Sponge Behavior and the Chemical Basis of Responses: A Post-Genomic View

On being a Hydra with, and without, a nervous system: what do neurons add?

The small freshwater cnidarian Hydra has been the subject of scientific inquiry for over 300 years due to its remarkable regenerative capacities and apparent immortality. More recently, Hydra has been recognized as an excellent model system within neuroscience because of its small size, transparency, and simple nervous system, which allow high-resolution imaging of its entire nerve net while behaving. In less than a decade, studies of Hydra's nervous system have yielded insights into the activity of neural circuits in vivo unobtainable in most other animals. In addition to these unique attributes, there is yet another lesser-known feature of Hydra that makes it even more intriguing: it does not require its neural hardware to live. The extraordinary ability to survive the removal and replacement of its entire nervous system makes Hydra uniquely suited to address the question of what neurons add to an extant organism. Here, I will review what early work on nerve-free Hydra reveals about the potential role of the nervous system in these animals and point towards future directions for this work.

Potential for host-symbiont communication via neurotransmitters and neuromodulators in an aneural animal, the marine sponge Amphimedon queenslandica

Interkingdom signalling within a holobiont allows host and symbionts to communicate and to regulate each other's physiological and developmental states. Here we show that a suite of signalling molecules that function as neurotransmitters and neuromodulators in most animals with nervous systems, specifically dopamine and trace amines, are produced exclusively by the bacterial symbionts of the demosponge Amphimedon queenslandica. Although sponges do not possess a nervous system, A. queenslandica expresses rhodopsin class G-protein-coupled receptors that are structurally similar to dopamine and trace amine receptors. When sponge larvae, which express these receptors, are exposed to agonists and antagonists of bilaterian dopamine and trace amine receptors, we observe marked changes in larval phototactic swimming behaviour, consistent with the sponge being competent to recognise and respond to symbiont-derived trace amine signals. These results indicate that monoamines synthesised by bacterial symbionts may be able to influence the physiology of the host sponge.

The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes

BACKGROUND

Explaining the emergence of the hallmarks of bilaterians is a central focus of evolutionary developmental biology-evodevo-and evolutionary genomics. For this purpose, we must both expand and also refine our knowledge of non-bilaterian genomes, especially by studying early branching animals, in particular those in the metazoan phylum Porifera.

RESULTS

We present a comprehensive analysis of the first whole genome of a glass sponge, Oopsacas minuta, a member of the Hexactinellida. Studying this class of sponge is evolutionary relevant because it differs from the three other Porifera classes in terms of development, tissue organization, ecology, and physiology. Although O. minuta does not exhibit drastic body simplifications, its genome is among the smallest of animal genomes sequenced so far, and surprisingly lacks several metazoan core genes (including Wnt and several key transcription factors). Our study also provides the complete genome of a symbiotic Archaea dominating the associated microbial community: a new Thaumarchaeota species.

CONCLUSIONS

The genome of the glass sponge O. minuta differs from all other available sponge genomes by its compactness and smaller number of encoded proteins. The unexpected loss of numerous genes previously considered ancestral and pivotal for metazoan morphogenetic processes most likely reflects the peculiar syncytial tissue organization in this group. Our work further documents the importance of convergence during animal evolution, with multiple convergent evolution of septate-like junctions, electrical-signaling and multiciliated cells in metazoans.

Is ABA the exogenous vector of interplant drought cuing?

We have recently demonstrated that root cuing from drought-stressed plants increased the survival time of neighboring plants under drought, which came at performance costs under benign conditions. The involvement of abscisic acid (ABA) was implicated from additional experiments in which interplant drought cuing was greatly diminished in ABA-deficient plants. Here, we tested the hypothesis that ABA is the exogenous vector of interplant drought cuing. Pisum sativum plants were grown in rows of three split-root plants. One of the roots of the first plant was subjected to either drought of benign conditions in one rooting vial, while its other root shared its rooting vial with one of the roots of an unstressed neighbor, which in turn shared its other rooting vial with an additional unstressed neighbor. One hour after subjecting one of the roots of the first plant to drought, ABA concentrations were 106% and 145% higher around its other root and the roots of its unstressed neighbor, compared to their respective unstressed controls; however, the absolute concentrations of ABA found in the rooting media were substantially low. The results may indicate that despite its involvement in interplant drought and the commonly observed exchange of ABA between drought-stressed plants and their rhizospheres, ABA is not directly involved in exogenous interplant drought cuing. However, previous studies have shown that even minute concentrations of ABA in the rhizosphere can prevent ABA leakage from roots and thus to significantly increase endogenous ABA levels. In addition, under drought conditions, plants tend to accumulate ABA, which could markedly increase internal ABA concentrations over time and ABA concentrations in close proximity to the root surface might be significantly greater than estimated from entire rooting volumes. Finally, phaseic acid, an ABA degradation product, is known to activate various ABA receptors, which could enhance plant drought tolerance. It is thus feasible that while the role of ABA is limited, its more stable degradation products could play a significant role in interplant drought cuing. Our preliminary findings call for an extensive investigation into the identity and modes of operation of the exogenous vectors of interplant drought cuing.

Molecular machineries of ciliogenesis, cell survival, and vasculogenesis are differentially expressed during regeneration in explants of the demosponge Halichondria panicea

Sponges are interesting animal models for regeneration studies, since even from dissociated cells, they are able to regenerate completely. In particular, explants are model systems that can be applied to many sponge species, since small fragments of sponges can regenerate all elements of the adult, including the oscula and the ability to pump water. The morphological aspects of regeneration in sponges are relatively well known, but the molecular machinery is only now starting to be elucidated for some sponge species. Here, we have used an explant system of the demosponge Halichondria panicea to understand the molecular machinery deployed during regeneration of the aquiferous system. We sequenced the transcriptomes of four replicates of the 5-day explant without an osculum (NOE), four replicates of the 17-18-day explant with a single osculum and pumping activity (PE) and also four replicates of field-collected individuals with regular pumping activity (PA), and performed differential gene expression analysis. We also described the morphology of NOE and PE samples using light and electron microscopy. Our results showed a highly disorganised mesohyl and disarranged aquiferous system in NOE that is coupled with upregulated pathways of ciliogenesis, organisation of the ECM, and cell proliferation and survival. Once the osculum is formed, genes involved in "response to stimulus in other organisms" were upregulated. Interestingly, the main molecular machinery of vasculogenesis described in vertebrates was activated during the regeneration of the aquiferous system. Notably, vasculogenesis markers were upregulated when the tissue was disorganised and about to start forming canals (NOE) and angiogenic stimulators and ECM remodelling machineries were differentially expressed once the aquiferous system was in place (PE and PA). Our results are fundamental to better understanding the molecular mechanisms involved in the formation of the aquiferous system in sponges, and its similarities with the early onset of blood-vessel formation in animal evolution.

Alternative neural systems: What is a neuron? (Ctenophores, sponges and placozoans)

How to make a neuron, a synapse, and a neural circuit? Is there only one 'design' for a neural architecture with a universally shared genomic blueprint across species? The brief answer is "No." Four early divergent lineages from the nerveless common ancestor of all animals independently evolved distinct neuroid-type integrative systems. One of these is a subset of neural nets in comb jellies with unique synapses; the second lineage is the well-known Cnidaria + Bilateria; the two others are non-synaptic neuroid systems in sponges and placozoans. By integrating scRNA-seq and microscopy data, we revise the definition of neurons as synaptically-coupled polarized and highly heterogenous secretory cells at the top of behavioral hierarchies with learning capabilities. This physiological (not phylogenetic) definition separates 'true' neurons from non-synaptically and gap junction-coupled integrative systems executing more stereotyped behaviors. Growing evidence supports the hypothesis of multiple origins of neurons and synapses. Thus, many non-bilaterian and bilaterian neuronal classes, circuits or systems are considered functional rather than genetic categories, composed of non-homologous cell types. In summary, little-explored examples of convergent neuronal evolution in representatives of early branching metazoans provide conceptually novel microanatomical and physiological architectures of behavioral controls in animals with prospects of neuro-engineering and synthetic biology.

Machine Learning Applications of Convolutional Neural Networks and Unet Architecture to Predict and Classify Demosponge Behavior

Biological data sets are increasingly becoming information-dense, making it effective to use a computer science-based analysis. We used convolution neural networks (CNN) and the specific CNN architecture Unet to study sponge behavior over time. We analyzed a large time series of hourly high-resolution still images of a marine sponge, Suberites concinnus (Demospongiae, Suberitidae) captured between 2012 and 2015 using the NEPTUNE seafloor cabled observatory, off the west coast of Vancouver Island, Canada. We applied semantic segmentation with the Unet architecture with some modifications, including adapting parts of the architecture to be more applicable to three-channel images (RGB). Some alterations that made this model successful were the use of a dice-loss coefficient, Adam optimizer and a dropout function after each convolutional layer which provided losses, accuracies and dice scores of up to 0.03, 0.98 and 0.97, respectively. The model was tested with five-fold cross-validation. This study is a first step towards analyzing trends in the behavior of a demosponge in an environment that experiences severe seasonal and inter-annual changes in climate. The end objective is to correlate changes in sponge size (activity) over seasons and years with environmental variables collected from the same observatory platform. Our work provides a roadmap for others who seek to cross the interdisciplinary boundaries between biology and computer science.

Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis

BACKGROUND

The ancestral presence of epithelia in Metazoa is no longer debated. Porifera seem to be one of the best candidates to be the sister group to all other Metazoa. This makes them a key taxon to explore cell-adhesion evolution on animals. For this reason, several transcriptomic, genomic, histological, physiological and biochemical studies focused on sponge epithelia. Nevertheless, the complete and precise protein composition of cell-cell junctions and mechanisms that regulate epithelial morphogenetic processes still remain at the center of attention.

RESULTS

To get insights into the early evolution of epithelial morphogenesis, we focused on morphogenic characteristics of the homoscleromorph sponge Oscarella lobularis. Homoscleromorpha are a sponge class with a typical basement membrane and adhaerens-like junctions unknown in other sponge classes. We took advantage of the dynamic context provided by cell dissociation-reaggregation experiments to explore morphogenetic processes in epithelial cells in a non-bilaterian lineage by combining fluorescent and electron microscopy observations and RNA sequencing approaches at key time-points of the dissociation and reaggregation processes.

CONCLUSIONS

Our results show that part of the molecular toolkit involved in the loss and restoration of epithelial features such as cell-cell and cell-matrix adhesion is conserved between Homoscleromorpha and Bilateria, suggesting their common role in the last common ancestor of animals. In addition, sponge-specific genes are differently expressed during the dissociation and reaggregation processes, calling for future functional characterization of these genes.

An Interesting Molecule: γ-Aminobutyric Acid. What Can We Learn from Hydra Polyps?

Neuronal excitability is controlled primarily by γ-aminobutyric acid (GABA) in the central and peripheral nervous systems of vertebrate as well as invertebrate organisms. Besides its recognized neurotransmitter functions, GABA also plays a fundamental role in neurogenesis and synaptogenesis during embryonic development. In addition, GABAergic mechanisms are also involved in disorders of various peripheral tissues, ranging from diabetes to hypothyroidism to inflammatory responses. The discovery of the molecule and the history of its biosynthetic pathways in vertebrate and invertebrate phyla are summarized here. The occurrence and distribution of GABA, GABA-synthesizing enzymes, and receptors to GABA in the freshwater polyp Hydra vulgaris (Cnidaria: Hydrozoa), endowed with an early evolved nervous system, are discussed in relation to possible interactions with the microbiota, a stable component of Hydra polyps; their contribution to the evolution of nervous systems through microbe-neuronal interactions is proposed.

Neural versus alternative integrative systems: molecular insights into origins of neurotransmitters

Transmitter signalling is the universal chemical language of any nervous system, but little is known about its early evolution. Here, we summarize data about the distribution and functions of neurotransmitter systems in basal metazoans as well as outline hypotheses of their origins. We explore the scenario that neurons arose from genetically different populations of secretory cells capable of volume chemical transmission and integration of behaviours without canonical synapses. The closest representation of this primordial organization is currently found in Placozoa, disk-like animals with the simplest known cell composition but complex behaviours. We propose that injury-related signalling was the evolutionary predecessor for integrative functions of early transmitters such as nitric oxide, ATP, protons, glutamate and small peptides. By contrast, acetylcholine, dopamine, noradrenaline, octopamine, serotonin and histamine were recruited as canonical neurotransmitters relatively later in animal evolution, only in bilaterians. Ligand-gated ion channels often preceded the establishment of novel neurotransmitter systems. Moreover, lineage-specific diversification of neurotransmitter receptors occurred in parallel within Cnidaria and several bilaterian lineages, including acoels. In summary, ancestral diversification of secretory signal molecules provides unique chemical microenvironments for behaviour-driven innovations that pave the way to complex brain functions and elementary cognition. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.

Uncovering cognitive similarities and differences, conservation and innovation

This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.