Biology subjects

Siegel, D. A.

Publications and source records attributed to Siegel, D. A..

10 recordsLinked to original sources

bioRxiv2026

Particle lability drives degradation dynamics and bacterial community assembly during a Phaeocystis bloom decline

Microbial degradation of suspended and sinking organic carbon regulates long-term oceanic carbon storage by controlling the efficiency of the biological pump. Yet microbial controls on carbon export and remineralization remain poorly constrained, limiting predictions of how ocean carbon cycling will respond to climate change. Here, we combined in situ sampling with ship-based incubations to quantify prokaryote-driven removal rates of suspended and sinking total organic carbon (TOC). Samples were collected below the mixed layer during three stages of a spring Phaeocystis pouchetii bloom in the Labrador Sea. Phaeocystis blooms can dominate regional phytoplankton biomass and are expected to increase under future climate. Removal rates were used as a proxy for carbon lability and combined with 16S rRNA metabarcoding and carbon composition analyses to link microbial community structure with substrate characteristics. Removal rates of sinking particles (0.02-0.06 d-1) were an order of magnitude higher than those of suspended TOC (0.002 d-1) during bloom-decline and non-bloom. In contrast, during late-bloom, suspended carbon exhibited rates of 0.01 d-1, comparable to sinking particles, and was enriched in exopolymer-rich colonies. Prokaryotic community composition varied primarily among bloom stages rather than carbon fractions, indicating that bloom stage-- and thus particle origin and composition--was the dominant control on bacterial degradation and assembly. Bacterial diversity peaked where carbon was refractory and originated from mixed phytoplankton. Together, these results demonstrate that suspended Phaeocystis-derived carbon can be rapidly remineralized when blooms produce exopolymer-rich colonies and highlight bloom stage as key regulator of microbial carbon processing and biological pump efficiency.

microbiology↗

bioRxiv2024

Intense storms affect sinking particle fluxes after the North Atlantic diatom spring bloom

The sinking of large particles (i.e., marine snow) has long been recognized as a key pathway for efficient particulate organic carbon (POC) export to the ocean interior during the decline of spring diatom blooms. Recent work has suggested that particles smaller than marine snow can also substantially contribute to POC export. However, a detailed characterization of small and large sinking particles at the end of blooms is missing. Here, we separately collected suspended and small and large sinking particles using Marine Snow Catchers and assessed their biogeochemical composition after the North Atlantic spring bloom in May 2021. During the three weeks of sampling, when four intense storms (maximum wind speeds 37 - 50 kts) created high turbulent energy dissipation rates and deepened the mixed layer, we observed two distinct sedimentation episodes. During the storm periods, sinking particles were dominated by small (diameter < 0.1 mm), slow-sinking (~18 m d-1), silica-rich particles that carried a moderate POC flux (< 6 mmol C m-2 d-1) to 500 m depth. Once the storms ceased, the volume of large (diameter > 0.1 mm), fast-sinking (> 75 m d-1), carbon-rich marine snow aggregates (not fecal pellets) increased exponentially and POC fluxes at 100 m depth were more than fourfold greater (30{+/-}12 mmol C m-2 d-1) than those during the previous event. The aggregates consisted of a mixed post-bloom plankton community. Our data suggest that the intense storms determined the timing, type, and magnitude of POC flux at the end of a spring phytoplankton bloom.

biochemistry↗

bioRxiv2023

Toward a synthesis of phytoplankton community composition methods for global-scale application

The composition of the marine phytoplankton community has been shown to impact many biogeochemical processes and marine ecosystem services. A variety of methods exist to characterize phytoplankton community composition (PCC), with varying degrees of taxonomic resolution. Accordingly, the resulting PCC determinations are dependent on the method used. Here, we use surface ocean samples collected in the North Atlantic and North Pacific Oceans to compare high performance liquid chromatography (HPLC) pigment-based PCC to four other methods: quantitative cell imaging, flow cytometry, and 16S and 18S rRNA amplicon sequencing. These methods allow characterization of both prokaryotic and eukaryotic PCC across a wide range of size classes. PCC estimates of many taxa resolved at the class level (e.g., diatoms) show strong positive correlations across methods, while other groups (e.g., dinoflagellates) are not well captured by one or more methods. Since variations in phytoplankton pigment concentrations are related to changes in optical properties, this combined dataset expands the potential scope of ocean color remote sensing by associating PCC at the genus- and species-level with group- or class-level PCC from pigments. Quantifying the strengths and limitations of pigment-based PCC methods compared to PCC assessments from amplicon sequencing, imaging, and cytometry methods is the first step toward the robust validation of remote sensing approaches to quantify PCC from space.

ecology↗

bioRxiv2023

Quantitative analysis of food web dynamics in a low export ecosystem

Food webs trace the flow of organic matter and energy among producers and consumers; for pelagic marine food webs, network complexity directly influences the amount and form of carbon exported to the deep ocean via the biological pump. Here we present a synoptic view of mixed layer food web dynamics observed during the late summer 2018 EXport Processes in the Ocean from Remote Sensing (EXPORTS) field campaign in the subarctic Northeast Pacific at the long-running time-series site, Ocean Station Papa. Carbon biomass reservoirs of phytoplankton, microzooplankton, and bacterioplankton, were approximately equal while mesozooplankton biomass was 70% lower. Live organisms composed [~]40% of the total particulate organic carbon within the mixed layer: the remainder was attributed to detritus. Rates of carbon transfer among reservoirs indicated production and assimilation rates were well balanced by losses, leaving little organic carbon available for export. The slight positive net community production rate generated organic carbon that was exported from the system in the form of food web byproducts, such as large fecal pellets generated by mesozooplankton. This characteristically regenerative food web had relatively slow turnover times with small-magnitude transfers of carbon relative to standing stocks that occurred amidst a high background concentration of detrital particles and dissolved organic matter. The concurrent estimation of food web components and rates revealed that separated processes dominated the transfer of carbon within the food web compared to those that contributed to export. Plain Language SummaryThe biological carbon pump drives a downward flux of organic matter from the sunlit surface ocean to the vast ocean interior. Ecological interactions in the surface ocean directly affect the amount and type of carbon that is exported to the deep ocean. In this study, we present a synthesis of the late summer mixed layer food web in the Northeast Pacific that was extensively characterized during the 2018 EXport Processes in the Ocean from Remote Sensing (EXPORTS) field campaign. We found the majority of carbon was recycled within the mixed layer by microbes through multiple transfers between producers and consumers. Larger organisms, mesozooplankton and salps, only consumed a small amount of carbon but through the formation of sinking fecal pellets were the main mechanism of transporting carbon out of the system. The study highlights the need to concurrently study microbial and large organism dynamics to develop a predictive understanding of the fate of organic carbon in the oceans. Key PointsO_LIThe microbial loop dominated carbon flow in the late summer mixed layer food web of the North Pacific, most net production was respired leaving little carbon available for export. C_LIO_LIActive production and consumption of organic carbon occurred amid a high background of detrital particulate organic carbon (58% of total) with slow turnover time, 66 d. C_LIO_LIMesozooplankton which had relatively minor carbon consumption rates created the majority of export production due to efficient repackaging of consumed material. C_LI

ecology↗

bioRxiv2023

Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection

The major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective antiretroviral therapy (ART). Most prior host genetic HIV studies have focused on identifying DNA polymorphisms (e.g., CCR5{Delta}32, MHC class I alleles) associated with viral load among untreated "elite controllers" (~1% of HIV+ individuals who are able to control virus without ART). However, there have been few studies evaluating host genetic predictors of viral control for the majority of people living with HIV (PLWH) on ART. We performed host RNA sequencing and HIV reservoir quantification (total DNA, unspliced RNA, intact DNA) from peripheral CD4+ T cells from 191 HIV+ ART-suppressed non-controllers. Multivariate models included covariates for timing of ART initiation, nadir CD4+ count, age, sex, and ancestry. Lower HIV total DNA (an estimate of the total reservoir) was associated with upregulation of tumor suppressor genes NBL1 (q=0.012) and P3H3 (q=0.012). Higher HIV unspliced RNA (an estimate of residual HIV transcription) was associated with downregulation of several host genes involving inflammasome (IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9, CXCL3, CXCL10) and innate immune (TLR7) signaling, as well as novel associations with potassium (KCNJ2) and gap junction (GJB2) channels, all q<0.05. Gene set enrichment analyses identified significant associations with TLR4/microbial translocation (q=0.006), IL-1{beta}/NRLP3 inflammasome (q=0.008), and IL-10 (q=0.037) signaling. HIV intact DNA (an estimate of the "replication-competent" reservoir) demonstrated trends with thrombin degradation (PLGLB1) and glucose metabolism (AGL) genes, but data were (HIV intact DNA detected in only 42% of participants). Our findings demonstrate that among treated PLWH, that inflammation, innate immune responses, bacterial translocation, and tumor suppression/cell proliferation host signaling play a key role in the maintenance of the HIV reservoir during ART. Further data are needed to validate these findings, including functional genomic studies, and expanded epidemiologic studies in female, non-European cohorts. Author SummaryAlthough lifelong HIV antiretroviral therapy (ART) suppresses virus, the major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective ART, "the HIV reservoir." HIV eradication strategies have focused on eliminating residual virus to allow for HIV remission, but HIV cure trials to date have thus far failed to show a clinically meaningful reduction in the HIV reservoir. There is an urgent need for a better understanding of the host-viral dynamics during ART suppression to identify potential novel therapeutic targets for HIV cure. This is the first epidemiologic host gene expression study to demonstrate a significant link between HIV reservoir size and several well-known immunologic pathways (e.g., IL-1{beta}, TLR7, TNF- signaling pathways), as well as novel associations with potassium and gap junction channels (Kir2.1, connexin 26). Further data are needed to validate these findings, including functional genomic studies and expanded epidemiologic studies in female, non-European cohorts.

genetics↗

bioRxiv2021

Host Variation in Interferon, MHC Class I, Glycosylation, and Viral Transcription Genes Predict HIV Persistence

ObjectivePrior genomewide association studies have identified variation in MHC Class I alleles and CCR5{Delta}32 as genetic predictors of viral control, especially in "elite" controllers, individuals who remain virally suppressed in the absence of therapy. DesignCross-sectional genomewide association study. MethodsWe analyzed custom whole exome sequencing and direct HLA typing from 202 ART-suppressed HIV+ non-controllers in relation to four measures of the peripheral CD4+ T cell reservoir: HIV intact DNA, total (t)DNA, unspliced (us)RNA, and RNA/DNA. Linear mixed models were adjusted for potential covariates including age, sex, nadir CD4+ T cell count, pre-ART HIV RNA, timing of ART initiation, and duration of ART suppression. ResultsPreviously reported "protective" host genetic mutations related to viral setpoint (e.g., among elite controllers) were found to predict smaller HIV reservoir size. The HLA "protective" B*57:01 was associated with significantly lower HIV usRNA (q=3.3x10-3), and among the largest subgroup, European ancestry individuals, the CCR5{Delta}32 deletion was associated with smaller HIV tDNA (p=4.3x10-3) and usRNA (p=8.7x10-3). In addition, genomewide analysis identified several SNPs in MX1 (an interferon stimulated gene) that were significantly associated with HIV tDNA (q=0.02), and the direction of these associations paralleled MX1 gene eQTL expression. ConclusionsWe observed a significant association between previously reported "protective" MHC class I alleles and CCR5{Delta}32 with the HIV reservoir size in non-controllers. We also found a novel association between MX1 and HIV total DNA (in addition to other interferon signaling relevant genes, PPP1CB, DDX3X). These findings warrant further investigation in future validation studies.

genomics↗

bioRxiv2021

Metazoans, migrations, and the ocean's biological carbon pump

The daily vertical migrations of fish and other metazoans actively transport organic carbon from the ocean surface to depth, contributing to the biological carbon pump. We use an oxygen-constrained, game-theoretic food-web model to simulate diel vertical migrations and estimate global carbon fluxes and sequestration by fish and zooplankton due to respiration, fecal pellets, and deadfalls. Our model provides estimates of the carbon export and sequestration potential for a range of pelagic functional groups, despite uncertain biomass estimates of some functional groups. While the export production of metazoans and fish is modest (~20% of global total), we estimate that their contribution to carbon sequestered by the biological pump (~ 800 PgC) is conservatively more than 50% of the estimated global total (~1300 PgC) and have a significantly longer sequestration time scale (~250 years) than previously reported for other components of the biological pump. Fish and multicellular zooplankton contribute about equally to this sequestered carbon pool. This essential ecosystem service could be at risk from both unregulated fishing on the high seas and ocean deoxygenation due to climate change.

ecology↗

bioRxiv2020

MPRAudit Quantifies the Fraction of Variance Described by Unknown Features in Massively Parallel Reporter Assays

Transformative advances in molecular technologies, such as massively parallel reporter assays (MPRAs) and CRISPR screens, can efficiently characterize the effects of genetic and genomic variation on cellular phenotypes. Analysis approaches to date have focused on identifying individual genomic regions or genetic variants that perturb a phenotype of interest. In this work, we develop a wholistic framework (MPRAudit) to determine the global contribution of sequence to phenotypic variation across subsets of the entire experiment, opening the door to myriad novel analyses. For example, MPRAudit can reliably estimate the upper limit of predictive performance, the fraction of variation attributed to specific biological categories, and the total contribution of experimental noise. We demonstrate through simulation and application to several types of real MPRA data sets how MPRAudit can lead to an improved understanding of experimental quality, molecular biology, and guide future research. Applying MPRAudit to real MPRA data, we observe that sequence variation is the primary driver of outcome variability, but that known biological categories explain only a fraction of this variance. We conclude that our understanding of how sequence variation impacts phenotype, even at the level of MPRAs, remains open to further scientific discovery.

bioinformatics↗

bioRxiv2020

No detectable alloreactive transcriptional responses during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells

Single-cell RNA sequencing (scRNA-seq) provides high-dimensional measurement of transcript counts in individual cells. However, high assay costs limit the study of large numbers of samples. Sample multiplexing technologies such as antibody hashing and MULTI-seq use sample-specific sequence tags to enable individual samples (e.g., different patients) to be sequenced in a pooled format before downstream computational demultiplexing. Critically, no study to date has evaluated whether the mixing of samples from different donors in this manner results in significant changes in gene expression resulting from alloreactivity (i.e., response to non-self immune antigens). The ability to demonstrate minimal to no alloreactivity is crucial to avoid confounded data analyses, particularly for cross-sectional studies evaluating changes in immunologic gene signatures. Here, we compared the expression profiles of peripheral blood mononuclear cells (PBMCs) from a single donor with and without pooling with PBMCs isolated from other donors with different blood types. We find that there was no evidence of alloreactivity in the multiplexed samples following three distinct multiplexing workflows (antibody hashing, MULTI-seq, and in silico genotyping using souporcell). Moreover, we identified biases amongst antibody hashing sample classification results in this particular experimental system, as well as gene expression signatures linked to PBMC preparation method (e.g., Ficoll-Paque density gradient centrifugation with or without apheresis using Trima filtration).

genomics↗

bioRxiv2020

Massively Parallel Analysis of Human 3' UTRs Reveals that AU-Rich Element Length and Registration Predict mRNA Destabilization

AU-rich elements (AREs) are 3' UTR cis-regulatory elements that regulate the stability of mRNAs. Consensus ARE motifs have been determined, but little is known about how differences in 3' UTR sequences that conform to these motifs affect their function. Here we use functional annotation of sequences from 3' UTRs (fast-UTR), a massively parallel reporter assay (MPRA), to investigate the effects of 41,288 3' UTR sequence fragments from 4,653 transcripts on gene expression and mRNA stability. The library included 9,142 AREs, and incorporated a set of fragments bearing mutations in each ARE. Our analyses demonstrate that the length of an ARE and its registration (the first and last nucleotides of the repeating ARE motif) have significant effects on gene expression and stability. Based on this finding, we propose improved ARE classification and concomitant methods to categorize and predict the effect of AREs on gene expression and stability. Our new approach explains 64{+/-}13% of the contribution of AREs to the stability of human 3' UTRs in Jurkat cells and predicts ARE activity in an unrelated cell type. Finally, to investigate the advantages of our general experimental design for annotating 3' UTR elements we examine other motifs including constitutive decay elements (CDEs), where we show that the length of the CDE stem-loop has a significant impact on steady-state expression and mRNA stability. We conclude that fast-UTR, in conjunction with our analytical approach, can produce improved yet simple sequence-based rules for predicting the activity of human 3' UTRs containing functional motifs.

genomics↗