Biology subjects

Burkhardt, P.

Publications and source records attributed to Burkhardt, P..

18 recordsLinked to original sources

bioRxiv2026

Precocious reproduction in the ctenophore Mnemiopsis leidyi is modulated by conspecific density and food availability

Precocious reproduction, prior to the acquisition of the final adult morphology, occurs in a variety of animals and represents a distinct life-history strategy with important consequences for growth and survival. Larval reproduction is far rarer and usually restricted to groups that go through metamorphosis. In ctenophores, Carl Chun described dissogeny more than 130 years ago, a distinctive life-history pattern involving larval and adult reproductive periods separated by gonadal regression. Yet, the potential plasticity of larval reproduction in ctenophores remains unresolved. Here, we developed a method to follow and quantify reproductive output in Mnemiopsis leidyi larvae and tested environmental factors that may regulate precocious reproduction. We found that conspecific density strongly influences its onset: low-density, well-fed animals can bypass reproduction at the cydippid stage and develop rapidly into the lobed form, whereas higher density promotes precocious reproduction. Food availability and associated growth rate also contribute but cannot alone explain the observed differences. Once reproduction is established, however, high conspecific density suppresses reproductive output, an effect reproduced by exposure to seawater incubated with high M. leidyi densities, consistent with water-borne chemical communication. Salinity and light conditions further modulate spawning. Together, our results reveal substantial environmental plasticity in precocious reproduction in M. leidyi, reconcile long-standing contradictory observations of ctenophore development, and highlight how environmental cues can reshape reproductive life-history transitions.

ecology↗

bioRxiv2026

Diversity and Spatial Segregation of TRP Channels in Choanoflagellates Provide Insight into the Evolutionary Origin of Animal Sensory Systems

Sensory systems, built around specialized cell types, are central to how animals perceive and respond to their environments. Yet many of the molecular components defining these systems predate the origin of animal multicellularity. Among these, transient receptor potential (TRP) channels form a polymodal and evolutionarily ancient superfamily of ion channels involved in diverse sensory processes. To better understand how sensory complexity emerged in animals, we investigated the diversity of TRP channels in choanoflagellates, the closest living relatives of animals. Using a combination of homology-based searches, phylogenetics, and structural predictions, we find extensive TRP channel repertoires across choanoflagellates, including representatives of most major animal TRP channel families. Comparative analyses across species revealed two distinct evolutionary patterns for TRP channel families: conserved, low-copy families with stable domain architectures, and lineage-specific expansions within the families TRPM and TRPW, indicative of functional diversification. Functional insights from fluorescent localization studies in the choanoflagellate Salpingoeca rosetta demonstrated that TRPA, TRPC, and TRPV channels are spatially segregated within the collar complex, a key interface for environmental sensing and feeding. Distinct localization domains, along with evidence for heteromeric interactions between TRPA paralogs, suggest that subcellular organization likely contributes to sensory specialization in these single cells. Together, our findings indicate that a diverse and functionally versatile TRP channel toolkit was already present in the last common ancestor of choanoflagellates and animals. We propose that the evolution of animal sensory systems involved both expansion and reorganization of this ancestral repertoire, with subcellular patterning in unicellular organisms representing a precursor to cell-type specialization in multicellular animals.

evolutionary biology↗

bioRxiv2026

Ancient nervous system architecture in a living ctenophore

The evolutionary origin of nervous systems in animals remains elusive and is largely hidden from the fossil record. Ctenophores, one of the earliest-branching animals possessing neurons, are instrumental to our understanding of nervous system origin, and a few rare ctenophore fossils preserve traces of nervous tissue as carbonaceous remains. Cambrian ctenophores appear to exhibit a more diverse neuroanatomy than that of modern species, suggesting secondary loss in extant ctenophores. However, much remains unknown about the origin and ontogeny giving rise to the structural organization of modern ctenophore nervous systems. Here, by investigating the neural anatomy of the ctenophore Mnemiopsis leidyi during development, we identified a ladder-like nerve net (LNN) beneath the comb rows that converges into condensed neurites and connects to the aboral organ. Examination of carbon-rich areas of Ctenorhabdotus capulus, an extinct ctenophore from the Burgess Shale, reveals a pattern similar to that of M. leidyi, consistent with a shared neural organization. Furthermore, M. leidyi exhibits a condensed comb nerve, resembling the longitudinal nerve preserved in the Cambrian ctenophore Fasciculus vesanus and the giant axon of extant Euplokamis dunlapae. Our study reveals conserved evolutionary constraints shaping nervous system architectures linked to locomotory organs and indicates that the different modes of nervous system organization observed in Cambrian ctenophores are variably retained in modern species.

neuroscience↗

bioRxiv2025

Neural Connectome of the Ctenophore Statocyst

Ctenophores possess a unique gravity receptor (statocyst) in their aboral organ formed by four clusters of ciliated balancer cells that collectively support a statolith. During reorientation, differential loads on the balancer cilia lead to altered beating of the ciliated comb rows to elicit turns. To study the neural bases of gravity sensing, we used volume electron microscopy (vEM) to image the aboral organ of the ctenophore Mnemiopsis leidyi. We reconstructed 1011 cells, including syncytial neurons that form a nerve net. The syncytial neurons synapse on the balancer cells and also form reciprocal connections with the bridge cells that span the statocyst. High-speed imaging revealed that balancer cilia beat and arrest in a coordinated manner but with differences between the sagittal and tentacular planes of the animal, reflecting nerve-net organisation. Our results suggest a coordinating rather than sensory-motor function for the nerve net and inform our understanding of the diversity of nervous-system organisation across animals.

animal behavior and cognition↗

bioRxiv2025

The 3D architecture of the ctenophore aboral organ and the evolution of complex integrative centers in animals

The ability to sense and respond to environmental cues is fundamental to animal behavior and survival. In ctenophores - early-branching marine animals - a syncytial nerve net underlies complex behaviors such as geotaxis, feeding, and escape. At the center of this system is the aboral organ (AO), a dense sensory hub that detects motion, light, and pressure and coordinates ciliary movement. However, the AOs cellular architecture and its integration with the nerve net remain poorly understood. Here, using volume electron microscopy in Mnemiopsis leidyi, we reveal that the syncytial nerve net converges and condenses around the AO, forming synaptic connections with diverse effector cells. We annotated 17 distinct cell types, including candidate light and pressure sensors, novel ciliated and secretory cells, and non-synaptic vesicle-rich cells likely involved in volume transmission. Our data shows that signal processing within the AO relies on both synaptic and non-synaptic communication. Gene expression profiling of conserved transcription factors indicates that the AO is a functionally convergent, evolutionarily distinct sensory structure that retains minimal homology. Our findings redefine the ctenophore AO as a highly integrated, multilayered sensory system critical for behavioral regulation.

evolutionary biology↗

bioRxiv2025

Emergent spatial structure in the gut microbiota is driven by bacterial growth and gut contractions

Spatial structure can determine function and evolution of bacterial communities. The gut microbiota is known to be spatially structured longitudinally along the many meters of the gastrointestinal tract, but micro-scale structure in the gut lumen has not been extensively explored. In samples from mice and humans, we show that upper large-intestinal content behaves as a non-Newtonian fluid that changes its viscoelastic properties under the force of gut contractions. This phenomenon is sufficient to explain micro-scale bacterial clustering in the murine cecum, resulting from growth within the gel-like structure of cecum content, and periodic disruption due to peristalsis-driven shear-thinning and clearance. Shear-thinning can also explain the surprising observation that fed beads enter the tip of the mouse cecum by flow along the epithelial cell layer before being mixed into the cecum content. Our study shows mechanistically how spatial structure in the gut emerges through the interplay of microbial and host physiology and highlights the possibility of host control over gut microbiota distribution via gut contractions. One sentence summaryWe show how spatial structure emerges in the gut microbiota through bacterial growth in the matrix of gut content.

systems biology↗

bioRxiv2024

Reverse development in the ctenophore Mnemiopsis leidyi

Reverse development, or the ability to rejuvenate by morphological reorganization into the preceding life cycle stage is thought to be restricted to a few species within Cnidaria. To date, the cnidarian Turritopsis dohrnii is the only known species capable of undergoing reverse development after the onset of sexual reproduction. Here, we demonstrate that the ctenophore Mnemiopsis leidyi is capable of reversal from mature lobate to early cydippid when fed following a period of stress. Our findings illuminate central aspects of ctenophore development, ecology, and evolution, and show the high potential of M. leidyi as a new model system to study reverse development and rejuvenation. Besides shedding light on the plasticity of developmental programs, our results raise fundamental questions about early animal development, body plans and life cycles.

ecology↗

bioRxiv2024

Electrical signaling and coordinated behavior in the closest relative of animals

The transition between simple to complex multicellularity involves large degrees of division of labor and specialization of cell types. In animals, complex sensory motor systems are primarily built around the fundamental cell types of muscles and neurons, though the evolutionary origin of these cells, and their integration, remains unclear. Here, in order to investigate sensory-behavior coupling in the closest relatives of animals, we established a line of the choanoflagellate, Salpingoeca rosetta, which stably expresses the calcium indicator RGECO1. Using this, we identify a novel cellular behavior associated with electrical signaling, in which ciliary arrest is coupled with apical-basal contraction of the cell. This behavior, and the associated calcium transients, are synchronized in the multicellular state and result in coordinated ciliary arrest and colony wide contraction, suggesting information is spread amongst the cells. Our work reveals fundamental insights into how choanoflagellates sense and respond to their environment and offer a new perspective into the integration of cellular and organism wide behavior in the closest protistan relatives of animals.

evolutionary biology↗

bioRxiv2024

Spatiotemporal visualization of DNA replication by click chemistry reveals bubbling of viral DNA in virion formation

The organisation of human chromosomes reversibly changes in cell division, and irreversibly in apoptosis or erythropoiesis by DNA condensation and fragmentation processes. Yet, how viral replication in the nucleus affects host and viral chromatin organisation remains poorly understood. Here we used dual-color click chemistry to image human adenovirus DNA replication, demonstrating host chromatin compaction during active expansion of the viral replication compartment (VRC). Early-replicated viral DNA (vDNA) segregated from VRC and lost phospho-serine5-RNA Pol-II and viral DNA-binding protein (DBP), while late-replicated vDNA retained active RNA Pol-II, besides viral RNA-splicing and DNA-packaging proteins. Depending on replication and the assembly protein 52K, the late-stage VRCs gave rise to progeny by droplet formation of vDNA with GFP-tagged virion protein V into 52K biomolecular condensates. The study reveals distinct functions of early and late-replicated vDNA and provides insight into active and passive liquid phase separated zones conducive to selective genome packaging of nascent virions.

microbiology↗

bioRxiv2023

Evolution of the ribbon-like organization of the Golgi apparatus in animal cells

The Golgi ribbon is a structural organization formed by linked Golgi stacks that is believed to be exclusive to vertebrate cells. Its functional contribution to cellular processes is unclear, yet its disruption is associated with several human pathologies. In this study we address the evolutionary origin of the Golgi ribbon, describe a potential molecular mechanism for its emergence and identify a cellular process in which it may be involved. We observed the ribbon-like architecture in the cells of several metazoan taxa, suggesting its early appearance during animal evolution before the emergence of vertebrates. Supported by AlphaFold2 modelling, we propose that the evolution of the complex between two Golgi resident proteins, Golgin-45 and GRASP, led to the tethering of Golgi stacks into the ribbon-like configuration. Finally, we find that the ribbon is assembled during the early embryogenesis of deuterostome animals, a strong indication of its role in development. Overall, our study indicates that the Golgi ribbon is functionally relevant beyond vertebrates and calls for further investigations to decipher its elusive functions. O_FIG O_LINKSMALLFIG WIDTH=89 HEIGHT=200 SRC="FIGDIR/small/528797v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@17a404forg.highwire.dtl.DTLVardef@11413b4org.highwire.dtl.DTLVardef@119c036org.highwire.dtl.DTLVardef@19a512f_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

cell biology↗

bioRxiv2022

Syncytial nerve net in a ctenophore sheds new light on the early evolution of nervous systems

A fundamental breakthrough in neurobiology has been the formulation of the neuron doctrine by Santiago Ramon y Cajal, which states that the nervous system is composed of discrete individual cells. Electron microscopy later confirmed the doctrine and allowed the identification of synaptic connections. Here we use volume electron microscopy and 3D reconstructions to characterize the nerve net of a cydippid-phase ctenophore, belonging to one of the earliest-branching animal lineages. We found that neurons of its subepithelial nerve net do not follow Cajals neuron doctrine but instead show a continuous plasma membrane forming a syncytium. This is more similar to the reticulate theory of the nervous system put forward by Camillo Golgi. Additionally, we were able to identify new sensory cell types and describe simple neuro-sensory circuits for cydippid-phase ctenophores. Together with the ctenophore-specific synaptic architecture and the presence of an extensive repertoire of lineage-specific neuropeptides our morphological data provide substantial evidence for the independent evolution of the nervous system of ctenophores and the remaining animals.

evolutionary biology↗

bioRxiv2021

The unique neuronal structure and neuropeptide repertoire in the ctenophore Mnemiopsis leidyi shed light on the evolution of animal nervous systems

The ctenophore nerve net represents one of the earliest evolved nervous system of animals. Due to the uncertainties of their phylogenetic placement of ctenophores and the absence of several key bilaterian neuronal genes, it has been hypothesized that their neurons have evolved independently. Whether this is indeed the case remains unclear, and thus the evolutionary history of neurons is still contentious. Here, we have characterized the neuropeptide repertoire of the ctenophore Mnemiopsis leidyi. Using the machine learning NeuroPID tool1 129 new putative neuropeptide precursors were predicted. Sixteen of them are detected in the subepithelial nerve net (SNN), aboral organ (AO) and epithelial sensory cells (ESC) of early cydippid-stage M. leidyi by in situ hybridization (ISH) and immunohistochemistry (IHC). Four of these neuropeptides increase the animals swimming velocity in a behavioral essay. The new neuropeptides were used as markers to identify neuronal cell types in single cell transcriptomic data2. To unravel the neuronal architecture, we 3D reconstructed the SNN underlying the comb plates using serial block-face scanning electron microscopy (SBF-SEM). For the first time, we confirm a more than 100 years old hypothesis about anastomoses between neurites of the same cell in ctenophores and reveal that they occur through a continuous membrane. Our findings reveal the unique neuronal structure and neuropeptide repertoire of ctenophores and are important for reconstructing the evolutionary origin of animal neurons and nervous systems.

evolutionary biology↗

bioRxiv2021

Colonial choanoflagellate isolated from Mono Lake harbors a microbiome

Choanoflagellates offer key insights into bacterial influences on the origin and early evolution of animals. Here we report the isolation and characterization of a new colonial choanoflagellate species, Barroeca monosierra, that, unlike previously characterized species, harbors a microbiome. B. monosierra was isolated from Mono Lake, California and forms large spherical colonies that are more than an order of magnitude larger than those formed by the closely related Salpingoeca rosetta. By designing fluorescence in situ hybridization probes from metagenomic sequences, we found that B. monosierra colonies are colonized by members of the halotolerant and closely related Saccharospirillaceae and Oceanospirillaceae, as well as purple sulfur bacteria (Ectothiorhodospiraceae) and non-sulfur Rhodobacteraceae. This relatively simple microbiome in a close relative of animals presents a new experimental model for investigating the evolution of stable interactions among eukaryotes and bacteria. IMPORTANCEThe animals and bacteria of Mono Lake (California) have evolved diverse strategies for surviving the hypersaline, alkaline, arsenic-rich environment. We sought to investigate whether the closest living relatives of animals, the choanoflagellates, exist among the relatively limited diversity of organisms in Mono Lake. We repeatedly isolated members of a single species of choanoflagellate, which we have named Barroeca monosierra, suggesting that it is a stable and abundant part of the ecosystem. Characterization of B. monosierra revealed that it forms large spherical colonies that each contain a microbiome, providing an opportunity to investigate the evolution of stable physical associations between eukaryotes and bacteria.

microbiology↗

bioRxiv2020

Choanoflagellates and the ancestry of neurosecretory vesicles

Neurosecretory vesicles are highly specialized trafficking organelles important for metazoan cell-cell signalling. Despite the high anatomical and functional diversity of neurons in metazoans, the protein composition of neurosecretory vesicles in bilaterians appears to be similar. This similarity points towards a common evolutionary origin. Moreover, many key neurosecretory vesicle proteins predate the origin of the first neurons and some even the origin of the first animals (metazoans). However, little is known about the molecular toolkit of these vesicles in non-bilaterian metazoans and their closest unicellular relatives, making inferences about the evolutionary origin of neurosecretory vesicles extremely difficult. By comparing 28 proteins of the core neurosecretory vesicle proteome in 13 different species, we demonstrate that most of the proteins are already present in unicellular organisms. Surprisingly, we find that the vesicle residing SNARE protein synaptobrevin is localized to the vesicle-rich apical and basal pole in the choanoflagellate Salpingoeca rosetta. Our 3D vesicle reconstructions reveal that the choanoflagellates Salpingoeca rosetta and Monosiga brevicollis exhibit a polarized and diverse vesicular landscape. This study sheds light on the ancestral molecular machinery of neurosecretory vesicles and provides a framework to understand the origin and evolution of secretory cells, synapses, and neurons.

evolutionary biology↗

bioRxiv2019

Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

The evolutionary origin of metazoan cell types such as neurons, muscles, digestive, and immune cells, remains unsolved. Using whole-body single-cell RNA sequencing in a sponge, an animal without nervous system and musculature, we identify 18 distinct cell types comprising four major families. This includes nitric-oxide sensitive contractile cells, digestive cells active in macropinocytosis, and a family of amoeboid-neuroid cells involved in innate immunity. We uncover presynaptic genes in an amoeboid-neuroid cell type, and postsynaptic genes in digestive choanocytes, suggesting asymmetric and targeted communication. Corroborating this, long neurite-like extensions from neuroid cells directly contact and enwrap choanocyte microvillar collars. Our data indicate a link between neuroid and immune functions in sponges, and suggest that a primordial neuro-immune system cleared intruders and controlled ciliary beating for feeding.

developmental biology↗

bioRxiv2019

Spatial cell disparity in the colonial choanoflagellate Salpingoeca rosetta

Choanoflagellates are the closest unicellular relatives of animals (Metazoa). These tiny protists display complex life histories that include sessile as well as different pelagic stages. Some choanoflagellates have the ability to form colonies as well. Up until recently, these colonies have been described to consist of mostly identical cells showing no spatial cell differentiation, which supported the traditional view that spatial cell differentiation, leading to specific cell types in animals, evolved after the split of the last common ancestor of the Choanoflagellata and Metazoa. The recent discovery of single cells in colonies of the choanoflagellate Salpingoeca rosetta that exhibit unique cell morphologies challenges this traditional view. We have now reanalyzed TEM serial sections, aiming to determine the degree of similarity of S. rosetta cells within a rosette colony. We investigated cell morphologies and nuclear, mitochondrial and food vacuole volumes of 40 individual cells from four different S. rosetta rosette colonies and compared our findings to previously published data on sponge choanocytes. Our analysis show that cells in a choanoflagellate colony differ from each other in respect to cell morphology and content ratios of nuclei, mitochondria and food vacuoles. Furthermore, cell disparity within S. rosetta colonies is higher compared to cell disparity within sponge choanocytes. Moreover, we discovered the presence of plasma membrane contacts between colonial cells in addition to already described intercellular bridges and filo-/pseudopodial contacts. Our findings indicate that the last common ancestor of Choanoflagellata and Metazoa might have possessed plasma membrane contacts and spatial cell disparity during colonial life history stages.

evolutionary biology↗

bioRxiv2019

Animal evolution coincides with a novel degree of freedom in exocytic transport processes

Exocytic transport of transmembrane receptors and secreted ligands provides the basis for cellular communication in animals. The RAB8/RAB3/RAB27 trafficking regulators function in transport processes towards the cell membrane. The small G-proteins recruit a diversity of effectors that mediate transport along microtubule and actin tracks, as well as membrane tethering and fusion. SPIRE actin nucleators organise local actin networks at exocytic vesicle membranes. By complex formation with class-5 myosins, vesicle transport track generation and motor protein activation are coordinated. Our phylogenetic analysis traced the onset of SPIRE function back to the origin of the Holozoa. We have identified SPIRE in the closest unicellular relatives of animals, the choanoflagellates, and the more distantly related ichthyosporeans. The discovery of a SPIRE-like protein encoding a KIND and tandem-WH2 domains in the amoebozoan Physarum polycephalum suggests that the SPIRE-type actin nucleation mechanism originated even earlier. Choanoflagellate SPIRE interacts with RAB8, the sole choanoflagellate representative of the metazoan RAB8/RAB3/RAB27 family. Major interactions including MYO5, FMN-subgroup formins and vesicle membranes are conserved between the choanoflagellate and mammalian SPIRE proteins and the choanoflagellate Monosiga brevicollis SPIRE protein can rescue mouse SPIRE1/2 function in melanosome transport. Genome duplications generated two mammalian SPIRE genes (SPIRE1 and SPIRE2) and allowed for the separation of SPIRE protein function in terms of tissue expression and RAB GTPase binding. SPIRE1 is highest expressed in the nervous system and interacts with RAB27 and RAB8. SPIRE2 shows high expression in the digestive tract and specifically interacts with RAB8. We propose that at the dawn of the animal kingdom a new transport mechanism came into existence, which bridges microtubule tracks, detached vesicles and the cellular actin cytoskeleton by organising actin/myosin forces directly at exocytic vesicle membranes. The new degree of freedom in transport may reflect the increased demands of the sophisticated cellular communications in animals.

cell biology↗

bioRxiv2018

The architecture of cell differentiation in choanoflagellates and sponge choanocytes

Collar cells are ancient animal cell types which are conserved across the animal kingdom [1] and their closest relatives, the choanoflagellates [2]. However, little is known about their ancestry, their subcellular architecture, or how they differentiate. The choanoflagellate Salpingoeca rosetta [3] expresses genes necessary for animal multicellularity and development [4] and can alternate between unicellular and multicellular states [3,5], making it a powerful model to investigate the origin of animal multicellularity and mechanisms underlying cell differentiation [6,7]. To compare the subcellular architecture of solitary collar cells in S. rosetta with that of multicellular \"rosettes\" and collar cells in sponges, we reconstructed entire cells in 3D through transmission electron microscopy on serial ultrathin sections. Structural analysis of our 3D reconstructions revealed important differences between single and colonial choanoflagellate cells, with colonial cells exhibiting a more amoeboid morphology consistent with relatively high levels of macropinocytotic activity. Comparison of multiple reconstructed rosette colonies highlighted the variable nature of cell sizes, cell-cell contact networks and colony arrangement. Importantly, we uncovered the presence of elongated cells in some rosette colonies that likely represent a distinct and differentiated cell type. Intercellular bridges within choanoflagellate colonies displayed a variety of morphologies and connected some, but not all, neighbouring cells. Reconstruction of sponge choanocytes revealed both ultrastructural commonalities and differences in comparison to choanoflagellates. Choanocytes and colonial choanoflagellates are typified by high amoeboid cell activity. In both, the number of microvilli and volumetric proportion of the Golgi apparatus are comparable, whereas choanocytes devote less of their cell volume to the nucleus and mitochondria than choanoflagellates and more of their volume to food vacuoles. Together, our comparative reconstructions uncover the architecture of cell differentiation in choanoflagellates and sponge choanocytes and constitute an important step in reconstructing the cell biology of the last common ancestor of the animal kingdom.

evolutionary biology↗