Biology subjects

Crowe, S. A.

Publications and source records attributed to Crowe, S. A..

10 recordsLinked to original sources

bioRxiv2024

Sulfur oxidation through rDsr in a novel Sox-free marine Roseobacter lineage

Sulfur oxidation drives nutrient and energy flow in marine sediments. Bacteria typically oxidize thiosulfate, a key sulfur intermediate, either through a complete Sox system or through an incomplete Sox system that feeds zero valent sulfur into the reverse dissimilatory sulfite reductase (rDsr) pathway. Whether rDsr alone can oxidize thiosulfate has been unclear. Here we show that ten intertidal Ruegeria strains carry a complete rDsr pathway but lack all sox genes. Under low oxygen (2% O2) but not under air, thiosulfate activates the pathway, enhances growth, and is associated with accelerated nitrate reduction. Using a CRISPR base editing tool for Ruegeria, we demonstrate that disrupting dsrA, which encodes a subunit of the core rDsr enzyme, significantly delays thiosulfate consumption, suggesting that rDsr is actively involved in oxidation. Previous work only documented rDsr acting downstream of an incomplete Sox system; our results establish that a standalone rDsr pathway is sufficient for thiosulfate consumption under oxygen limitation and that this activity can feed electrons into the denitrification pathway. Metagenomic surveys show rDsr genes from this group are widespread in low oxygen marine environments, including coastal sediments where they account for up to 26% of all rDsr genes. These findings revise the view that thiosulfate oxidation depends on Sox and highlight rDsrs ecological role in deoxygenated habitats.

ecology↗

bioRxiv2023

Emergence of Prochlorococcus in the Tonian oceans and the initiation of Neoproterozoic oxygenation

Prochlorococcus are the smallest and most abundant photosynthetic organisms on Earth, contributing up to 50% of the chlorophyll in the oligotrophic oceans. Despite being important in regulating the carbon cycle in todays ocean, the ecological significance of Prochlorococcus in Earths history remains elusive. Our new robustly calibrated molecular clock analysis reveals that Prochlorococcus emerged in the deep photic zone of the Tonian (1,000-720 Mya) oceans. The classical light-harvesting antenna complex in Cyanobacteria, i.e., the phycobilisome, was replaced in Prochlorococcus by the chlorophyll{square}based antenna, enabling more efficient use of blue light that penetrates into deeper water. Importantly, Prochlorococcus colonization of deep water enhanced access to phosphate, which was abundant in upwelled seawater, but likely scarce in the Tonian surface ocean, promoting expansion of Prochlorococcus, displacement of incumbent low-light adapted anoxygenic photoferrotrophs, and associated increases in photosynthetic oxygen production. Colonization of deeper waters would also have improved access to ammonium, leading to the neutral loss of nitrate utilization genes. Our research thus documents the conspicuous emergence of new photosynthetic bacterial lineages in the run-up to the Neoproterozoic oxygenation event, implying an additional layer of eco-evolutionary complexity during this pivotal interval in Earths history.

microbiology↗

bioRxiv2022

The dietary fiber guar gum ameliorates experimental autoimmune encephalomyelitis via attenuated Th1 activation and differentiation

Dietary fibers are potent modulators of immune responses that can restrain inflammation in multiple disease contexts. However, dietary fibers encompass a biochemically diverse family of carbohydrates, and it remains unknown how different fiber sources influence immunity. In a head-to-head comparison of four different high-fiber diets, we demonstrate a unique and potent ability of guar gum to reduce neuroinflammation in experimental autoimmune encephalomyelitis (EAE), a T cell-mediated mouse model of multiple sclerosis. CD4+ T cells from guar gum-fed mice have blunted Th1-skewing, reduced migratory capacity, and limited activation and proliferative capabilities. These changes are not explained by guar gum-specific alterations to the microbiota at the 16S rRNA level, nor by specific alterations in short chain fatty acids. These findings demonstrate specificity in the host response to fiber sources, and define a new pathway of fiber-induced CD4+ T cell immunomodulation that protects against pathologic neuroinflammation.

immunology↗

bioRxiv2022

Virus Infection Causes Intestinal Dysbiosis to Promote Type 1 Diabetes Onset

Autoimmune disorders like type 1 diabetes (T1D) are complex diseases caused by numerous factors including both genetic variance and environmental influences. Two such exogenous factors, intestinal microbial composition and enterovirus infection, have been independently associated with T1D onset in both humans and animal models. Since environmental factors rarely work in isolation, we examined the cross-talk between the microbiome and Coxsackievirus B4 (CVB4), an enterovirus that accelerates T1D onset in non-obese diabetic (NOD) mice. We demonstrate that CVB4-infection induced restructuring of the intestinal microbiome prior to T1D onset that was associated with thinning of the mucosal barrier, bacterial translocation to the pancreatic lymph node, and increased detection of circulating and intestinal commensal-reactive antibodies. Notably, the CVB4-induced change in community composition was strikingly similar to that of uninfected NOD mice that spontaneously developed diabetes, thus implying a mutual "diabetogenic" microbiome. Furthermore, fecal microbiome transfer (FMT) of the diabetogenic microbiota from CVB4-infected mice was sufficient to enhance T1D susceptibility in naive NOD recipients. These findings support a model whereby CVB infection disrupts the microbiome and intestinal homeostasis in a way that promotes activation of autoreactive immune cells and T1D.

microbiology↗

bioRxiv2020

Snowball Earths, population bottlenecks, and the evolution of marine photosynthetic bacteria

Prochlorococcus are the most abundant photosynthetic organisms in the modern ocean. A massive DNA loss event occurred in their early evolutionary history, leading to highly reduced genomes in nearly all lineages, as well as enhanced efficiency in both nutrient uptake and light absorption. The environmental landscape that shaped this ancient genome reduction, however, remained unknown. Through careful molecular clock analyses, we established that this Prochlorococcus genome reduction occurred during the Neoproterozoic Snowball Earth climate catastrophe. The lethally low temperature and exceedingly dim light during the Snowball Earth event would have inhibited Prochlorococcus growth and proliferation and caused severe population bottlenecks. These bottlenecks are recorded as an excess of deleterious mutations that accumulated across genomic regions in the descendant lineages. Prochlorococcus adaptation to extreme environmental conditions during Snowball Earth intervals can be inferred by tracing the evolutionary paths of genes that encode key metabolic potential. This metabolic potential includes modified lipopolysaccharide structure, strengthened peptidoglycan biosynthesis, the replacement of a sophisticated circadian clock with an hourglass-like mechanism that resets daily for dim light adaption, and the adoption of ammonia diffusion as an efficient membrane transporter-independent mode of nitrogen acquisition. In this way, the Neoproterozoic Snowball Earth event altered the physiological characters of Prochlorococcus, shaping their ecologically vital role as the most abundant primary producers in the modern oceans.

microbiology↗

bioRxiv2020

STAT1-dependent tolerance of intestinal viral infection

Recent evidence indicates that viral components of the microbiota can contribute to intestinal homeostasis and protection from local inflammatory or infectious insults. However, host-derived mechanisms that maintain tolerance to the virome remain largely unknown. Here, we use colonization with the model commensal murine norovirus (MNV CR6) to interrogate host-directed mechanisms of viral tolerance, and show that STAT1 is a central coordinator of tolerance following CR6 colonization. STAT1 restricts CR6 replication to the intestinal tract, prevents systemic viral-induced tissue damage and disease, and regulates antiviral CD4+ and CD8+ T cell responses. In contrast to systemic viral pathogens that drive T cell mediated immunopathology in STAT1-deficient mice, our data indicates that loss of CD4+ or CD8+ T cells and their associated effector functions has no effect on CR6-induced disease. However, therapeutic administration of an antiviral compound to limit viral replication prevented viral-induced tissue damage and death despite ongoing dysregulated antiviral T cell responses. Collectively, our data uncouple the requirement for STAT1-mediated regulation of antiviral T cell responses from innate immune-mediated restriction of viral replication that is necessary for intestinal viral tolerance.

immunology↗

bioRxiv2019

Expression of extracellular multiheme cytochromes discovered in a betaproteobacterium during Mn(III) reduction

Soluble ligand-bound Mn(III) can support anaerobic microbial respiration in diverse aquatic environments. Thus far, Mn(III) reduction has only been associated with certain Gammaproteobacteria. Here, we characterized microbial communities enriched from Mn-replete sediments of Lake Matano, Indonesia. Our results provide the first evidence for biological reduction of soluble Mn(III) outside the Gammaproteobacteria. Metagenome assembly and binning revealed a novel betaproteobacterium, which we designate "Candidatus Dechloromonas occultata." This organism dominated the enrichment and expressed a porin-cytochrome c complex typically associated with iron-oxidizing Betaproteobacteria and a novel cytochrome c-rich protein cluster (Occ), including an undecaheme putatively involved in extracellular electron transfer. This occ gene cluster was also detected in diverse aquatic bacteria, including uncultivated Betaproteobacteria from the deep subsurface. These observations provide new insight into the taxonomic and functional diversity of microbially-driven Mn(III) reduction in natural environments. Originality-Significance StatementRecent observations suggest that Mn(III)-ligand complexes are geochemically important in diverse aquatic environments. Thus far, microbially-driven Mn(III) reduction has only been associated with Gammaproteobacteria encoding three-component outer-membrane porin-cytochrome c conduits. Here, we demonstrate that Betaproteobacteria dominate in abundance and with respect to protein expression during biologically-mediated Mn(III) reduction in an enrichment culture from an anoxic lacustrine system. Using metaproteomics, we detect for the first time that Betaproteobacteria express a two-component porin-cytochrome c conduit, and an uncharacterized extracellular undecaheme (11-heme) c-type cytochrome. Although this is the first definitive report of an undecaheme within the Betaproteobacteria, we find evidence that they are widespread in uncultivated strains. These results widen the phylogenetic diversity of Mn(III)-reducing bacteria, and provide new insights into potential molecular mechanisms for soluble Mn(III) reduction

microbiology↗

bioRxiv2019

In vitro prototyping and rapid optimization of biosynthetic enzymes for cellular design

Microbial cell factories offer an attractive approach for production of biobased products. Unfortunately, designing, building, and optimizing biosynthetic pathways remains a complex challenge, especially for industrially-relevant, non-model organisms. To address this challenge, we describe a platform for in vitro Prototyping and Rapid Optimization of Biosynthetic Enzymes (iPROBE). In iPROBE, cell lysates are enriched with biosynthetic enzymes by cell-free protein synthesis and then metabolic pathways are assembled in a mix-and-match fashion to assess pathway performance. We demonstrate iPROBE with two examples. First, we tested and ranked 54 different pathways for 3-hydroxybutyrate production, improving in vivo production in Clostridium by 20-fold to 14.63 {+/-} 0.48 g/L and identifying a new biosynthetic route to (S)-(+)-1,3-butanediol. Second, we used iPROBE and data-driven design to optimize a 6-step n-butanol pathway, increasing titers 4-fold across 205 pathways, and showed strong correlation between cell-free and cellular performance. We expect iPROBE to accelerate design-build-test cycles for industrial biotechnology.

synthetic biology↗

bioRxiv2019

Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes

Electroactive type IV pili, or e-pili, are used by some microbial species for extracellular electron transfer. Recent studies suggest that e-pili may be more phylogenetically and structurally diverse than previously assumed. Here, we used updated aromatic density thresholds ([≥]9.8% aromatic amino acids, [≤]22-aa aromatic gaps, and aromatic amino acids at residues 1, 24, 27, 50 and/or 51, and 32 and/or 57) to search for putative e-pilin genes in metagenomes from diverse ecosystems with active microbial metal cycling. Environmental putative e-pilins were diverse in length and phylogeny, and included truncated e-pilins in Geobacter spp., as well as longer putative e-pilins in Fe(II)-oxidizing Betaproteobacteria and Zetaproteobacteria.\n\nOriginality and SignificanceElectroactive pili (e-pili) are used by microorganisms to respire solid metals in their environment through extracellular electron transfer. Thus, e-pili enable microbes to occupy specific environmental niches. Additionally, e-pili have important potential for biotechnological applications. Currently the repertoire of known e-pili is small, and their environmental distribution is largely unknown. Using sequence analysis, we identified numerous genes encoding putative e-pili from diverse anoxic, metal-rich ecosystems. Our results expand the diversity of putative e-pili in environments where metal oxides may be important electron acceptors for microbial respiration.

microbiology↗

bioRxiv2016

Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment incubations

Reactive Fe(III) minerals can influence methane (CH4) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH4 oxidation. The balance between Fe(III) reduction, methanogenesis, and methane oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH4 fluxes to the atmosphere, thereby regulating the capacity for CH4 to warm the early Earth under the Faint Young Sun. We studied CH4 and Fe cycling in anoxic incubations of ferruginous sediment from the ancient ocean analogue Lake Matano, Indonesia over three successive transfers (500 days total). Iron reduction, methanogenesis, methane oxidation, and microbial taxonomy were monitored in treatments amended with ferrihydrite or goethite. After three dilutions, Fe(III) reduction persisted only in bottles with ferrihydrite. Enhanced CH4 production was observed in the presence of goethite, highlighting the potential for reactive Fe(III)-oxides to inhibit methanogenesis. Supplementing the media with hydrogen, nickel and selenium did not stimulate methanogenesis. There was limited evidence for Fe(III)-dependent CH4 oxidation, although some incubations displayed CH4-stimulated Fe(III)-reduction. 16S rRNA profiles continuously changed over the course of enrichment, with ultimate dominance of unclassified members of the order Desulfuromonadales in all treatments. Microbial diversity decreased markedly over the course of incubation, with subtle differences between ferrihydrite and goethite amendments. These results suggest that Fe(III)-oxide mineralogy and availability of electron donors could have led to spatial separation of Fe(III)-reducing and methanogenic microbial communities in ferruginous marine sediments, potentially explaining the persistence of CH4 as a greenhouse gas throughout the first half of Earth history.

microbiology↗