A holobiont is an assemblage of a host and the many other species living in or around it, which together form a discrete ecological unit through symbiosis, though there is controversy over its discreteness. The components of a holobiont are individual species or bionts, while the combined genome of all bionts is the hologenome. The holobiont concept was initially introduced by the German theoretical biologist Adolf Meyer-Abich in 1943, and then apparently independently by Dr. Lynn Margulis in her 1991 book Symbiosis as a Source of Evolutionary Innovation. The concept has evolved since the original formulations. Holobionts include the host, virome, microbiome, and any other organisms which contribute in some way to the functioning of the whole. Well-studied holobionts include reef-building corals and humans.
A Cell So Minimal That It Challenges Definitions of Life | Quanta Magazine
The newly described microbe represents a world of parasitic, intercellular biodiversity only beginning to be revealed by genome sequencing.
A diverse and distinct microbiome inside living trees
Nature - Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood...
Symbiotic organs in insects: diversity, functional implications, and terminology
Abstract With over a million described species, insects represent the most successful group of animals on Earth. One of the drivers of insect diversity is their ability to engage in multifold beneficial symbioses with microorganisms, often involving specialized host organs to accommodate intra- or extracellular symbionts. The existence of such organs and their importance for sustaining and transmitting beneficial symbionts has been known for over a century, and specific terms have been established for categorizing organs harbouring intracellular bacteria (bacteriomes) or fungi (mycetomes), or cuticular crypts containing extracellular fungi (mycetangia). For others, however, general terms are lacking, e.g. organs containing extracellular bacteria associated with the cuticle or with the digestive tract. Furthermore, previously established terms have been misused in other contexts. Notably, ‘bacteriome’ has been increasingly employed in the microbiome field to refer to bacterial communities, instead of the term’s original meaning of specialized organs housing intracellular bacterial symbionts. Here, we review and categorize the diversity of symbiotic organs in insects and propose a unified terminology. Our hope is that this common language will facilitate communication and thereby support the field of symbiosis research in unravelling commonalities and differences in the evolution, ecology, development, physiology and molecular basis across symbiotic interactions. This article is part of the theme issue ‘Life in natural microcosms’.
The cognitive cell: bacterial behavior reconsidered
Research on how bacteria adapt to changing environments underlies the contemporary biological understanding of signal transduction, and signal transduction provides the foundation of the information-processing approach that is the hallmark of the ‘cognitive revolution,’ which began in the mid-20th century. Yet cognitive scientists largely remain oblivious to research into microbial behavior that might provide insights into problems in their own domains, while microbiologists seem equally unaware of the potential importance of their work to understanding cognitive capacities in multicellular organisms, including vertebrates. Evidence in bacteria for capacities encompassed by the concept of cognition is reviewed. Parallels exist not only at the heuristic level of functional analogue, but also at the level of molecular mechanism, evolution and ecology, which is where fruitful cross-fertilization among disciplines might be found.
Cognition without brains? Learning and memory in microorganisms
Memory and learning are cognitive abilities typically associated with animals that possess a complex nervous system. Interestingly, recent studies suggest that microorganisms might also display learning-like behaviours. However, a factor limiting progress in this field is the lack of shared, microbe-specific frameworks that allow microbiologists to easily compare discoveries with concepts developed in cognitive sciences. In this review, we aim to bridge this gap by providing a conceptual overview of the definitional requirements for memory and learning to classify microbial behaviours and capabilities. Additionally, we identify and address problems that cause conceptual ambiguity in the microbial cognition literature, thereby facilitating more productive debates on the topic. Finally, we provide a novel perspective on how microbes might ‘learn’ from each other.
Principles of Minimal Cognition: Casting Cognition as Sensorimotor Coordination
Within the cognitive sciences, cognition tends to be interpreted from an anthropocentric perspective, involving a stringent set of human capabilities. Instead, we suggest that cognition is better explicated as a much more general biological phenomenon, allowing the lower bound of cognition to extend much further down the phylogenetic scale. We argue that elementary forms of cognition can already be witnessed in prokaryotes possessing a functional sensorimotor analogue of the nervous system. Building on a case-study of the Escherichia coli bacterium and its sensorimotor system, the TCST-system, we home in on the characteristics of minimal cognition, and distinguish it from more basic forms of ontogenetic adaptation. In our view, minimal cognition requires an embodiment consisting of a sensorimotor coupling mechanism that subsumes an autopoietic organization; this forms the basis of the growing consensus that the core of cognition revolves around sensorimotor coupling. We discuss the relevance of our interpretation of minimal cognition for the study of cognition in general
Biosphere
The biosphere, also called the ecosphere, is the worldwide sum of all ecosystems. It can also be termed the zone of life on the Earth. The biosphere is virtually a closed system with regard to matter, with minimal inputs and outputs. Regarding energy, it is an open system, with photosynthesis capturing solar energy at a rate of around 100 terawatts. By the most general biophysiological definition, the biosphere is the global ecological system integrating all living beings and their relationships, including their interaction with the elements of the lithosphere, cryosphere, hydrosphere, and atmosphere. The biosphere is postulated to have evolved, beginning with a process of biopoiesis or biogenesis, at least some 3.5 billion years ago.
The biogenic approach to cognition
After half a century of cognitive revolution we remain far from agreement about what cognition is and what cognition does. It was once thought that these questions could wait until the data were in. Today there is a mountain of data, but no way of making sense of it. The time for tackling the fundamental issues has arrived. The biogenic approach to cognition is introduced not as a solution but as a means of approaching the issues. The traditional, and still predominant, methodological stance in cognitive inquiry is what I call the anthropogenic approach: assume human cognition as the paradigm and work ‘down’ to a more general explanatory concept. The biogenic approach, on the other hand, starts with the facts of biology as the basis for theorizing and works ‘up’ to the human case by asking psychological questions as if they were biological questions. Biogenic explanations of cognition are currently clustered around two main frameworks for understanding biology: self-organizing complex systems and autopoiesis. The paper describes the frameworks and infers from them ten empirical principles—the biogenic ‘family traits’—that constitute constraints on biogenic theorizing. Because the anthropogenic approach to cognition is not constrained empirically to the same degree, I argue that the biogenic approach is superior for approaching a general theory of cognition as a natural phenomenon.
Lectures on Perception: An Ecological Perspective
Lectures on Perception: An Ecological Perspective addresses the generic principles by which each and every kind of life form—from single celled organisms (e.g., difflugia) to multi-celled organisms (e.g., primates)—perceives the circumstances of their living so that they can behave adaptively. It focuses on the fundamental ability that relates each and every organism to its surroundings, namely, the ability to perceive things in the sense of how to get about among them and what to do, or not
Growth, metabolic partitioning, and the size of microorganisms
Population growth rate is a fundamental ecological and evolutionary characteristic of living organisms, but individuals must balance the metabolism devoted to biosynthesis and reproduction against the maintenance of existing structure and other functionality. Here we present a mathematical model that relates metabolic partitioning to the form of growth. The model captures the observed growth trajectory of single cells and individuals for a variety of species and taxa spanning prokaryotes, unicellular eukaryotes, and small multicellular eukaryotes. Our analysis suggests that the per-unit costs of biosynthesis and maintenance are conserved across prokaryotes and eukaryotes. However, the relative metabolic expenditure on growth and maintenance of whole organisms clearly differentiates taxa: prokaryotes spend an increasing fraction of their entire metabolism on growth with increasing cell size, whereas eukaryotes devote a diminishing fraction. These differences allow us to predict the minimum and maximum size for each taxonomic group, anticipating observed evolutionary life-history transitions. The framework provides energetic insights into taxonomic tradeoffs related to growth and metabolism and constrains traits that are important for size-structured modeling of microbial communities and their ecological and biogeochemical effects.
A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome
Abstract Defining the minimal genetic requirements for cellular life remains a fundamental question in biology. Genomic exploration continually reveals novel microbial lineages, often exhibiting extreme genome reduction, particularly within symbiotic relationships. Here, we report the discovery of Candidatus Sukunaarchaeum mirabile, a novel archaeon with an unprecedentedly small genome of only 238 kbp —less than half the size of the smallest previously known archaeal genome— from a dinoflagellate-associated microbial community. Phylogenetic analyses place Sukunaarchaeum as a deeply branching lineage within the tree of Archaea, representing a novel major branch distinct from established phyla. Environmental sequence data indicate that sequences closely related to Sukunaarchaeum form a diverse and previously overlooked clade in microbial surveys. Its genome is profoundly stripped-down, lacking virtually all recognizable metabolic pathways, and primarily encoding the machinery for its replicative core: DNA replication, transcription, and translation. This suggests an unprecedented level of metabolic dependence on a host, a condition that challenges the functional distinctions between minimal cellular life and viruses. The discovery of Sukunaarchaeum pushes the conventional boundaries of cellular life and highlights the vast unexplored biological novelty within microbial interactions, suggesting that further exploration of symbiotic systems may reveal even more extraordinary life forms, reshaping our understanding of cellular evolution. Graphical Abstract
Controlled Mold
A blog about fermentation, engineering, and cell-ag. We run wild experiments on microbes and try to eat them, all with the help of computers and math.
Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications
Agriculture is under pressure to provide food for a growing population and the feedstock required to drive the bioeconomy. Methods to breed and genetically modify plants are inadequate to keep pace. When engineering crops, traits are painstakingly introduced into plants one-at-a-time, combine unpredictably, and are continuously expressed. Synthetic biology is changing these paradigms with new genome construction tools, computer aided design (CAD), and artificial intelligence (AI). “Smart plants” contain circuits that respond to environmental change, alter morphology, or respond to threats. Further, the plant and associated microbes (fungi, bacteria, archaea) are now being viewed by genetic engineers as a holistic system. Historically, plant health has been enhanced by many natural and laboratory-evolved soil microbes marketed to enhance growth or provide nutrients, or pest/stress resistance. Synthetic biology has expanded the number of species that can be engineered, increased the complexity of engineered functions, controlled environmental release, and can assemble stable consortia. New CAD tools will manage genetic engineering projects spanning multiple plant genomes (nucleus, chloroplast, mitochondrion) and the thousands of genomes of associated bacteria/fungi. This review covers advanced genetic engineering techniques to drive the next agricultural revolution, as well as push plant engineering into new realms for manufacturing, infrastructure, sensing, and remediation.
Chondrilla nucula (Porifera, Demospongiae) : an example of successful plasticity ; ecological and morphological aspects
Sponges (Porifera) represent an important component of the Mediterranean sessile benthic community. They are present both in shallow and deeper waters, on soft and hard bottoms and some species, namely the bath sponges, has an application in human life since a long time. In the last few decades, they also assumed an importance among the organisms producing bioactive compounds which application goes from the homeopathy to the classical medicine to the industry. The study of the taxonomy, ecology and biology of sponges has an history hundreds years old. Now, due to the new findings that render sponges an exploitable marine resource, a coupling of the traditional sciences with the new emerging applications (biotechnology) is urgently needed. The Northern Adriatic Sea was the craddle of the sponge science hosting 36% of the sponge species present in the whole Mediterranean Sea. For the present work, the sponge fauna of a channel-like bay called Limski kanal (Croatia) has been intensively studied for the first time and a list of sponges, including species new for this area, is the result of a series of surveys in twelve sampling sites along the channel. As an introduction to the classification of sponges, a guide to the identification of the most common Mediterranean species has been written and included. A study on the temporal dynamic of a sponge community (Limski kanal, Croatia) was made by using fixed frames that have been photographed along a period of two years. Either seasonality, morphological variability, growth and degeneration phenomena have been observed, providing one more evidence of the incredible plasticity of the Porifera. Among the species in the Limski kanal, Chondrilla nucula (Porifera, Demospongiae) has been chosen as model organism. Firstly, its distribution, abundance and average coverage have been studied, showing that this species is very common along the channel, also in areas with a high sedimentation. Its distribution pattern depends mainly on light availability and kind of substrate. C. nucula is known as a very plastic species: here some macromorphological aspects related to the locomotion, the fragmentation events, the elimination of the sediment and the epibiosis are described in the attempt to give an overview on the successful life strategies of this sponge. Up to now only morphological studies on the oogenesis and spermatogenesis are available but the complete life cycle is unknown. In this study, macromorphological variations in specimens of C. nucula in reproduction and the first stages of embryogenesis have been described for the first time. Finally, in view of a biotechnological use of sponges as bioremediator organisms, the filtration and the bacterial retention rates of C. nucula have been investigated using clearance tests. In spite of a low filtration rate, the sponge showed high bacterial retention rates. This, together with the easy techniques required to farm it, makes of this sponge an eligible candidate for bioremediation. To achieve an effective conservation management plan and a sustainable exploitation of the marine resources, the knowledge on the biological and ecological characteristics of the benthic community and of the single species is absolutely necessary.