Biology subjects

Crowley, C. A.

Publications and source records attributed to Crowley, C. A..

5 recordsLinked to original sources

bioRxiv2026

Bloom-forming bacteria heavily invest in anti-phage defense

Bacterial blooms are characterized by unusually high cell densities and exceptionally low diversity and can profoundly alter ecosystem function and services. Bacteriophages have long been considered an important cause of mortality in blooms, acting as a mechanism for control. Here, we characterize the viral ecology of a long-lasting estuarine bloom of green sulfur bacteria (Chlorobiota). We combined direct cell and viral counts with metagenomic and metaproteomic data to characterize host and phage activity at different time points. The abundance of virus-like particles (VLPs) decreased at high cell densities, suggesting reduced lytic infection rates. The dominant organism, GSB-TRL01 (genus Prosthecochloris), apparently contained a large conjugative plasmid encoding five different anti-phage defense systems. The organism's genome encoded 13 additional defense systems. Compared to the average of five defense systems per microbial genome, this enrichment suggests robust anti-phage defense capabilities. Proteins from ten different defense systems on GSB-TRL01's genome and four systems from the conjugative plasmid were expressed in the proteome. This suggests that GSB-TRL01 invests heavily in anti-phage defense, leading to reduced lysis at high cell densities and allowing blooms to persist for weeks to months. To determine whether this ability is widespread among bloom forming organisms, we compared genomes of putative bloomers to those of non-blooming organisms. We found that bloomer genomes were significantly enriched with anti-phage defense systems. This challenges traditional paradigms of phage ecology in bloom-forming systems and suggests that microbes adapted to high-density growth may have evolved mechanisms to reduce their susceptibility to phage attack.

microbiology↗

bioRxiv2026

Anoxygenic phototrophic Chlorobi use broad metabolic and resource acquisition strategies to support stable near-clonal blooms

Anoxygenic phototrophic green sulfur bacteria (GSB; Chlorobiia) are important primary producers in anoxic and sulfidic environments, whose significance in aquatic ecosystems will expand with coastal deoxygenation. Here, we employed a uniquely comprehensive analytical approach to investigate the formation, maintenance, and collapse of a GSB bloom. We combined multi-omics -- V4V5 and synthetic long read 16S rRNA amplicon sequencing, metagenomics, and metaproteomics -- with total and GSB-specific cell counts, biogeochemical measurements, and isotopic analysis. The GSB bloom exceeded 109 cells ml-1, among the highest environmental cell densities reported to date, with up to 96 % of the bloom consisting of a single strain-level Prosthecochloris lineage (GSB-TRL01). Extreme sulfide concentrations (> 17 mM) coincided with peaking cell density and a shift in isotopic composition. Bloom persistence is supported by tightly coupled sulfur cycling, high rates of nitrogen fixation, mechanisms to tolerate oxidative stress and maintain redox balance, and nutrient acquisition through outer membrane transport systems. A shift in sulfur oxidizing enzymes towards enzymes with higher sulfide affinity proceeded bloom demise. Prosthecochloris GSB-TRL01 differs from closely related lineages in several outer membrane transport systems, including porins to transport phosphate and tonB-dependent transporters. Collectively, these findings identify physiological and metabolic strategies that may enable near-clonal Prosthecochloris populations to attain extraordinary biomass while coupling the sulfur, carbon, and nitrogen cycles in coastal euxinic environments.

microbiology↗

bioRxiv2025

Host species and body site equally impact microbiome structure between sympatric Atlantic sea cucumber species

Sea cucumbers are key members in the marine ecosystem, food webs, and support valuable commercial fisheries, yet their microbiomes, which likely influence host health and function, are relatively understudied. There is specifically a paucity of microbiome studies of echinoderm coelomic fluid (CF), which is centrally involved in circulation, digestion, and immunity. This study analyzed the microbiomes of two sympatric holothurians (sea cucumbers), Leptosynapta tenuis, and Sclerodactyla briareus, found in coastal, temperate waters of the Northeast Atlantic. First, we found unexpectedly high levels (approaching 107 cells/ml) of prokaryotic-sized cells in the coelomic fluid of the sympatric sea star Asterias forbesi. Amplicon sequencing of the 16S rRNA gene revealed significant differences in alpha and beta diversity of sea cucumber microbiomes. This included differences in CF communities between the two sea cucumber species and among body sites--CF, epidermis, and gut--of S. briareus. Host and body sites explained roughly equal amounts of microbial community variation (22% and 27%, respectively). We identified particular taxa associated with differences in community composition, including enrichment of anaerobic taxa (e.g., Desulftobacterota) in gut samples and Proteobacteria (including Burkholderiales and Pseudomonadales) in epidermis samples. We also uncovered higher levels of Synechococcales cyanobacteria in CF relative to the gut, epidermis, and background seawater samples. CF is thought to exchange with surrounding seawater, so these results highlight an apparent selective retention of CF microbial communities. This work adds to our growing knowledge of echinoderm microbiomes and highlights the need for additional surveys of their microbiomes. ImportanceMicrobiomes influence the function and health of animal hosts, but basic characterization of sea cucumber microbiomes is lacking. Furthermore, there are few studies on the microbiomes of echinoderm coelomic fluid that interacts with the respiratory, digestion, locomotion, and reproduction systems of these animals. To fill these gaps in knowledge, we analyzed the microbiomes of two sea cucumber and one sea star species from the North Atlantic. We found unexpectedly high abundances of bacteria-sized cells in the coelomic fluid of all three species. Using DNA sequencing, we uncovered differences in bacterial communities across the two sea cucumber species and across body sites (the epidermis, gut, and coelomic fluid) within one host species. This is consistent with patterns of host and body-site specificity seen in animal other microbiome studies. These results build important information for sea cucumbers that play important roles in natural marine ecosystems and support globally important fisheries.

microbiology↗

bioRxiv2021

VAMPIRE: A model blood cell trait focused annotation tool for interpretation and prioritization of complex trait genome-wide association study results

Genome-wide association studies (GWAS) have identified hundreds of thousands of genetic variants associated with complex diseases and traits. However, most variants are noncoding and not clearly linked to genes, making it challenging to interpret these GWAS signals. We present a systematic variant-to-function study, prioritizing the most likely functional elements of the genome for experimental follow-up, for >148,000 variants identified for hematological traits. Specifically, we developed VAMPIRE: Variant Annotation Method Pointing to Interesting Regulatory Effects, an interactive web application implemented in R Shiny (http://shiny.bios.unc.edu/vampire/). This tool efficiently integrates and displays information from multiple complementary sources, including epigenomic signatures from blood cell relevant tissues or cells, functional and conservation summary scores, variant impact on protein and gene expression, chromatin conformation information, as well as publicly available GWAS and phenome-wide association study (PheWAS) results. Leveraging data generated from independently performed functional validation experiments, we demonstrate that our prioritized variants, genes, or variant-gene links are significantly more likely to be experimentally validated. This study not only has important implications for systematic and efficient revelation of functional mechanisms underlying GWAS variants for hematological traits, but also provides a prototype that can be adapted to many other complex traits, paving the path for efficient variant to function (V2F) analyses.

genetics↗

bioRxiv2020

Neuronal and glial 3D chromatin architecture illustrates cellular etiology of brain disorders

Cellular heterogeneity in the human brain obscures the identification of robust cellular regulatory networks. Here we integrated genome-wide chromosome conformation in purified neurons and glia with transcriptomic and enhancer profiles to build the gene regulatory landscape of two major cell classes in the human brain. Within glutamatergic and GABAergic neurons, we were able to link enhancers to their cognate genes via neuronal chromatin interaction profiles. These cell-type-specific regulatory landscapes were then leveraged to gain insight into the cellular etiology of several brain disorders. We found that Alzheimers disease (AD)-associated epigenetic dysregulation was linked to neurons and oligodendrocytes, whereas genetic risk factors for AD highlighted microglia as a central cell type, suggesting that different cell types may confer risk to the disease via different genetic mechanisms. Moreover, neuronal subtype-specific annotation of genetic risk factors for schizophrenia and bipolar disorder identified shared (parvalbumin-expressing interneurons) and distinct cellular etiology (upper layer neurons for bipolar and deeper layer projection neurons for schizophrenia) between these two closely related psychiatric illnesses. Collectively, these findings shed new light on cell-type-specific gene regulatory networks in brain disorders.

neuroscience↗