Biology subjects

Wallace, B. A.

Publications and source records attributed to Wallace, B. A..

7 recordsLinked to original sources

bioRxiv2026

Temperate and filamentous bacteriophages as reservoirs of bacterial virulence in stony coral tissue loss disease

Lysogenic conversion, in which bacteriophages (viruses that infect bacteria) integrate into bacterial genomes and confer new phenotypic traits on their hosts, is a well-established mechanism for the emergence of pathogens. While this process underpins many bacterial diseases in humans and other animals, its role in coral disease remains largely unexplored. Here, we investigate the potential role of lysogenic conversion in stony coral tissue loss disease (SCTLD), which has caused unprecedented mortality of Caribbean corals since 2014 and for which the etiological agent remains unknown. Across 27 original coral samples and 178 publicly available metagenomes from the Florida Reef Tract spanning seven coral species, we detected a greater number of unique viral genomes capable of lysogeny in diseased corals or visually healthy portions of diseased corals (DD and HD, respectively) compared to visually healthy (VH) corals. SCTLD-associated bacteriophages were primarily predicted to infect bacterial taxa previously implicated in the disease, such as Vibrionales, Rhodobacterales, and Flavobacteriia, and carried abundant and widespread virulence genes with the potential to enhance bacterial colonization, competition, or direct host damage, including homologs of Tse2, Zot, RTX, pneumolysin, and cytolytic delta-endotoxin. Although causal relationships remain unresolved, our findings indicate that phages capable of lysogenic conversion have the genomic capacity to laterally transfer bacterial virulence genes in SCTLD-affected corals. The acquisition of genes via lysogenic conversion could contribute to bacterial virulence while maintaining community taxonomic profiles, helping to explain previous community profiling observations and providing a mechanistic framework for disease pathogenesis.

genomics↗

bioRxiv2026

Prophage induction shifts community composition and functional capacity in a Sargassum-derived multispecies biofilm

BackgroundPelagic Sargassum has undergone significant range expansion and dramatic blooms in the Atlantic over the past 15 years. This algaes microbiome provides symbiotic functions that are believed to contribute to its ecological success. Recent research shows that Sargassum-associated bacteria are enriched in integrated prophages compared to the surrounding seawater and that these prophages are inducible by chemical and ultraviolet treatment. ResultsHere, we investigated a Sargassum-derived in vitro multispecies biofilm encompassing the dominant heterotrophic microbial members associated with Sargassum to probe the impacts of prophage induction on the composition of Sargassum microbiomes. Induction was quantified by coverage-based virus-to-host ratios in chemically induced treatments with Mitomycin C and non-induced controls, and the community composition and metabolic profiles were analyzed after a period of recovery post-induction. Chemical induction led to a significant increase in abundance and virus-to-host ratio of viral genomes linked to Vibrio metagenome-assembled genomes. This was accompanied by altered biofilm community composition, with a reduction in Vibrio bacterial abundance that opened niche space for other biofilm members in the genera Pseudoalteromonas, Alteromonas, and Cobetia. The induced Vibrio-associated phages encoded genes involved in quorum sensing, biofilm formation, virulence, and host metabolism. Induction led to a relative loss of 17 metabolic modules, including functions related to energy metabolism and nitrogen utilization. ConclusionDue to the high frequency of lysogeny in the Sargassum microbiome and the susceptibility of prophages to chemical and ultraviolet light induction, these results suggest that prophage integration and induction are mechanisms that significantly contribute to structuring the Sargassum microbiome and its functional profiles, potentially aiding in microbiome flexibility in changing environmental contexts.

microbiology↗

bioRxiv2026

Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes

Meromictic lakes serve as analogs for redox-stratified ancient oceans with well-mixed surface waters and anoxic bottoms. Purple and green sulfur bacteria (PSB, GSB) dominate the anoxic zones where light penetrates, and their biosignatures can be used to guide interpretations of geologic records. However, PSB and GSB biosignatures do not directly reflect the microbial community composition of modern lakes, posing a challenge for their interpretation. Here, we investigate this decoupling by integrating metagenomics, metatranscriptomics, and metaHi-C virus-host linkages with the geochemical profiles of three meromictic lakes. In the phototrophic microbial plates, PSBs transcriptional activity far exceeded their abundance (73% of the total microbial community activity versus 30% of the abundance), while GSBs displayed the opposite pattern. Concurrently, PSBs were exclusively associated with temperate viruses, while GSBs were targeted by lytic infections. Sulfate-reducing bacteria (SRB) and viruses encoding genes for sulfate reduction were most active where sulfide concentration was lowest. These results reveal that viral replication strategies are associated with the decoupling between abundance and activity in anoxygenic phototrophs and sulfate reducers. These relationships could accelerate sulfur regeneration, contribute to sustaining phototrophy, and ultimately reflect in the lakes bulk biosignatures.

microbiology↗

bioRxiv2025

Viral and bacterial traits associated with the success of the yellow pencil coral, Madracis mirabilis, in Curacaos coral reefs

Coral reefs have experienced extensive coral loss and shifts in community composition worldwide. Despite this, some coral species appear naturally more resistant, such as Madracis mirabilis (herein Madracis). Madracis has emerged as the dominant hard coral in Curacao, comprising 26% of coral cover in reefs that declined by 78% between 1973 and 2015. Although life history traits and competitive mechanisms contribute to Madracis success, these factors alone may not fully explain it, as other species with similar traits have not shown comparable success. Here, we investigated the potential role of microbial communities in the success of Madracis on Curacao reefs by leveraging a low-bias bacterial and viral enrichment method for metagenomic sequencing of coral samples, resulting in 77 unique bacterial metagenome-assembled genomes and 2,820 viral genomic sequences. Our analyses showed that Madracis-associated bacterial and viral communities are 1.24-fold and 1.61-fold richer than the communities of five sympatric coral species combined. The Madracis-associated bacterial community was dominated by Ruegeria and Sphingomonas, genera that have previously been associated with coral health, defense against pathogens, and bioremediation. The viral community exhibited a 50% enrichment of proviruses relative to the viral communities of other corals. These proviruses have the genomic capacity to laterally transfer genes involved in antibiotic resistance, central metabolism, and oxidative stress responses, potentially enhancing the adaptive capacity of the Madracis microbiome and contributing to Madracis success on Curacaos reefs. IMPORTANCEUnderstanding why some coral species persist and thrive while most are in fast decline is critical. Madracis mirabilis is increasingly dominant on degraded reefs in Curacao, yet the role of microbial communities in its success remains underexplored. This study highlights the potential role of Madracis-associated bacterial and viral communities in supporting coral resilience and competitive success. By identifying key microbial partners and viral genes that may enhance host stress tolerance and defense against pathogens, we broaden the understanding of how the coral holobiont contributes to species persistence under environmental stress. These insights are valuable for predicting reef community shifts in a changing climate and open avenues for microbiome-informed strategies to support coral conservation and restoration.

microbiology↗

bioRxiv2024

Functionally important binding site for a volatile anesthetic in a voltage-gated sodium channel identified by X-ray crystallography

Voltage-gated sodium channels (VGSCs), key mediators of excitability and synaptic transmission, are established and functionally relevant targets for volatile anaesthetic (VA) action. Using the structurally homologous prokaryotic VGSCs NavMs and NaChBac as models, we present a structure-function analysis of VGSC-VA interactions. We report that multiple VAs compete for binding sites on NavMs, and that these direct interactions mediate functional effects of sevoflurane on NavMs that mirror those attributed to VA effects in eukaryotic VGSCs, including human isoforms. Using X-ray crystallography, we determined the first atomic-resolution structure of a VA bound to a VGSC, showing sevoflurane displacing lipids to bind in an intramembranous hydrophobic pocket of NavMs. A conserved tyrosine residue within this binding site is critical for channel gating, and its substitution with alanine abolishes sevoflurane binding and selectively eliminates the characteristic anaesthetic-induced hyperpolarising shift of steady-state inactivation that reduces neuronal excitability at physiological membrane potentials. Finally, we provide evidence supporting VA action at the conserved sites in human VGSC isoforms. These findings define the first VA binding site in a VGSC. A membrane-mediated access pathway to the binding site leads to negative modulation of channel function that reduces neuronal activity and excitatory synaptic transmission in general anaesthesia.

biophysics↗

bioRxiv2024

Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions

Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. Bacteriophages are the most abundant and diverse members of these communities, yet very little is known about their functions in the holobiont due to methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size-fractionation approach which increased bacterial and viral recovery in coral metagenomes by 9-fold and 3-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a Global Coral Virome Database of over 20,000 viral genomes and genome fragments spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Ackermannviridae were the most abundant, replacing the since-abolished groups Podoviridae and Siphoviridae. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to eavesdrop and modulate bacterial quorum sensing, interfere with sulfur cycling, and direct molecular interactions with eukaryotic cells through the release of extracellular effectors. This study reveals the basis of bacteriophage roles in modulating ecological interactions not only among bacterial community members but also directly affecting tripartite interactions with the coral host and its endosymbiotic algae.

genomics↗

bioRxiv2020

Cannabidiol Interactions with Voltage-Gated Sodium Channels

Voltage-gated sodium channels are targets for a range of pharmaceutical drugs developed for treatment of neurological diseases. Cannabidiol (CBD), the non-psychoactive compound isolated from cannabis plants, was recently approved for treatment of two types of epilepsy associated with sodium channel mutations. This study used high resolution X-ray crystallography to demonstrate the detailed nature of the interactions between CBD and the NavMs voltage-gated sodium channel, showing CBD binds at a novel site at the interface of the fenestrations and the central hydrophobic cavity of the channel. Binding at this site blocks the transmembrane-spanning sodium ion translocation pathway, providing a molecular mechanism for channel inhibition. Modelling studies illuminate why the closely-related psychoactive compound THC may not bind to these channels. Finally, comparisons are made with the TRPV2 channel, also recently proposed as a target site for CBD. In summary, this study provides novel insight into a possible mechanism for CBD with sodium channels.

biophysics↗