 mbsf across six cold seep sites from around the world. These species were predicted to participate in methane oxidation and sulfate reduction, and based on their metabolic capabilities, grouped as aerobic methane-oxidizing bacteria (MOB), anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). These physiologically and phylogenetically diverse MOB, ANME and SRB display different degrees of intrapopulation sequence divergence and different evolutionary trajectories. Populations were in general characterized by low rates of homologous recombination and strong purifying selection with most of the nucleotide variation being synonymous. Functional genes related to methane (pmoA and mcrA) and sulfate (dsrA) metabolisms were found to be under strong purifying selection in the vast majority of species investigated, although examples of active positive selection were also observed. These genes differed in evolutionary trajectories across phylogenetic clades but are functionally conserved across cold seep sites. Intrapopulation diversification of MOB, ANME and SRB species as well as their mcrA and dsrA genes was observed to be depth-dependent and undergo divergent selection pressures throughout the sediment column. These results highlight the role of the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep sediments and shed light on how microbial populations adapt in the subseafloor biosphere.

microbiology↗

bioRxiv2022

Spatiotemporal landscape of SARS-CoV-2 pulmonary infection reveals Slamf9+Spp1+ macrophages promoting viral clearance and inflammation resolution

While SARS-CoV-2 pathogenesis has been intensively investigated, the host mechanisms of viral clearance and inflammation resolution are still elusive because of the ethical limitation of human studies based on COVID-19 convalescents. Here we infected Syrian hamsters by authentic SARS-CoV-2 and built an ideal model to simulate the natural recovery process of SARS-CoV-2 infection from severe pneumonia1,2. We developed and applied a spatial transcriptomic sequencing technique with subcellular resolution and tissue-scale extensibility, i.e., Stereo-seq3, together with single-cell RNA sequencing (scRNA-seq), to the entire lung lobes of 45 hamsters and obtained an elaborate map of the pulmonary spatiotemporal changes from acute infection, severe pneumonia to the late viral clearance and inflammation resolution. While SARS-CoV-2 infection caused massive damages to the hamster lungs, including naive T cell infection and deaths related to lymphopenia, we identified a group of monocyte-derived proliferating Slamf9+Spp1+ macrophages, which were SARS-CoV-2 infection-inducible and cell death-resistant, recruiting neutrophils to clear viruses together. After viral clearance, the Slamf9+Spp1+ macrophages differentiated into Trem2+ and Fbp1+ macrophages, both responsible for inflammation resolution and replenishment of alveolar macrophages. The existence of this specific macrophage subpopulation and its descendants were validated by RNAscope in hamsters, immunofluorescence in hACE2 mice, and public human autopsy scRNA-seq data of COVID-19 patients. The spatiotemporal landscape of SARS-CoV-2 infection in hamster lungs and the identification of Slamf9+Spp1+ macrophages that is pivotal to viral clearance and inflammation resolution are important to better understand the critical molecular and cellular players of COVID-19 host defense and also develop potential interventions of COVID-19 immunopathology.

immunology↗

bioRxiv2022

CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer

Prostate cancer (PCa) harboring BRCA1/2 mutations is often exquisitely sensitive to PARP inhibition. However, genomic alterations in other DNA damage response genes have not been consistently predictive of clinical response to PARP inhibitors (PARPis). Here, we perform genome-wide CRISPR-Cas9 knockout screens in BRCA1/2-proficient PCa cell lines and identify novel genes whose loss has a profound impact on PARPi sensitivity and resistance. Specifically, MMS22L deletion, frequently observed (up to 14%) in PCa, renders cells hypersensitive to PARPis by disrupting RAD51 loading required for homologous recombination repair, although this response is TP53-dependent. Unexpectedly, loss of CHEK2 confers resistance rather than sensitivity to PARPis in PCa cells through increased expression of BRCA2, a target of CHEK2-TP53-E2F7-mediated transcriptional repression. Combined PARP and ATR inhibition overcomes PARPi resistance caused by CHEK2 loss. Our findings may inform the use of PARPis beyond BRCA1/2-deficient tumors and support reevaluation of currently used biomarkers for PARPi treatment in PCa.

cancer biology↗

bioRxiv2022

Tomographic-encoded multiphoton (TEMP) microscopy

Axial scanning in multiphoton microscopy (MPM) is typically realized by mechanically shifting either the objective or the sample. However, the scan speed is usually hindered by the mechanical inertia of the bulky mass. Although the extended depth of field provided by the non-diffracting beam allows fast volumetric imaging, it abandons the axial resolution. Here, we demonstrate a novel and powerful tomographic technique using the Bessel droplet in MPM, termed Tomographic-Encoded MultiPhoton (TEMP) microscopy. We show that benefiting from the high-order nonlinear excitation in MPM, the side-lobes cancellation and smaller beam focus of the Bessel droplet realize better image quality. The TEMP microscopy allows fast axial scanning, less risks of photodamage and photobleaching, and high-resolution and high-contrast imaging. Furthermore, fewer raw images are required for the 3D image reconstruction. To demonstrate its usability and advantages for scattering tissues and biomedical applications, we showcase the TEMP microscopy with highly scattering fluorescence microspheres and mouse brain slice. More details can be visualized by the Bessel droplet compared with the conventional Gaussian and Bessel beam. More importantly, the TEMP technique is an easy-plug-in method for the current microscopy system. The TEMP microscopy is promising for fast volumetric multiphoton imaging, especially for highly scattering tissues.

bioengineering↗

bioRxiv2022

Effects of seasonal changes on the carbon dynamics in mixed coniferous forests

We characterized seasonal changes in the residual rate and mass-loss rate of litter, as well as the carbon release dynamics of litter and soil, in mixed coniferous forests in the Xiaoxinganling region by conducting a controlled freeze-thaw experiment. The carbon release rate and mass-loss rate of litter at two levels of decomposition (undecomposed and semi-decomposed) were measured during four seasons: the unfrozen season, freeze-thaw season, frozen season, and thaw season. The temperature was higher, the mass-loss rate was faster, and the overall mass-loss rate of litter was higher in the unfrozen season than in the other three seasons; litter organic carbon increased and soil organic carbon increased due to the strong carbon sequestration capacity of plants. The temperature fluctuated above and below 0{degrees}C during the freeze-thaw season, which results in the physical breakage of the undecomposed litter and increases in the mass-loss rate. This leads to increases in the organic carbon of undecomposed litter and decreases in the soil organic carbon of undecomposed litter; the opposite patterns were observed for changes in the organic carbon of semidecomposed litter and soil organic carbon. There was noticeable mass loss of litter during the frozen season, and the rate of mass loss of litter during the thaw season was the lowest. Litter organic carbon decreased and soil organic carbon increased in both seasons. The organic carbon of undecomposed litter was highest in the thaw season, followed by the freeze-thaw season, frozen season, and unfrozen season. The organic carbon of semi-decomposed litter was highest in the frozen season, followed by the thaw season, freeze-thaw season, unfrozen season to freeze-thaw season, frozen season, thaw season, and unfrozen season. After freeze-thaw treatment, the organic carbon in deadfall soil was highest in the unfrozen season, freeze-thaw season, frozen season, thaw season to unfrozen season, frozen season, thaw season, and freeze-thaw season. The findings of this study provide new insights into the material cycling process under freeze-thawing, as well as information on the effect of seasonal freeze-thaws on the forest carbon cycle.

ecology↗

bioRxiv2022

Frequency of change determines effectiveness of microbial response strategies in sulfidic stream microbiomes

Nature challenges microbes with change at different frequencies and demands an effective response for survival. Here, we used controlled laboratory experiments to investigate the ecological success of different response strategies, such as post-translational modification, transcriptional regulation, and specialized versus adaptable metabolisms. For this, we inoculated replicated chemostats with an enrichment culture obtained from sulfidic stream microbiomes 16 weeks prior. The chemostats were submitted to alternatingly oxic and anoxic conditions at three frequencies, with periods of 1 day, 4 days and 16 days. The microbial response was recorded with 16S rRNA gene amplicon sequencing, shotgun metagenomics, transcriptomics and proteomics. Metagenomics resolved 26 nearly complete genomes of bacterial populations, mainly affiliated with Proteobacteria and Bacteroidetes. Almost all these populations maintained a steady growth rate under both redox conditions at all three frequencies of change. Apparently, oscillating oxic/anoxic conditions selected for generalistic species, rather than species specializing in only a single condition. Rapid (1-day) dynamics yielded more stochasticity, both in community dynamics and gene expression, indicating that bet-hedging might be an effective coping strategy for relatively rapid environmental change. Codon-usage bias, previously associated with copiotrophic and oligotrophic lifestyles, was found to be a powerful predictor of ecological success at different frequencies, with copiotrophs and oligotrophs more successful at a rapid and a slow pace of change, respectively, independent of growth rate.

microbiology↗