Biology subjects

McFall-Ngai, M.

Publications and source records attributed to McFall-Ngai, M..

7 recordsLinked to original sources

bioRxiv2025

Nanoscale imaging of native symbiotic animal tissue using amultimodal large volume imaging pipeline for cryo-electrontomography

The field of cryo-EM offers the possibility to gain high-resolution structural information of biomolecules in their native state. Advances in sample thinning of cryo-EM samples allows the study of proteins inside intact cells using tomography, opening the door for visual proteomics. However, thicker samples such as tissues or entire organisms are still largely unsuitable for cryo-electron tomography (cryo-ET). Therefore, significant efforts are directed toward developing and improving preparation methods to enable cryo-ET of such complex samples. We focused on the binary association between the Hawaiian bobtail squid Euprymna scolopes and the luminous bacteria Vibrio fischeri. The Squid-Vibrio system has long been studied to understand host-symbiont interactions. Our goal is to study the bacterial-host interface using cryo-ET, at a resolution previously unattainable by conventional EM methods. Here, we present a multi-modal preparation and correlative imaging workflow--including cryo- fluorescence microscopy, microCT, freeze-substitution electron tomography (FS-ET), and serial blockface SEM--to localize and prepare specific regions of the dissected symbiotic light organs for cryo-ET. This approach enabled us to directly visualize symbiotic V. fischeri within the internal host crypts at macromolecular resolution, revealing spatial organization, physical contact, and putative exchange interfaces between host and microbe. Our findings provide structural insights into a foundational model of host-microbe symbiosis and demonstrate the feasibility of cryo-ET for investigating intact tissues at the nanoscale.

microbiology↗

bioRxiv2025

Climate-driven warming disrupts the symbiosis of bobtail squid Euprymna scolopes and the luminous bacterium Vibrio fischeri

Under the current climate crisis, marine heatwaves (MHW) are expected to intensify and become more frequent in the future, leading to adverse effects on marine life. Here, we aimed to investigate the impact of environmental warming on the symbiotic relationship between the Hawaiian bobtail squid (Euprymna scolopes) and the bioluminescent bacterium Vibrio fischeri. We exposed eggs of E. scolopes to three different temperatures during the embryogenesis, namely: i) 25 {degrees}C (yearly average), ii) 27 {degrees}C (average summer), or iii) 30 {degrees}C (category IV MHW), followed by a colonisation assay under the same conditions. Decreased hatching success and reduced developmental time were observed across warmer conditions compared to 25 {degrees}C. Moreover, exposure to the category IV MHW led to a significant decrease in survival after 48 hours. With increasing temperature, bobtail squids required more bacteria in the surrounding seawater for successful colonisation. When colonised, the regression of the light organs appendages was not dependent on temperature, but the opposite was found in non-colonised bobtail squids. Furthermore, the capacity to maintain the symbiosis diminished significantly with temperature. Finally, the capacity for crypt 3 formation in the squids light organ, which is crucial for enhancing resilience under stress, also declined with warming conditions. This study emphasises the critical need to study the dynamics of microbial symbiosis under the projected conditions for the ocean of tomorrow.

ecology↗

bioRxiv2025

Diversity, connectivity and negative interactions define robust microbiome networks across land, stream, and sea

In this era of rapid global change, factors influencing the stability of ecosystems and their functions have come into the spotlight. For decades the relationship between stability and complexity has been investigated in modeled and empirical systems, yet results remain largely context dependent. To overcome this we leverage a multiscale inventory of fungi and bacteria ranging from single sites along an environmental gradient, to habitats inclusive of land, sea and stream, to an entire watershed. We use networks to assess the relationship between microbiome complexity and robustness and identify fundamental principles of stability. We demonstrate that while some facets of complexity are positively associated with robustness, others are not. Beyond positive biodiversity x robustness relationships we find that the number of "gatekeeper" species or those that are highly connected and central within their networks, and the proportion of predicted negative interactions are universal indicators of robust microbiomes. With the potential promise of microbiome engineering to address global challenges ranging from human to ecosystem health we identify properties of microbiomes for future experimental studies that may enhance their stability. We emphasize that features beyond biodiversity and additional characteristics beyond stability such as adaptability should be considered in these efforts.

ecology↗

bioRxiv2023

Flow Physics Explains Morphological Diversity of Ciliated Organs

Organs that pump fluids by the coordinated beat of motile cilia through the lumen are integral to animal physiology. Such organs include the human air-ways, brain ventricles, and reproductive tracts. Although cilia organization and duct morphology vary drastically in the animal kingdom, ducts are typically classified as either carpet or flame designs. The reason behind this di-chotomy and how duct design relates to fluid pumping remain unclear. Here, we demonstrate that two structural parameters - lumen diameter and cilia-to-lumen ratio - organize the observed duct diversity into a continuous spectrum that connects carpets to flames across all animal phyla. Using a unified fluid model, we show that carpet and flame designs maximize flow rate and pressure generation, respectively. We propose that convergence of ciliated organ designs follows functional constraints rather than phylogenetic distance, along with universal design rules for ciliary pumps.

biophysics↗

bioRxiv2021

Transitioning to confined spaces impacts bacterial swimming and escape response

Symbiotic bacteria often navigate complex environments before colonizing privileged sites in their host organism. Chemical gradients are known to facilitate directional taxis of these bacteria, guiding them towards their eventual destination. However, less is known about the role of physical features in shaping the path the bacteria take and defining how they traverse a given space. The flagellated marine bacterium Vibrio fischeri,which forms a binary symbiosis with the Hawaiian bobtail squid, Euprymna scolopes, must navigate tight physical confinement, squeezing through a bottleneck constricting to ~2 m in width on the way to its eventual home. Using microfluidic in vitro experiments, we discovered that V. fischeri cells alter their behavior upon entry into confined space, straightening their swimming paths and promoting escape from confinement. Using a computational model, we attributed this escape response to two factors: reduced directional fluctuation and a refractory period between reversals. Additional experiments in asymmetric capillary tubes confirmed that V. fischeri quickly escape from tapered ends, even when drawn into the ends by chemoattraction. This avoidance was apparent down to a limit of confinement approaching the diameter of the cell itself, resulting in a balance between chemoattraction and evasion of physical confinement. Our findings demonstrate that non-trivial distributions of swimming bacteria can emerge from simple physical gradients in the level of confinement. Tight spaces may serve as an additional, crucial cue for bacteria while they navigate complex environments to enter specific habitats. Significance StatementSymbiotic bacteria that navigate to and through specific host tissues often face tight physical confinement. This work reveals that confinement-associated changes in swimming can dramatically alter taxis, shaping bacterial localization in conjuncture with other motility-directing cues. This work helps explain how bacteria can avoid getting stuck in confined areas while transiting to privileged spaces, adding confinement as an environmental cue that symbiotic bacteria use to shape their motility behavior.

biophysics↗

bioRxiv2019

The Trichoplax microbiome: the simplest animal lives in an intimate symbiosis with two intracellular bacteria

Summary paragraphPlacozoa is an enigmatic phylum of simple, microscopic, marine metazoans. Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host. We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax H2 lives in symbiosis with two intracellular bacteria. One symbiont forms a new genus in the Midichloriaceae (Rickettsiales) and has a genomic repertoire similar to that of rickettsial parasites, but does not appear to express key genes for energy parasitism. Correlative microscopy and 3-D electron tomography revealed that this symbiont resides in an unusual location, the rough endoplasmic reticulum of its hosts internal fiber cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations. This symbiont lives in the ventral epithelial cells of Trichoplax, likely metabolizes algal lipids digested by its host, and has the capacity to supplement the placozoans nutrition. Our study shows that even the simplest animals known have evolved highly specific and intimate associations with symbiotic, intracellular bacteria, and highlights that symbioses with microorganisms are a basal trait of animal life.

microbiology↗

bioRxiv2018

Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast

Light field microscopy provides an efficient means to collect 3D images in a single acquisition, as its plenoptic detection captures an extended image volume in one snapshot. The ability of light field microscopy to simultaneously capture image data from a volume of interest, such as a functioning brain or a beating heart, is compromised by inadequate contrast and effective resolution, due, in large part, to light scattering by the tissue. Surprisingly, a major contribution to the image degradation is the signal scattered into the volume of interest by the typical wide-field illumination that excites the sample region outside the volume of interest. Here, we minimize this degradation by employing selective volume illumination, using a modified light sheet approach to illuminate preferentially the volume of interest. This minimizes the unavoidable background generated when extraneous regions of the sample are illuminated, dramatically enhancing the contrast and effective resolution of the captured and reconstructed images. Light Field Selective Volume Illumination Microscopy (LF-SVIM, SVIM for short) dramatically improves the performance of light field microscopy, and offers an unprecedented combination of synchronous z-depth coverage, lateral and axial resolution, and imaging speed.

biophysics↗