Evolutionary transitions revisited: Holobiont evo-devo

Adapting the rhizome concept to an extended definition of viral quasispecies and the implications for molecular evolution

The rhizome concept proposed by Gilles Deleuze and Félix Guattari offers a novel perspective on the organization and interdependence of complex constellations of heterogeneous entities, their mapping and their ruptures. The emphasis of the present study is placed on the dynamics of contacts and communication among such entities that arise from experimentation, without any favored hierarchy or origin. When applied to biological evolution, the rhizome concept integrates all types of heterogeneity resulting from "symbiotic" relationships among living beings (or their genomic material), horizontal genetic transfer, recombination and mutation, and breaks away from the approach that gives rise to the phylogenetic tree of life. It has already been applied to describe the dynamics and evolution of RNA viruses. Thus, here we introduce a novel framework for the interpretation the viral quasispecies concept, which explains the evolution of RNA virus populations as the result of dynamic interconnections and multifaceted interdependence between highly heterogeneous viral sequences and its inherently heterogeneous host cells. The rhizome network perspective underlines even further the medical implications of the broad mutant spectra of viruses that are in constant flow, given the multiple pathways they have available for fitness loss and gain.

The Evolution, Assembly, and Dynamics of Marine Holobionts

The holobiont concept (i.e., multiple living beings in close symbiosis with one another and functioning as a unit) is revolutionizing our understanding of biology, especially in marine systems. The earliest marine holobiont was likely a syntrophic partnership of at least two prokaryotic members. Since then, symbiosis has enabled marine organisms to conquer all ocean habitats through the formation of holobionts with a wide spectrum of complexities. However, most scientific inquiries have focused on isolated organisms and their adaptations to specific environments. In this review, we attempt to illustrate why a holobiont perspective-specifically, the study of how numerous organisms form a discrete ecological unit through symbiosis-will be a more impactful strategy to advance our understanding of the ecology and evolution of marine life. We argue that this approach is instrumental in addressing the threats to marine biodiversity posed by the current global environmental crisis.

Rapid acquisition of microorganisms and microbial genes can help explain punctuated evolution

The punctuated mode of evolution posits that evolution occurs in rare bursts of rapid evolutionary change followed by long periods of genetic stability (stasis). The accepted cause for the rapid changes in punctuated evolution is special ecological circumstances – selection forces brought about by changes in the environment. This article presents a complementary explanation for punctuated evolution by the rapid formation of genetic variants in animals and plants by the acquisition of microorganisms from the environment into microbiomes and microbial genes into host genomes by horizontal gene transfer. Several examples of major evolutionary events driven by microorganisms are discussed, including the formation of the first eukaryotic cell, the ability of some animals to digest cellulose and other plant cell-wall complex polysaccharides, dynamics of root system architecture, and the formation of placental mammals. These changes by cooperation were quantum leaps in the evolutionary development of complex bilolgical systems and can contribute to an understanding of the mechanisms underlying punctuated evolution.

The enteric nervous system of the C. elegans pharynx is specified by the Sine oculis-like homeobox gene ceh-34

Overarching themes in the terminal differentiation of the enteric nervous system, an autonomously acting unit of animal nervous systems, have so far eluded discovery. We describe here the overall regulatory logic of enteric nervous system differentiation of the nematode Caenorhabditis elegans that resides within the foregut (pharynx) of the worm. A C. elegans homolog of the Drosophila Sine oculis homeobox gene, ceh-34, is expressed in all 14 classes of interconnected pharyngeal neurons from their birth throughout their life time, but in no other neuron type of the entire animal. Constitutive and temporally controlled ceh-34 removal shows that ceh-34 is required to initiate and maintain the neuron type-specific terminal differentiation program of all pharyngeal neuron classes, including their circuit assembly. Through additional genetic loss of function analysis, we show that within each pharyngeal neuron class, ceh-34 cooperates with different homeodomain transcription factors to individuate distinct pharyngeal neuron classes. Our analysis underscores the critical role of homeobox genes in neuronal identity specification and links them to the control of neuronal circuit assembly of the enteric nervous system. Together with the pharyngeal nervous system simplicity as well as its specification by a Sine oculis homolog, our findings invite speculations about the early evolution of nervous systems.

Environmentality in biomedicine: microbiome research and the perspectival body

Microbiome research shows that human health is foundationally intertwined with the ecology of microbial communities living on and in our bodies. This challenges the categorical separation of organisms from environments that has been central to biomedicine, and questions the boundaries between them. Biomedicine is left with an empirical problem: how to understand causal pathways between host health, microbiota and environment? We propose a conceptual tool - environmentality - to think through this problem. Environmentality is the state or quality of being an environment for something else in a particular context: a fully perspectival proposition. Its power lies partly in what Isabelle Stengers has called the efficacy of the word itself, contrasting the dominant sense of the word environment as something both external and fixed. Through three case studies, we argue that environmentality can help think about the causality of microbiota vis-a-vis host health in a processual, relational and situated manner, across scales and temporalities. We situate this intervention within historical trajectories of thought in biomedicine, focusing on the challenge microbiome research poses to an aperspectival body. We argue that addressing entanglements between microbial and human lives requires that the environment is brought into the clinic, thus shortening the conceptual gap between medicine and public health.

Development, Diversity, and Neurogenic Capacity of Enteric Glia

Enteric glia are a fascinating population of cells. Initially identified in the gut wall as the "support" cells of the enteric nervous system, studies over the past 20 years have unveiled a vast array of functions carried out by enteric glia. They mediate enteric nervous system signalling and play a vital role in the local regulation of gut functions. Enteric glial cells interact with other gastrointestinal cell types such as those of the epithelium and immune system to preserve homeostasis, and are perceptive to luminal content. Their functional versatility and phenotypic heterogeneity are mirrored by an extensive level of plasticity, illustrated by their reactivity in conditions associated with enteric nervous system dysfunction and disease. As one of the hallmarks of their plasticity and extending their operative relationship with enteric neurons, enteric glia also display neurogenic potential. In this review, we focus on the development of enteric glial cells, and the mechanisms behind their heterogeneity in the adult gut. In addition, we discuss what is currently known about the role of enteric glia as neural precursors in the enteric nervous system.

Social networking in crop plants: Wired and wireless cross-plant communications

The plant-associated microbial community (microbiome) has an important role in plant-plant communications. Plants decipher their complex habitat situations by sensing the environmental stimuli and molecular patterns and associated with microbes, herbivores and dangers. Perception of these cues generates inter/intracellular signals that induce modifications of plant metabolism and physiology. Signals can also be transferred between plants via different mechanisms, which we classify as wired- and wireless communications. Wired communications involve direct signal transfers between plants mediated by mycorrhizal hyphae and parasitic plant stems. Wireless communications involve plant volatile emissions and root exudates elicited by microbes/insects, which enable inter-plant signalling without physical contact. These producer-plant signals induce microbiome adaptation in receiver plants via facilitative or competitive mechanisms. Receiver plants eavesdrop to anticipate responses to improve fitness against stresses. An emerging body of information in plant-plant communication can be leveraged to improve integrated crop management under field conditions.

Animal development in the microbial world: Re-thinking the conceptual framework

Animals have evolved within the framework of the microbes and are constantly exposed to diverse microbiota. This dominance of the microbial world is forcing all fields of biology to question some of their most basic premises, with developmental biology being no exception. While animals under laboratory conditions can develop and live without microbes, they are far from normal, and would not survive under natural conditions, where their fitness would be strongly compromised. Since much of the undescribed biodiversity on Earth is microbial, any consideration of animal development in the absence of the recognition of microbes will be incomplete. Here, we show that animal development may never have been autonomous, rather it requires transient or persistent interactions with the microbial world. We propose that to formulate a comprehensive understanding of embryogenesis and post-embryonic development, we must recognize that symbiotic microbes provide important developmental signals and contribute in significant ways to phenotype production. This offers limitless opportunities for the field of developmental biology to expand.

Developmental Symbiosis: A Sponge Larva Needs Symbiotic Bacteria to Succeed on the Benthos

Settlement and metamorphosis of marine invertebrate larvae are processes of profound developmental, morphological, physiological and ecological change. That these processes in larvae of a marine sponge critically rely on products supplied by endosymbiotic bacteria signals the importance of developmental symbiosis among the most basal metazoans.

Nest Architecture and Colony Growth of Atta bisphaerica Grass-Cutting Ants

Atta grass-cutting ants (Formicidae: Myrmicinae: Attini) are found in the Cerrado biome and build giant nests with hundreds or thousands of large chambers. We assessed for Atta bisphaerica grass-cutting ants whether the total volume of fungus chambers and other nest parameters grow at close or similar proportions to worker numbers in the colony. Data on fungus garden biomass, population, external area, number of entrance holes, number of fungus chambers, total fungus chambers volume, and nest depth were obtained during colony growth/nest development. Our results reveal that the fungus garden biomass, external area, and total fungus chamber volume increased at rates similar to the increase in the number of workers. The total volume of chambers, and external area increased at a similar proportion to the increase in number of workers, probably due to the fungus garden allocation needs of the colony. The number of fungus chambers, number of entrance holes, and nest depth increased less than 4-fold for every 10-fold increase in the worker number. In addition, the height of the fungus chambers increased as the width increased, a pattern not observed for tunnel height and length, and the chamber volume increased according to worker number. Thus, this study demonstrates for A. bisphaerica that nest development in terms of chamber volume is similar to the increase in number of colony workers, and this contributes to a better understanding of Atta nest architecture.

"Microbiota, symbiosis and individuality summer school" meeting report

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, symbiosis and individuality: conceptual and philosophical issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of incorporating into meetings experts from other disciplines, such as philosophy and history of science. Video Abstract.

The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis

John Tyler Bonner's call to re-evaluate evolutionary theory in light of major transitions in life on Earth (e.g., from the first origins of microbial life to the evolution of sex, and the origins of multicellularity) resonate with recent discoveries on epigenetics and the concept of the hologenome. Current studies of genome evolution often mistakenly focus only on the inheritance of DNA between parent and offspring. These are in line with the widely accepted Neo-Darwinian framework that pairs Mendelian genetics with an emphasis on natural selection as explanations for the evolution of biodiversity on Earth. Increasing evidence for widespread symbioses complicates this narrative, as is seen in Scott Gilbert's discussion of the concept of the holobiont in this series: Organisms across the tree of life coexist with substantial influence on one another through endosymbiosis, symbioses, and host-associated microbiomes. The holobiont theory, coupled with observations from molecular studies, also requires us to understand genomes in a new way-by considering the interactions underlain by the genome of a host plus its associated microbes, a conglomerate entity referred to as the hologenome. We argue that the complex patterns of inheritance of these genomes coupled with the influence of symbionts on host gene expression make the concept of the hologenome an epigenetic phenomenon. We further argue that the aspects of the hologenome challenge of the modern evolutionary synthesis, which requires updating to remain consistent with Darwin's intent of providing natural laws that underlie the evolution of life on Earth.