Morphological consequences for multi-partner chimerism in Botrylloides, a colonial urochordate

Physiological changes during torpor favor association with Endozoicomonas endosymbionts in the urochordate Botrylloides leachii

Environmental perturbations evoke down-regulation of metabolism in some multicellular organisms, leading to dormancy, or torpor. Colonies of the urochordate Botrylloides leachii enter torpor in response to changes in seawater temperature and may survive for months as small vasculature remnants that lack feeding and reproductive organs but possess torpor-specific microbiota. Upon returning to milder conditions, the colonies rapidly restore their original morphology, cytology and functionality while harboring re-occurring microbiota, a phenomenon that has not been described in detail to date. Here we investigated the stability of B. leachii microbiome and its functionality in active and dormant colonies, using microscopy, qPCR, in situ hybridization, genomics and transcriptomics. A novel lineage of Endozoicomonas, proposed here as Candidatus Endozoicomonas endoleachii, was dominant in torpor animals (53-79% read abundance), and potentially occupied specific hemocytes found only in torpid animals. Functional analysis of the metagenome-assembled genome and genome-targeted transcriptomics revealed that Endozoicomonas can use various cellular substrates, like amino acids and sugars, potentially producing biotin and thiamine, but also expressing various features involved in autocatalytic symbiosis. Our study suggests that the microbiome can be linked to the metabolic and physiological states of the host, B. leachii, introducing a model organism for the study of symbioses during drastic physiological changes, such as torpor.

Phylogeographic and Morphological Analysis of Botrylloides niger Herdman, 1886 from the Northeastern Mediterranean Sea

Botrylloides niger (class Ascidiacea) is an invasive marine filter-feeding invertebrate that is believed to originate from the West Atlantic region. This species of colonial tunicate has been observed in several locations along the coasts of Israel and around the Suez Canal, but it has not yet been reported on the coasts of the Northeastern Mediterranean Sea (NEMS), suggesting an ongoing Lessepsian migration. However, the extent of this invasion might be concealed by reports of other potentially misidentified species of Botrylloides, given that the strong morphological similarities within this genus renders taxonomical identification particularly challenging. In this study, we performed a phylogeographic and morphological analysis of B. niger in the NEMS. We collected 238 samples from 8 sampling stations covering 824 km of the coastlines of NEMS. We reported 14 different morphotypes, of which the orange-brown, orange, and brown-striped morphs were the most abundant. Using the mitochondrial cytochrome C oxidase I (COI) as a DNA barcode marker, we identified 4 haplotypes. The COI haplotypes clustered with the reference B. niger sequences from GenBank and differed significantly from the sister Botrylloides species. We confirmed our identification using three additional barcoding markers (Histone 3, 18S rRNA, and 28S rRNA), which all matched with over 99% similarity to reference sequences. In addition, we monitored a station for a year and conducted a temporal analysis of the collected colonies. The colonies were absent during the winter and spring, while new colonies were established in the summer and expanded during autumn. We performed demographic population analysis on our spatial data that identified a possible population subdivision at a sampling site, which might have been caused by local freshwater input. Herein, we present the first report on the presence of Botrylloides niger in the NEMS. This study represents a key step toward understanding the diversity and the propagation of this highly invasive species of colonial ascidians, both within the Mediterranean basin as well as globally.

Using RNA-Seq for Transcriptome Profiling of Botrylloides sp. Regeneration

The decrease in sequencing costs and technology improvements has led to the adoption of RNA-sequencing to profile transcriptomes from further non-traditional regeneration model organisms such as the colonial ascidian Botrylloides leachii. The relatively unbiased way in which transcripts are identified and quantified makes this technique suitable to detect large-scale changes in expression, and the identification of novel transcripts and isoforms. Of particular interest to many researchers is the discovery of differentially expressed transcripts across different treatment conditions or stages of regeneration. This protocol describes a workflow starting from processing raw sequencing reads, mapping reads, assembly of transcripts, and measuring their abundance, creating lists of differentially expressed genes and their biological interpretation using gene ontologies. All programs used in this protocol are open-source software tools and freely available.

Artificial seawater based long-term culture of colonial ascidians

Tunicates are highly diverse marine invertebrate filter-feeders that are vertebrates' closest relatives. These organisms, despite a drastically different body plan during their adulthood, have a tissue complexity related to that of vertebrates. Ascidians, which compose most of the Tunicata, are benthic sessile hermaphrodites that reproduce sexually through a motile tadpole larval stage. Over half of the known ascidians species are able to reproduce asexually by budding, typically leading to the formation of colonies where animals, called zooids, are interconnected through an external vascular system. In addition, colonial ascidians are established models for important biological processes including allorecognition, immunobiology, aging, angiogenesis and whole-body regeneration. However, the current paucity in breeding infrastructures limits the study of these animals to coastal regions. To promote a wider scientific spreading and popularity of colonial ascidians, we have developed a flexible recirculating husbandry setup for their long-term in-lab culture. Our system is inspired both by the flow-through aquariums used by coastal ascidian labs, as well as by the recirculating in-lab systems used for zebrafish research. Our hybrid system thus combines colony breeding, water filtering and food culturing in a semi-automated system where specimens develop on hanging microscopy glass slides. Temperature, light/dark cycles, flow speed and feeding rates can be controlled independently in four different breeding environments to provide room for species-specific optimization as well as for running experiments. This setup is complemented with a quarantine for the acclimatization of wild isolates. Herein we present our success in breeding Botrylloides diegensis, a species of colonial ascidians, for more than 3 years in recirculating artificial seawater over 600 ​km away from their natural habitat. We show that colonies adapt well to in-lab culturing provided that a suitable marine microbiome is present, and that a specific strain can be isolated, propagated and efficiently used for research over prolonged periods of time. The flexible and modular structure of our system can be scaled and adapted to the needs of specific species, such as Botryllus schlosseri, as well as of particular laboratory spaces. Overall, we show that Botrylloides diegensis can be proficiently bred in-land and suggest that our results can be extended to other species of colonial ascidians to promote research on these fascinating animals.

High fusibility and chimera prevalence in an invasive colonial ascidian

The formation of chimeric entities through colony fusion has been hypothesized to favour colonisation success and resilience in modular organisms. In particular, it can play an important role in promoting the invasiveness of introduced species. We studied prevalence of chimerism and performed fusion experiments in Mediterranean populations of the worldwide invasive colonial ascidian Didemnum vexillum. We analysed single zooids by whole genome amplification and genotyping-by-sequencing and obtained genotypic information for more than 2,000 loci per individual. In the prevalence study, we analysed nine colonies and identified that 44% of them were chimeric, composed of 2–3 different genotypes. In the fusion experiment 15 intra- and 30 intercolony pairs were assayed but one or both fragments regressed and died in ~45% of the pairs. Among those that survived for the length of the experiment (30 d), 100% isogeneic and 31% allogeneic pairs fused. Fusion was unlinked to global genetic relatedness since the genetic distance between fused or non-fused intercolony pairs did not differ significantly. We could not detect any locus directly involved in allorecognition, but we cannot preclude the existence of a histocompatibility mechanism. We conclude that chimerism occurs frequently in D. vexillum and may be an important factor to enhance genetic diversity and promote its successful expansion.

Whole-Body Regeneration in the Colonial Tunicate Botrylloides leachii

The colonial marine invertebrate Botrylloides leachii belongs to the Tunicata subphylum, the closest invertebrate relatives to the vertebrate group and the only known class of chordates that can undergo whole-body regeneration (WBR). This dramatic developmental process allows a minute isolated fragment of B. leachii's vascular system, or a colony excised of all adults, to restore a functional animal in as little as 10 days. In addition to this exceptional regenerative capacity, B. leachii can reproduce both sexually, through a tadpole larval stage, and asexually, through palleal budding. Thus, three alternative developmental strategies lead to the establishment of filter-feeding adults. Consequently, B. leachii is particularly well suited for comparative studies on regeneration and should provide novel insights into regenerative processes in chordates.Here, after a short introduction on regeneration, we overview the biology of B. leachii as well as the current state of knowledge on WBR in this species and in related species of tunicates. Finally, we highlight the possible future directions that research might take in the study of WBR, including thoughts on technological approaches that appear most promising in this context. Overall, we provide a synthesis of the current knowledge on WBR in B. leachii to support research in this chordate species.

Invasiveness, chimerism and genetic diversity

Adaptation for invasiveness should comprise the capability to exploit and prosper in a wide range of ecological conditions and is therefore expected to be associated with a certain level of genetic diversity. Paradoxically, however, invasive populations are established by only a few founders, resulting in low genetic diversity. As a conceivable way of attaining high genetic diversity and high variance of gene expression even when a small number of founders is involved in invasiveness, I suggest here chimerism, a fusion between different individuals-a common phenomenon found in numerous phyla. The composite entity offers the chimeric organism genetic flexibility and higher inclusive fitness that depends on the joint genomic fitness of the original partners. The ability to form a chimeric entity is also applied to subsequent generations, and consequently, the level of genetic diversity does not decline over generations of population establishment following invasion.

Quo vadis chimerism?

Although immunity in multicellular organisms is efficient in dealing with alien agents, it may fail for allogeneic chimerism. Natural chimerism is widely documented in nature, distributed in at least ten phyla of protists, invertebrates and plants, vertebrates and mammals, including humans; it is an important ecological/evolutionary tool manipulating metazoans' life history portraits. Instead of purging allogeneic nascent selfish cells, a 'double edged sword' chimerism emerges, displaying environmental dictated costs and benefits for the genotypes involved. Benefits include the development of synergistic complementation, the increase of genetic variability, the assurance of mate location, improved size-dependent ecological qualities (growth rates, reproduction, survivorship, competition, environmental tolerance) and more. Costs include the threat of somatic and germ cell parasitism, developmental instability, death, diseases, autoimmunity, sexual sterility and organ malformations, which develop as well in mammalian natural chimerism, including humans. Because of its importance, medical sciences should study and harness natural chimerism properties for clinical purposes.

Neglected biological features in cnidarians self-nonself recognition

Cnidarian taxa, currently of the most morphologically simplest extant metazoans, exhibit many salient properties of innate immunity that are shared by most Animalia. One hallmark constituent of immunity exhibit by most cnidarians is histocompatibility, marked by wide spectrum of allogeneic and xenogeneic effector arms, progressing into tissue fusions or inflammatory rejections. Scientific propensity on cnidarians immunity, while discussing historecognition as the ground for immunity in these organisms, concentrates on host-parasitic and disease oriented studies, or focuses on genome approaches that search for gene homologies with the vertebrates. Above tendency for mixing up between historecognition and host-parasitic/disease, highlights a serious obstacle for the progress in our understanding of cnidarian immunobiology. Here I critically overview four 'forgotten' cnidarian immune features, namely, specificity, immunological memory, allogeneic maturation and natural chimerism, presenting insights into perspectives that are prerequisite for any discussion on cnidarian evolution. It is evident that cnidarian historecognition embraces elements that the traditional field of vertebrate immunology has never encountered (i.e., variety of cytotoxic outcomes, different types of effector mechanisms, chimerism, etc.). Also, cnidarian immune features dictating that different individuals within the same species seem to respond differently to the same immunological challenge, is far from that recorded in the vertebrates' adaptive immunity. While above features may be connected to host-parasitic and disease phenomena and effector arms, they clearly attest to their unique critical roles in shaping cnidarians historecognition, calling for improved distinction between historecognition and host-response/ disease disciplines. The research on cnidarians immunity still suffers from the lack of accepted synthesis of what historecognition is or does. Mounting of an immune response against conspecifics or xenogeneic organisms should therefore be clearly demarcated from other paths of immunity, till cnidarian innate immunity as a whole is expounded.

Asexual propagation and regeneration in colonial ascidians

Regeneration is widely distributed among the metazoans. However, clear differences exist as to the degree of regenerative capacity: some phyla can only replace missing body parts, whereas others can generate entirely new individuals. Ascidians are animals that possess a remarkable regenerative plasticity and exhibit a great diversity of mechanisms for asexual propagation and survival. They are marine invertebrate members of the subphylum Tunicata and represent modern-day descendants of the chordate ancestor; in their tadpole stage they exhibit a chordate body plan that is resorbed during metamorphosis. Solitary species grow into an adult that can reach several centimeters in length, whereas colonial species grow by asexual propagation, creating a colony of genetically identical individuals. In this review, we present an overview of the biology of colonial ascidians as a paradigm for study in stem cell and regenerative biology. Focusing on botryllid ascidians, we introduce the potential roles played by multipotent epithelia and multipotent/pluripotent stem cells as source of asexual propagation and regenerative plasticity in the different budding mechanisms, and consider the putative mechanism of body repatterning in a non-embryonic scenario. We also discuss the involvement of intra-colony homeostatic processes in regulating budding potential, and the functional link between allorecognition, chimerism, and regenerative potential.

Coral kin aggregations exhibit mixed allogeneic reactions and enhanced fitness during early ontogeny

Background

Aggregated settlement of kin larvae in sessile marine invertebrates may result in a complex array of compatible and incompatible allogeneic responses within each assemblage. Each such aggregate can, therefore, be considered as a distinct self-organizing biological entity representing adaptations that have evolved to maximize the potential benefits of gregarious settlement. However, only sparse information exists on the selective forces and ecological consequences of allogeneic coalescence.

Results

We studied the consequences of aggregated settlement of kin larvae of Stylophora pistillata (a Red Sea stony coral), under controlled laboratory settings. When spat came into contact, they either fused, establishing a chimera, or rejected one another. A one-year study on growth and survivorship of 544 settled S. pistillata genotypes revealed six types of biological entities: (1) Single genotypes (SG); (2) Bi-chimeras (BC); (3) Bi-rejecting genotypes (BR); (4) Tri-chimera entities (TC); (5) Three-rejecting genotypes (TR); and (6) Multi-partner entities (MP; consisting of 7.5 ± 2.6 partners). Analysis of allorecognition responses revealed an array of effector mechanisms: real tissue fusions, transitory fusions and six other histoincompatible reactions (borderline formation, sutures, overgrowth, bleaching, rejection, and partner death), disclosing unalike onsets of ontogeny and complex modes of appearance within each aggregate. Evaluations at the entity level revealed that MP entities were the largest, especially in the first two months (compared with SG: 571% in the first month and 162% in the seventh month). However, at the genotype level, the SG entities were the largest and the colonies with the highest-cost-per-genotype were the TR and the MP colonies. The cost was calculated as reduced average genotype size, from 27% and 12% in the first month to 67% and 64% in the seventh month, respectively. In general, MP exhibited the highest survivorship rate (85%, after one year) and SG the lowest (54%).

Conclusion

In view of the above, we suggest that the driving force behind gregarious kin settlements in Stylophora pistillata stems from gained benefits associated with the immediate and long-term increase in total size of the MP entity, whereas survivorship rates did not draw a parallel link. Furthermore, the biological organization of MP entity exhibits, simultaneously, an intricate network of rejecting and fusible interactions in a single allogeneic intimate arena, where proposed benefits surpass costs incurred by discord among founders. Above results and documentations on gregarious settlement in other marine taxa bring us to suggest that the 'group level' of kin aggregates may serve as a ubiquitous legitimate selection entity in the evolution of a sessile mode of life in marine organisms.

Stem cells are units of natural selection in a colonial ascidian

Stem cells are highly conserved biological units of development and regeneration. Here we formally demonstrate that stem cell lineages are also legitimate units of natural selection. In a colonial ascidian, Botryllus schlosseri, vascular fusion between genetically distinct individuals results in cellular parasitism of somatic tissues, gametes, or both. We show that genetic hierarchies of somatic and gametic parasitism following fusion can be replicated by transplanting cells between colonies. We prospectively isolate a population of multipotent, self-renewing stem cells that retain their competitive phenotype upon transplantation. Their single-cell contribution to either somatic or germline fates, but not to both, is consistent with separate lineages of somatic and germline stem cells or pluripotent stem cells that differentiate according to the niche in which they land. Since fusion is restricted to individuals that share a fusion/histocompatibility allele, these data suggest that histocompatibility genes in Botryllus evolved to protect the body from parasitic stem cells usurping asexual or sexual inheritance.

Primitive immune systems: Are your ways my ways?

Although vertebrate immune systems have been commonly conceived as exquisitely developed to combat pervasiveness by pathogens, they are not infallible. The enigmatic expression of histocompatibility in vertebrates, the manifestation of natural chimerism, autoimmunity, malignancy, and other puzzling outcomes hint that immunity did not arise in evolution to fight infections and that this capacity is a late evolutionary appendage, owing its appearance to the redeployment of a system developed for other reasons. Allorecognition in the colonial tunicate Botryllus schlosseri serves here as a platform for a contending paradigm, advocating that immunity has developed as a surveillance machinery against and for purging of nascent selfish cells (stemmed from a kin organism or from transformed cells within the organism of origin). Defense against pathogens (always representing xenogeneic aliens) appeared later, revealing the multiplicity of newly developed phenomena. Allorecognition events characteristic of the Botryllus primitive immune system, such as fusion versus rejection, the morphological resorption with its expressed hierarchy, and the somatic/germ-cell parasitic outcomes, provide clues to the evolutionary basis of allorecognition. Recent work on Botryllus immunity that highlights the cost of littering individuality by somatic variants/allogeneic cells is discussed.