Microorganisms as scaffolds of host individuality: an eco-immunity account of the holobiont

There is currently a great debate about whether the holobiont, i.e. a multicellular host and its residential microorganisms, constitutes a biological individual. We propose that resident microorganisms have a general and important role in the individuality of the host organism, not the holobiont. Drawing upon the Equilibrium Model of Immunity (Eberl in Nat Rev Immunol 16:524–532, 2016), we argue that microorganisms are scaffolds of immune capacities and processes that determine the constituency and persistence of the host organism. A scaffolding perspective accommodates the contingency and heterogeneity of resident microorganisms while accounting for their necessity and unifying contributions to host individuality. In our symbiotic view of life, holobionts may not be organisms or units of selection, but macroorganisms cannot persist nor function as individuals without their scaffolding microorganisms.     

Biological individuality: the case of biofilms

This paper examines David Hull’s and Peter Godfrey-Smith’s accounts of biological individuality using the case of biofilms. Biofilms fail standard criteria for individuality, such as having reproductive bottlenecks and forming parent-offspring lineages. Nevertheless, biofilms are good candidates for individuals. The nature of biofilms shows that Godfrey-Smith’s account of individuality, with its reliance on reproduction, is too restrictive. Hull’s interactor notion of individuality better captures biofilms, and we argue that it offers a better account of biological individuality. However, Hull’s notion of interactor needs more precision. We suggest some ways to make Hull’s notion of interactor and his account of individuality more precise. Generally, we maintain that biofilms are a good test case for theories of individuality, and a careful examination of biofilms furthers our understanding of biological individuality.     

The seaweed holobiont: from microecology to biotechnological applications

In the ocean, seaweed and microorganisms have coexisted since the earliest stages of evolution and formed an inextricable relationship. Recently, seaweed has attracted extensive attention worldwide for ecological and industrial purposes, but the function of its closely related microbes is often ignored. Microbes play an indispensable role in different stages of seaweed growth, development and maturity. A very diverse group of seaweed-associated microbes have important functions and are dynamically reconstructed as the marine environment fluctuates, forming an inseparable ‘holobiont’ with their host. To further understand the function and significance of holobionts, this review first reports on recent advances in revealing seaweed-associated microbe spatial and temporal distribution. Then, this review discusses the microbe and seaweed interactions and their ecological significance, and summarizes the current applications of the seaweed–microbe relationship in various environmental and biological technologies. Sustainable industries based on seaweed holobionts could become an integral part of the future bioeconomy because they can provide more resource-efficient food, high-value chemicals and medical materials. Moreover, holobionts may provide a new approach to marine environment restoration.     

Systems biology of eukaryotic superorganisms and the holobiont concept

The founders of modern biology (Jean Lamarck, Charles Darwin, August Weismann etc.) were organismic life scientists who attempted to understand the morphology and evolution of living beings as a whole (i.e., the phenotype). However, with the emergence of the study of animal and plant physiology in the nineteenth century, this “holistic view” of the living world changed and was ultimately replaced by a reductionistic perspective. Here, I summarize the history of systems biology, i.e., the modern approach to understand living beings as integrative organisms, from genotype to phenotype. It is documented that the physiologists Claude Bernard and Julius Sachs, who studied humans and plants, respectively, were early pioneers of this discipline, which was formally founded 50 years ago. In 1968, two influential monographs, authored by Ludwig von Bertalanffy and Mihajlo D. Mesarovi?, were published, wherein a “systems theory of biology” was outlined. Definitions of systems biology are presented with reference to metabolic or cell signaling networks, analyzed via genomics, proteomics, and other methods, combined with computer simulations/mathematical modeling. Then, key insights of this discipline with respect to epiphytic microbes (Methylobacterium sp.) and simple bacteria (Mycoplasma sp.) are described. The principles of homeostasis, molecular systems energetics, gnotobiology, and holobionts (i.e., complexities of host–microbiota interactions) are outlined, and the significance of systems biology for evolutionary theories is addressed. Based on the microbe—Homo sapiens—symbiosis, it is concluded that human biology and health should be interpreted in light of a view of the biomedical sciences that is based on the holobiont concept.     

Cell individuality: the bistability of competence development

Heterogeneous development of competence among cells of the bacterium Bacillus subtilis provides an appealing model of cell individuality, an area that is currently attracting considerable research interest. Under appropriate conditions, only a fraction of cells in an isogenic culture become competent for transformation. Two experimental studies have now pinpointed the same auto-stimulatory feedback loop of gene expression as the principal requirement for the establishment of this 'bistable' response.     

Microbiome-mediated signal transduction within the plant holobiont

Microorganisms colonizing the plant rhizosphere and phyllosphere play crucial roles in plant growth and health. Recent studies provide new insights into long-distance communication from plant roots to shoots in association with their commensal microbiome. In brief, these recent advances suggest that specific plant-associated microbial taxa can contribute to systemic plant responses associated with the enhancement of plant health and performance in face of a variety of biotic and abiotic stresses. However, most of the mechanisms associated with microbiome-mediated signal transduction in plants remain poorly understood. In this review, we provide an overview of long-distance signaling mechanisms within plants mediated by the commensal plant-associated microbiomes. We advocate the view of plants and microbes as a holobiont and explore key molecules and mechanisms associated with plant–microbe interactions and changes in plant physiology activated by signal transduction.     

Bacterial assemblages differ between compartments within the coral holobiont

It is widely accepted that corals are associated with a diverse and host species-specific microbiota, but how they are organized within their hosts remains poorly understood. Previous sampling techniques (blasted coral tissues, coral swabs and milked mucus) may preferentially sample from different compartments such as mucus, tissue and skeleton, or amalgamate them, making comparisons and generalizations between studies difficult. This study characterized bacterial communities of corals with minimal mechanical disruption and contamination from water, air and sediments from three compartments: surface mucus layer (SML), coral tissue and coral skeleton. A novel apparatus (the ‘snot sucker’) was used to separate the SML from tissues and skeleton, and these three compartments were compared to swab samples and milked mucus along with adjacent environmental samples (water column and sediments). Bacterial 16S rRNA gene diversity was significantly different between the various coral compartments and environmental samples (PERMANOVA, F = 6.9, df = 8, P = 0.001), the only exceptions being the complete crushed coral samples and the coral skeleton, which were similar, because the skeleton represents a proportionally large volume and supports a relatively rich microflora. Milked mucus differed significantly from the SML collected with the ‘snot sucker’ and was contaminated with zooxanthellae, suggesting that it may originate at least partially from the gastrovascular cavity rather than the tissue surface. A common method of sampling the SML, surface swabs, produced a bacterial community profile distinct from the SML sampled using our novel apparatus and also showed contamination from coral tissues. Our results indicate that microbial communities are spatially structured within the coral holobiont, and methods used to describe these need to be standardized to allow comparisons between studies.     

More than words: the chemistry behind the interactions in the plant holobiont

Plants and microbes have evolved sophisticated ways to communicate and coexist. The simplest interactions that occur in plant-associated habitats, i.e., those involved in disease detection, depend on the production of microbial pathogenic and virulence factors and the host's evolved immunological response. In contrast, microbes can also be beneficial for their host plants in a number of ways, including fighting pathogens and promoting plant growth. In order to clarify the mechanisms directly involved in these various plant–microbe interactions, we must still deepen our understanding of how these interkingdom communication systems, which are constantly modulated by resident microbial activity, are established and, most importantly, how their effects can span physically separated plant compartments. Efforts in this direction have revealed a complex and interconnected network of molecules and associated metabolic pathways that modulate plant–microbe and microbe–microbe communication pathways to regulate diverse ecological responses. Once sufficiently understood, these pathways will be biotechnologically exploitable, for example, in the use of beneficial microbes in sustainable agriculture. The aim of this review is to present the latest findings on the dazzlingly diverse arsenal of molecules that efficiently mediate specific microbe–microbe and microbe–plant communication pathways during plant development and on different plant organs.     

Stable isotope probing of carbon flow in the plant holobiont

Stable isotope probing (SIP) approach in plant rhizosphere to analyse structure, diversity and function of active microorganisms through carbon utilisation.

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The dialectics of socialization: A tentative formulation

Conclusion A cognitive anthropological approach helps us to understand that children's conceptions are antithetical to adult conceptions. Furthermore, socialization is a dialectical process involving an interplay of these antithetical child conceptions and adult conceptions. As indicated in the field observations, change in the child is internal but the transition from one stage of growth to another occurs only through interaction with the environment. One sees elements of adult conceptions created in the child but they are and remain child conceptions until such time as the Leap has occurred. Babs' teacher, for example, misunderstood this antithetical quality in Babs and assumed her mature behavior indicated she was really mature, really an adult. Qualitatively and quantitatively Babs was still a child and had to initiate action on her own part to prove that. She exhibited behavior that was misconstrued as adult-like, but because she was still a child, her conceptions of herself, her environment and correlatively, of her behavior remained child-like.Carol was obviously quite resourceful and adept at moving in and out of various behavioral patterns appropriate to social situations in which she found herself. This was necessary for survival, particularly when she was forced into situations where prejudicial people controlled her life and her future. The antithetical qualities of her conceptual framework and that of her teacher are overshadowed by the real historical circumstances of race relations in this society. But those antithetical conceptual qualities are still clearly evident. Adult conceptions from the outside intrude on Carol's life and her thinking. And, elements of adult conceptions are being created within her. Yet these autonomous creations will remain child conceptions as long as she remains a child. She responds to her environment, but she responds as a child, subjectified/objectified. She is still qualitatively and quantitatively a childClearly much of what children learn from the environment — from school — is harmful to their autonomy. Through current socialization processes, the dialectics of learning remain incomplete. The interaction whereby children's categories antithetical to adult categories are transformed into a new synthesis of adult categories is missing. Instead, the adult conceptions created in and by the children merely replicate the adult categories of their socializers. Therefore, the current socialization process is a reactionary one. Children are increasingly objectified as their adult categories are less and less new categories, but merely replications of already formalized adult categories. Because the dialectical process of socialization is left incomplete, incomplete adults reach physical maturity. Such people are incapable of governing their own lives, of living out the complexities and inconsistencies of adulthood.Reformists are correct in calling for change in educational methods but not with the methods they suggest. Children should be educated for democracy, but the methods utilized should not result in chaos and disorder because they lack discipline.In fact, although ideologically at odds with each other, methodologically conventional and emancipated teachers differ only in locus of control. Conventional teachers see socialization as a unidirectional process in which they provide the stimulus and the students provide the response. Emancipated teachers see socialization as a dialectical process and deploy that process to educate children for greater autonomy, social and self-understanding. But, in rejecting conventional modes of thought, unconventional teachers do not necessarily reject sensible pedagogical methods. The processes and methods of education are more complex than a simple liberal (soft)/conservative (strict) theoretical dichotomy of education would suggest. Children can still be respected even as their teachers realize their conceptual categories are incomplete and inferior. Relativists who insist, for example, that all speech patterns, because they exhibit internal consistency and structural regularity are inherently equal, fail to recognize or to uncover the true source of social inequality. Relativistic revelations only mystify that inequality and contribute nothing to social liberation.Education for liberation is a slow, arduous task and will not occur by using short-cuts, or pop-psych approaches. It will come from strict adherence to exacting and demanding methods. It will be facilitated through a recognition of the dialectical nature of the socialization process and a cognitive anthropological investigation into the nature of conceptual categories of children. And it will have to be part of a general transformation of this society, while, at the same time, remaining an index of the succes of any such transformation. This means, among other things, that children must be taught to govern their own lives and to govern others. It does not mean, of course, that every person would govern; only that every person should understand the mechanics of governing — that every person, as Gramsci held, could govern.Maribeth Durst is Assistant Professor of Sociology, at St. John's University, Staten Island, New York.

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Nose thyself: individuality in the human olfactory genome

A recent study using cell-based assays together with an olfactory psychophysical survey in humans has established a link between a genetic polymorphism in an odorant receptor and variability in perception of the smell of the steroid androstenone.