Biology subjects

Nyholm, S. V.

Publications and source records attributed to Nyholm, S. V..

5 recordsLinked to original sources

bioRxiv2026

Paired metagenomics and metatranscriptomics reveal metabolic capabilities of uncultivated Verrucomicrobia and other bacteria in the Hawaiian bobtail squid reproductive symbiosis

Host-associated microbiomes often consist of complex bacterial consortia, many of whose members remain uncultivated and/or have poorly characterized functions. In this study, we used metagenomics and metatranscriptomics to better understand the reproductive defensive symbiosis of the accessory nidamental gland (ANG) of the Hawaiian bobtail squid, Euprymna scolopes. We recovered 23 high- and medium-quality metagenome-assembled genomes (MAGs) from the four major ANG symbiont taxa (Alphaproteobacteria, Verrucomicrobia, Gammaproteobacteria, and Flavobacteriia) that dominate the E. scolopes ANG community. Three Puniceicoccaceae MAGs represent the first Verrucomicrobia genomes from a cephalopod ANG and are potentially novel species in Verrucomicrobia subdivision four. These Verrucomicrobia encode the highest diversity of carbohydrate-active enzymes (CAZymes) among the analyzed strains. Metatranscriptomes revealed no differential expression between the ANG and eggs, indicating metabolic stability during symbiont transfer from the ANG tubules to egg jelly coats. Community-wide expression of glycoside hydrolases may enable shared degradation of host O- and N-glycosylated mucins. Genes often important in host-association, such as motility, chemotaxis, and quorum sensing, were broadly expressed amongst the major taxa. Expression of diverse secondary metabolite clusters (e.g., NRPS, PKS, bacteriocins) and competitive mechanisms, like the T6SS, were also expressed and may contribute to mediating competition within the ANG or in egg defense. Overall, this work reveals the genomic and transcriptomic repertoire of the E. scolopes ANG microbiome and provides insight on members of the marine Verrucomicrobia, a group with growing recognition as important in symbiotic associations. SignificanceThe Verrucomicrobia are a ubiquitous group of growing interest, particularly due to the role of Akkermansia in the human gut. However, little is known about aquatic Verrucomicrobia, especially those that switch between a free-living and host associated lifestyle. This study furthers our understanding of potential mucin degradation among novel Puniceicoccaceae of the E. scolopes ANG reproductive symbiosis. Shared expression of carbohydrate utilization pathways among ANG symbionts may reveal networks of competition and cooperation that parallel the complex networks found in the human gut. As well, this study lays the groundwork for further understanding the mechanisms of bacteria-mediated host egg defense, serving as a model for study of other marine defensive symbioses.

microbiology↗

bioRxiv2025

A versatile dual-color bacterial reporter system highlights two distinct Pseudomonas aeruginosa Type 3 secretion system intracellular populations.

Since their discovery, fluorescent reporters have revolutionized our ability to track gene and protein expression in real time. Ideally, two reporters are used, one constitutive signal for tracking viable bacteria and the other for measuring the expression of the gene/protein of interest. Unfortunately, these valuable tools are not available for most bacterial species, and if available are often not optimized for fluorophore protein folding rates and fluorescence intensity. Here we present a versatile dual reporter system, pCG-VmS, optimized for both transcriptional and translation fusions in Gram-negative bacteria. Using the important pathogen Pseudomonas aeruginosa for proof of concept, we demonstrate pCG-VmS utility in tracking transcriptional expression with flow cytometry and within a complex biofilm, and using a translational reporter fusion, monitor protein expression and visualize subcellular protein localization. We then analyzed T3SS-associated exoS toxin expression in infected host cells, which highlighted two distinct T3SS-dependent intracellular populations, one where the exoS promoter is turned on and the other where it is turned off in a smaller sub-population of bacterial cells (hereon referred to as T3SS-on and T3SS-off, respectively). Finally, we demonstrate the feasibility of spatiotemporal imaging in whole animals by using our system to monitor expression of an alternative sigma factor during Vibrio fischeri colonization of its squid host. Our findings demonstrate the versatile uses for the pCG-VmS vectors in microbiology, and that this vector can be used to visualize and separate distinct populations with precision for both in vitro and in vivo applications.

microbiology↗

bioRxiv2025

Euprymna berryi as a comparative model host for Vibrio fischeri light organ symbiosis

Functional studies of host-microbe interactions benefit from natural model systems that enable exploration of molecular mechanisms at the host-microbe interface. Bioluminescent Vibrio fischeri colonize the light organ of the Hawaiian bobtail squid, Euprymna scolopes, and this binary model has enabled advances in understanding host-microbe communication, colonization specificity, in vivo biofilms, intraspecific competition, and quorum sensing. The hummingbird bobtail squid, Euprymna berryi, can be generationally bred and maintained in lab settings and has had multiple genes deleted by CRISPR approaches. The prospect of expanding the utility of the light organ model system by producing multigenerational host lines led us to determine the extent to which the E. berryi light organ symbiosis parallels known processes in E. scolopes. However, the nature of the E. berryi light organ, including its microbial constituency and specificity for microbial partners, have not been examined. In this report, we isolate bacteria from E. berryi animals and tank water. Assays of bacterial behaviors required in the host, as well as host responses to bacterial colonization, illustrate largely parallel phenotypes in E. berryi and E. scolopes hatchlings. This study reveals E. berryi to be a valuable comparative model to complement studies in E. scolopes. IMPORTANCEMicrobiome studies have been substantially advanced by model systems that enable functional interrogation of the roles of the partners and the molecular communication between those partners. The Euprymna scolopes-Vibrio fischeri system has contributed foundational knowledge, revealing key roles for bacterial quorum sensing broadly and in animal hosts, for bacteria in stimulating animal development, for bacterial motility in accessing host sites, and for in vivo biofilm formation in development and specificity of an animals microbiome. Euprymna berryi is a second bobtail squid host, and one that has recently been shown to be robust to laboratory husbandry and amenable to gene knockout. This study identifies E. berryi as a strong symbiosis model host due to features that are conserved with those of E. scolopes, which will enable extension of functional studies in bobtail squid symbioses.

microbiology↗

bioRxiv2024

Multi-omics Analysis Reveals Important Role for Microbial-derived Metabolites from Botryllus schlosseri in Metal Interactions

Marine microbial communities govern many of the biological and chemical processes in the ocean, including element cycles, ecosystem health, and disease. Marine organisms are surrounded by microbes and complex molecular interactions occur between bacterial symbionts, eukaryotic hosts, and their pathogens or prey. Trace metals in the ocean can be either beneficial or detrimental to marine life depending on their concentrations and bioavailability. Multiple marine tunicate species are known to bioaccumulate trace metals in their mantel, and research suggests tunicate microbiota plays an important role in this process. Botryllus schlosseri, a marine colonial tunicate, has become a model organism for cellular and developmental studies, yet its ecological interactions are still not well understood. Using an integrated multidisciplinary approach, we established a comprehensive baseline and explored correlations between members of the B. schlosseri microbiome, metabolome, and metallome to elucidate the ecological effects of trace metals in host-microbe-pathogen interactions. We identified significant correlations between metals, including manganese, nickel, cerium, zinc, and cobalt, with various metabolites and bacterial taxa. These findings offer insights into B. schlosseri biological and chemical interactions with their symbionts and their environment, contributing to bridging the knowledge gap of host-microbiome-environment interactions and establishing a foundation for continuing research on the ecological effects of trace metals in these biological systems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/622856v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@190204org.highwire.dtl.DTLVardef@1d36c40org.highwire.dtl.DTLVardef@168150eorg.highwire.dtl.DTLVardef@3e4ce7_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBotryllus schlosseri tissue was highly enriched in metals compared to seawater C_LIO_LIB. schlosseri microbiome {beta}-diversity significantly different from seawater C_LIO_LIPan-metabolome indicated microbial metabolites in core and flexible metabolome C_LIO_LIMulti-omics revealed interactions between metals, metabolites, and microbes C_LI

systems biology↗

bioRxiv2024

Organ structure and bacterial microbiogeography in a reproductive organ of the Hawaiian bobtail squid reveal dimensions of a defensive symbiosis

Many plants and animals house symbiotic microorganisms in specialized tissues or organs. Here, we used multidimensional in-situ imaging techniques to illuminate how host organ structure and bacterial microbiogeography contribute to the symbiotic function of an organ in the Hawaiian bobtail squid, Euprymna scolopes. Along with the well-studied light organ, female E. scolopes harbor a community of bacteria in the accessory nidamental gland (ANG). The ANG is a dense network of epithelium-lined tubules, some of which are dominated by a single bacterial taxon. These bacteria are deposited into squid eggs, where they defend the developing embryos from harmful biofouling. This study used a combination of imaging techniques to visualize different dimensions of the ANG and its bacterial communities. Imaging entire organs with light sheet microscopy revealed that the ANG is a composite tissue of individual, non-intersecting tubules that each harbor their own bacterial population. The organ is bisected, with tubules converging towards two points in the organ. At these points, tubules empty in a space where bacteria can mix with squid jelly to be deposited onto eggs. Observations of bacterial populations correlated bacterial taxa with cell morphology and show that tubule populations varied: some contained populations of mixed phyla while some tubules contained only one genus of bacteria. Together, these data shed light on how bacterial populations interact within the ANG and how the host uses physical structure to maintain and employ a symbiotic bacterial population in a defensive context. IMPORTANCESequence-based microbiome studies have revealed much about how hosts interact with communities of symbiotic microbiota, but often lack a spatial understanding of how microbes relate with each other and the host in which they reside. This study used a combination of microscopy techniques to reveal how the structure of a symbiotic organ in the female bobtail squid, Euprymna scolopes houses diverse, beneficial bacterial populations and deploys them for egg defense. These findings suggest that spatial partitioning may be key to harboring a diverse population of antimicrobial-producing bacteria and establish a foundation for further understanding how host structures mediate symbiotic interactions.

microbiology↗