Science is now studying biodiversity on a massive scale. These studies are occurring not just at the scale of larger plants and animals, but also at the scale of minute entities such as bacteria and viruses. This expansion has led to the development of a specific sub-field of “microbial diversity”. In this paper, I investigate how microbial diversity faces two of the classical issues encountered by the concept of “ biodiversity ”: the issues of defining the (...) units of biodiversity and of choosing a mathematical measure of diversity. I also show that the extension of the scope of biodiversity to microbial entities such as viruses and many other not-clearly-alive entities raises yet another foundational issue: that of defining a “lower-limit” of biodiversity. (shrink)

Despite their diversity and ecological importance, many areas of the SAR—Stramenopila, Alveolata, and Rhizaria—clade are poorly understood as the majority of SAR species lack molecular data and only 5% of species are from well-sampled families. Here, we review and summarize the state of knowledge about the three major clades of SAR, describing the diversity within each clade and identifying synapomorphies when possible. We also assess the “dark area” of SAR: the morphologically described species that are missing molecular data. (...) The majority of molecular data for SAR lineages are characterized from marine samples and vertebrate hosts, highlighting the need for additional research effort in areas such as freshwater and terrestrial habitats and “non-vertebrate” hosts. We also describe the paucity of data on the biogeography of SAR species, and point to opportunities to illuminate diversity in this major eukaryotic clade. See also the video abstract here: https://youtu.be/_VUXqaX19Rw. Despite their diversity, abundance, and importance, fewer than 10% of the species within the SAR—Stramenopila, Alveolata, and Rhizaria—clade have been assessed using molecular tools. Only a small percentage of the molecular records contain information on ecology or have associate location data, indicating a tremendous dark area. (shrink)

Despite their diversity and ecological importance, many areas of the SAR—Stramenopila, Alveolata, and Rhizaria—clade are poorly understood as the majority (90%) of SAR species lack molecular data and only 5% of species are from well‐sampled families. Here, we review and summarize the state of knowledge about the three major clades of SAR, describing the diversity within each clade and identifying synapomorphies when possible. We also assess the “dark area” of SAR: the morphologically described species that are missing molecular (...) data. The majority of molecular data for SAR lineages are characterized from marine samples and vertebrate hosts, highlighting the need for additional research effort in areas such as freshwater and terrestrial habitats and “non‐vertebrate” hosts. We also describe the paucity of data on the biogeography of SAR species, and point to opportunities to illuminate diversity in this major eukaryotic clade. (shrink)

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or (...) features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)

The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth’s biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called “omic” techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These ‘omic methods have been used to describe (...) the taxonomic structure of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the ‘omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel ‘omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment. (shrink)

: Despite its amazing morphological diversity, life as we know it on Earth today is remarkably similar in its basic molecular architecture and biochemistry. The assumption that all life on Earth today shares these molecular and biochemical features is part of the paradigm of modern biology. This paper examines the possibility that this assumption is false, more specifically, that the contemporary Earth contains as yet unrecognized alternative forms of microbial life. The possibility that more than one form of (...) life arose on Earth is consistent with our current understanding of conditions on the early Earth and the biochemical and molecular possibilities for life. Arguments that microbial descendents of an alternative origin of life could not co-exist with familiar life are belied by what we know of the complexity and diversity of microbial communities. Furthermore, the tools that are currently used to explore the microbial world – microscopy (with the aid of techniques such as DAPI staining and fluorescence in situ hybridization), cultivation and PCR amplification of rRNA genes – could not detect such organisms if they existed. Thus, the fact that we have not discovered any alternative life forms cannot be taken as evidence that they do not exist. (shrink)

Microbial diversity has become a leitmotiv of contemporary microbiology, as epitomized in the concept of the microbiome, with significant consequences for the classification of microbes. In this paper, I contrast microbiology’s current diversity ideal with its influential predecessor in the twentieth century, that of purity, as epitomized in Robert Koch’s bacteriological culture methods. Purity and diversity, the two polar opposites with regard to making sense of the microbial world, have been operationalized in microbiological practice by (...) tools such as the “clean” Petri dish versus the “dirty” Winogradsky column, the latter a container that mimics, in the laboratory, the natural environment that teems with diverse microbial life. By tracing the impact of the practices and concepts of purity and diversity on microbial classification through a history of techniques, tools, and manuals, I show the shifts in these concepts over the last century. Juxtaposing the dominant purity ideal with the more restricted, but continuously articulated, diversity ideal in microbial ecology not only provides a fresh perspective on microbial classification that goes beyond its intellectual history, but also contextualizes the present focus on diversity. By covering the period of a century, this paper outlines a revised longue durée historiography that takes its inspiration from artifacts, such as Petri dish and the Winogradsky column, and thereby simple, but influential technologies that often remain invisible. This enables the problem of historical continuity in modern science to be addressed and the accelerationist narratives of its development to be countered. (shrink)

Microbial diversity has become a leitmotiv of contemporary microbiology, as epitomized in the concept of the microbiome, with significant consequences for the classification of microbes. In this paper, I contrast microbiology’s current diversity ideal with its influential predecessor in the twentieth century, that of purity, as epitomized in Robert Koch’s bacteriological culture methods. Purity and diversity, the two polar opposites with regard to making sense of the microbial world, have been operationalized in microbiological practice by (...) tools such as the “clean” Petri dish versus the “dirty” Winogradsky column, the latter a container that mimics, in the laboratory, the natural environment that teems with diverse microbial life. By tracing the impact of the practices and concepts of purity and diversity on microbial classification through a history of techniques, tools, and manuals, I show the shifts in these concepts over the last century. Juxtaposing the dominant purity ideal with the more restricted, but continuously articulated, diversity ideal in microbial ecology not only provides a fresh perspective on microbial classification that goes beyond its intellectual history, but also contextualizes the present focus on diversity. By covering the period of a century, this paper outlines a revised longue durée historiography that takes its inspiration from artifacts, such as Petri dish and the Winogradsky column, and thereby simple, but influential technologies that often remain invisible. This enables the problem of historical continuity in modern science to be addressed and the accelerationist narratives of its development to be countered. (shrink)

In this review, we provide an overview of the dynamic changes within the microbiota and its metabolites that are implicated in establishing and maintaining gastrointestinal homeostasis during various stages of microbial colonization. The gradual conversion of the gut microbiota toward a mutualistic microbial community involves replacement of pioneer gut colonizers with bacterial taxa that are characteristic for the adult gut. An important microbial signature of homeostasis in the adult gut is the prevalence and activity of a diverse (...) spectrum of bacterial species that produce beneficial metabolites through metabolic interactions between microbial groups. Deciphering these microbial signatures and their metabolites that govern short and long‐term equilibrium, as well as imbalances in host‐microbial relationships, may provide novel diagnostic tools and/or therapeutic targets for specific disorders associated with intestinal dysbiosis and loss of homeostasis. (shrink)

While examples of bacteria benefiting eukaryotes are increasingly documented, studies examining effects of eukaryote hosts on microbial fitness are rare. Beneficial bacteria are often called “mutualistic” even if mutual reciprocity of benefits has not been demonstrated and despite the plausibility of other explanations for these microbes' beneficial effects on host fitness. Furthermore, beneficial bacteria often occur in diverse communities, making mutualism both empirically and conceptually difficult to demonstrate. We suggest reserving the terms “mutualism” and “parasitism” for pairwise interactions where (...) the relationship is largely independent of other species and can be verified by measuring the fitness effect experienced by both partners. In hosts with diverse microbial communities, we propose re‐formulating some of the essential questions of symbiosis research – e.g. concerning specificity, transmission mode, and common evolutionary fates – as questions of community ecology and ecosystem function, allowing important biological interactions to be investigated without making assumptions about reciprocity. Understanding the fitness of host‐associated bacteria is a crucial component of investigations into the role of microbes in eukaryote evolution. (shrink)

Bacteria have developed an impressive ability to survive and propagate in highly diverse and changing environments by evolving phenotypic heterogeneity. Phenotypic heterogeneity ensures that a subpopulation is well prepared for environmental changes. The expression bet hedging is commonly (but often incorrectly) used by molecular biologists to describe any observed phenotypic heterogeneity. In evolutionary biology, however, bet hedging denotes a risk‐spreading strategy displayed by isogenic populations that evolved in unpredictably changing environments. Opposed to other survival strategies, bet hedging evolves because the (...) selection environment changes and favours different phenotypes at different times. Consequently, in bet hedging populations all phenotypes perform differently well at any time, depending on the selection pressures present. Moreover, bet hedging is the only strategy in which temporal variance of offspring numbers per individual is minimized. Our paper aims to provide a guide for the correct use of the term bet hedging in molecular biology. (shrink)

Current work in experimental biology revolves around a handful of animal species. Studying only a few organisms limits science to the answers that those organisms can provide. Nature has given us an overwhelming diversity of animals to study, and recent technological advances have greatly accelerated the ability to generate genetic and genomic tools to develop model organisms for research on host–microbe interactions. With the help of such models the authors therefore hope to construct a more complete picture of the (...) mechanisms that underlie crucial interactions in a given metaorganism (entity consisting of a eukaryotic host with all its associated microbial partners). As reviewed here, new knowledge of the diversity of host–microbe interactions found across the animal kingdom will provide new insights into how animals develop, evolve, and succumb to the disease. (shrink)

Latin American countries have an extensive biological diversity and a tropical or subtropical climate. This condition has advantages for development and for the implementation of biotechnological solutions for environmental problems. Environmental biotechnology could be used to enhance biodegradation, waste recovery, and also for the development of biotechnology-based products to diagnose and reduce environmental impacts such as biosensors, biopesticides, biofertilizers and biofuels. To generate new environmental biotechnological products, Latin American countries must not only overcome the known limitations associated with investment (...) in science and technology and in human resource training, but also develop their own vision of using environmental biotechnology, adapted to the economic, and environmental context. Biotechnology used wisely as a tool for promoting sustainable development in Latin American countries may also contribute to the solution of problems that represent potential risks to society and the environment in general. This document discusses the context of the research and innovation in Latin American countries around environmental biotechnology and also reviews perspectives for the improvement of these developments. (shrink)

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models (...) and concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease. (shrink)

Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on (...) both the molecular and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are genetically distinct and (ii) morphologically distinct individuals that are genetically the same. We argue that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis. -/- . (shrink)

Biological diversity - or ‘biodiversity’ - is the degree of variation of life within an ecosystem. It is a relatively new topic of study but has grown enormously in recent years. Because of its interdisciplinary nature the very concept of biodiversity is the subject of debate amongst philosophers, biologists, geographers and environmentalists. The Routledge Handbook of Philosophy of Biodiversity is an outstanding reference source to the key topics and debates in this exciting subject. Comprising twenty-three chapters by a team (...) of international contributors the _Handbook_ is divided into six parts: Historical and sociological contexts, focusing on the emergence of the term and early attempts to measure biodiversity _What is biodiversity? _How should biodiversity be defined? How can biodiversity include entities at the edge of its boundaries, including microbial diversity and genetically engineered organisms? _Why protect biodiversity? _What can traditional environmental ethics_ _contribute to biodiversity?_ _Topics covered include anthropocentrism, intrinsic value, and ethical controversies surrounding the economics of biodiversity _Measurement and methodology: _including decision-theory and conservation, the use of indicators for biodiversity, and the changing use of genetics in biodiversity conservation _Social contexts and global justice: _including conservation and community conflicts and biodiversity and cultural values _Biodiversity and other environmental values_: How does biodiversity relate to other values like ecological restoration or ecological sustainability? Essential reading for students and researchers in philosophy, environmental science and environmental studies, and conservation management, it will also be extremely useful to those studying biodiversity in subjects such as biology and geography. (shrink)

Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new ontology. By (...) reducing the dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ‘‘hardening’’ into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ‘‘core microbiome,’’ typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of per- sonalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM. (shrink)

Research on the human microbiome has generated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and enterotype—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statistical methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing the dimensionality (...) of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ‘‘hardening’’ into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ‘‘core microbiome,’’ typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of personalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM. (shrink)

Metagenomics is a culture‐ and PCR‐independent approach that is now widely exploited for directly studying microbial evolution, microbial ecology, and developing biotechnologies. Observations and discoveries are critically dependent on DNA extraction methods, sequencing technologies, and bioinformatics tools. The potential pitfalls need to be understood and, to some degree, mastered if the resulting data are to survive scrutiny. In particular, methodological variations appear to affect results from different ecosystems differently, thus increasing the risk of biological and ecological misinterpretation. Part (...) of the difficulty is derived from the lack of knowledge concerning the true microbial diversity and because no approach can guarantee accessing microorganisms in the same proportion in which they exist in the environment. However, the variation between different approaches (e.g. DNA extraction techniques, sequence annotation systems) can be used to evaluate whether observations are meaningful. These methodological variations can be integrated into the error analysis before comparing microbial communities. (shrink)

Metagenomics is a culture‐ and PCR‐independent approach that is now widely exploited for directly studying microbial evolution, microbial ecology, and developing biotechnologies. Observations and discoveries are critically dependent on DNA extraction methods, sequencing technologies, and bioinformatics tools. The potential pitfalls need to be understood and, to some degree, mastered if the resulting data are to survive scrutiny. In particular, methodological variations appear to affect results from different ecosystems differently, thus increasing the risk of biological and ecological misinterpretation. Part (...) of the difficulty is derived from the lack of knowledge concerning the true microbial diversity and because no approach can guarantee accessing microorganisms in the same proportion in which they exist in the environment. However, the variation between different approaches (e.g. DNA extraction techniques, sequence annotation systems) can be used to evaluate whether observations are meaningful. These methodological variations can be integrated into the error analysis before comparing microbial communities. (shrink)

Diverse living systems possess the capacity for regeneration; that is, they can under some circumstances repair, re-produce, and maintain themselves in the face of disturbance or damage. Think of systems as diverse as forests, microbial biofilms, corals, salamanders, hydra, and human skin cells. This capacity is fundamental to life—without it, many biological systems would be too fragile to cope with stress and would frequently collapse—but because it is multiply realized in wildly different living systems at many scales, finding a (...) common understanding may seem futile, and in fact research has proceeded along independent lines. For example, the sciences of organismal regeneration and ecological regeneration appear to have little more than a nominal relationship. Progress towards unification can be made, we think, by turning to evolutionary theory, specifically by synthesizing recent discussions of the evolution of individuals versus collectives with older literature about replicators versus interactors. This allows us to provide a partial answer in response to MacCord and Maienschein’s call for “basic units and mechanisms” of regeneration, relevant when that process is “adaptive.” We argue that the basics of adaptive regeneration can be understood and generalized through a modification of David Hull’s replicator-interactor framework. (shrink)

Microbial genome sequencing has entered a new phase, where DNA sequence information is gathered from entire microbial communities (metagenomics or environmental genomics) rather than from individual microorganisms. By providing access to the genetic material of vast numbers of organisms, most of which are organisms that have never been isolated or cultivated, a new level of insight is being gained into the diversity and extent of the microbial processes that are presently occuring in environmental communities. By extending (...) metagenomic‐based approaches to the study of very complex and methodologically recalcitrant soil environments, a recent study has found that ammonia‐oxidizing archaea are more abundant in many soils than bacteria.1 These findings not only highlight the undoubtedly critical yet unknown roles that archaea play in global nutrient cycles but illustrate the importance of genomic studies for informing us about the functional capacity of life on Earth. BioEssays 29: 11–14, 2007. © 2006 Wiley Periodicals, Inc. (shrink)

Diverse micro‐organisms populate a global deep biosphere hosted by rocks and sediments beneath land and sea, containing more biomass than any other biome except forests. This paper reviews an emerging palaeobiological archive of these dark habitats: microfossils preserved in ancient pores and fractures in the crust. This archive, seemingly dominated by mineralized filaments (although rods and coccoids are also reported), is presently far too sparsely sampled and poorly understood to reveal trends in the abundance, distribution, or diversity of deep (...) life through time. New research is called for to establish the nature and extent of the fossil record of Earth's deep biosphere by combining systematic exploration, rigorous microanalysis, and experimental studies of both microbial preservation and the formation of abiotic pseudofossils within the crust. It is concluded that the fossil record of Earth's largest microbial habitat may still have much to tell us about the history of life, the evolution of biogeochemical cycles, and the search for life on Mars. (shrink)

How significant is social evolution theory for the maintenance of virulence in natural populations? We assume that secreted, distantly acting virulence factors are highly likely to be cooperative public goods. Using this assumption, we discuss and critically assess the potential importance of social interactions for understanding the evolution, diversity and distribution of virulence in the Bacillus cereus group, a novel study system for microbial social biology. We conclude that dynamic equilibria in Cry toxin production, as well as strong (...) spatial structure and population bottlenecks in hosts are the main ecological factors maintaining the cooperative secretion of virulence factors and argue that collective action has contributed to the evolution of narrow host range. Non‐linearities in the benefits associated with public goods, as well as the lack of private secretion systems in the Firmicutes may also explain the prevalence and importance of distantly acting virulence factors in B. cereus and its relatives. (shrink)

Enzyme directed genetic mechanisms causing random DNA sequence alterations are ubiquitous in both eukaryotes and prokaryotes. A number of molecular geneticist have invoked adaptation through natural selection to account for this fact, however, alternative explanations have also flourished. The population geneticist G.C. Williams has dismissed the possibility of selection for mutator activity on a priori grounds. In this paper, I attempt a refutation of Williams' argument. In addition, I discuss some conceptual problems related to recent claims made by microbiologists on (...) the adaptiveness of molecular variety generators in the evolution of prokaryotes. A distinction is proposed between selection for mutations caused by a mutator activity and selection for the mutator activity proper. The latter requires a concept of fitness different from the one commonly used in microbiology. (shrink)

Holobionts, consisting of a host and diverse microbial symbionts, function as distinct biological entities anatomically, metabolically, immunologically, and developmentally. Symbionts can be transmitted from parent to offspring by a variety of vertical and horizontal methods. Holobionts can be considered levels of selection in evolution because they are well-defined interactors, replicators/reproducers, and manifestors of adaptation. An initial mathematical model is presented to help understand how holobionts evolve. The model offered combines the processes of horizontal symbiont transfer, within-host symbiont proliferation, vertical (...) symbiont transmission, and holobiont selection. The model offers equations for the population dynamics and evolution of holobionts whose hologenomes differ in gene copy number, not in allelic or loci identity. The model may readily be extended to include variation among holobionts in the gene identities of both symbionts and host. (shrink)

The last decade has seen an explosion of research on the gut microbiota—the trillions of microorganisms that colonize the human gut. It is now clear that interindividual diversity in microbiota composition plays an important role in determining susceptibility to a wide variety of diseases. However, identifying the precise changes in microbiota composition that play causal roles has remained a largely unrealized goal. Here, we propose that functional classifications of microbes based on their interactions with and effects on the host—particularly (...) the host immune system—will illuminate the role of the microbiota in shaping human physiology. We outline the benefits of “functional” classification compared to phylogenetic classifications, and review current efforts at functional classification of the microbiota. Finally, we outline a theoretical framework for classifying host-microbiota interactions. Future advances enabling broader functional classifications of the microbiota promise to revolutionize our understanding of the role of gut microbes in health and disease. Functional classifications of the human microbiota reveal previously hidden patterns and will be key to cracking the microbiota composition code. This figure shows a theoretical comparison between phylogenetic classification and functional classification of a host-associated microbial community. (shrink)

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, (...) between species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory. (shrink)

In multicellular organisms, cells are frequently programmed to die. This makes good sense: cells that fail to, or are no longer playing important roles are eliminated. From the cell’s perspective, this also makes sense, since somatic cells in multicellular organisms require the cooperation of clonal relatives. In unicellular organisms, however, programmed cell death poses a difficult and unresolved evolutionary problem. The empirical evidence for PCD in diverse microbial taxa has spurred debates about what precisely PCD means in the case (...) of unicellular organisms. In this article, we survey the concepts of PCD in the literature and the selective pressures associated with its evolution. We show that definitions of PCD have been almost entirely mechanistic and fail to separate questions concerning what PCD fundamentally is from questions about the kinds of mechanisms that realize PCD. We conclude that an evolutionary definition is best able to distinguish PCD from closely related phenomena. Specifically, we define “true” PCD as an adaptation for death triggered by abiotic or biotic environmental stresses. True PCD is thus not only an evolutionary product but must also have been a target of selection. Apparent PCD resulting from pleiotropy, genetic drift, or trade-offs is not true PCD. We call this “ersatz PCD.”. (shrink)

The geosciences include a wide spectrum of disciplines ranging from paleontology to climate science, and involve studies of a vast range of spatial and temporal scales, from the deep-time history of microbial life to the future of a system no less immense and complex than the entire Earth. Modeling is thus a central and indispensable tool across the geosciences. Here, we review both the history and current state of model-based inquiry in the geosciences. Research in these fields makes use (...) of a wide variety of models, such as conceptual, physical, and numerical models, and more specifically cellular automata, artificial neural networks, agent-based models, coupled models, and hierarchical models. We note the increasing demands to incorporate biological and social systems into geoscience modeling, challenging the traditional boundaries of these fields. Understanding and articulating the many different sources of scientific uncertainty – and finding tools and methods to address them – has been at the forefront of most research in geoscience modeling. We discuss not only structuralmodel uncertainties, parameter uncertainties, and solution uncertainties, but also the diverse sources of uncertainty arising from the complex nature of geoscience systems themselves. Without an examination of the geosciences, our philosophies of science and our understanding of the nature of model-based science are incomplete. (shrink)

Rhodopsins are one of the most studied photoreceptor protein families, and ion‐translocating rhodopsins, both pumps and channels, have recently attracted broad attention because of the development of optogenetics. Recently, a new functional class of ion‐pumping rhodopsins, an outward Na+ pump, was discovered, and following structural and functional studies enable us to compare three functionally different ion‐pumping rhodopsins: outward proton pump, inward Cl− pump, and outward Na+ pump. Here, we review the current knowledge on structure‐function relationships in these three light‐driven pumps, (...) mainly focusing on Na+ pumps. A structural and functional comparison reveals both unique and conserved features of these ion pumps, and enhances our understanding about how the structurally similar microbial rhodopsins acquired such diverse functions. We also discuss some unresolved questions and future perspectives in research of ion‐pumping rhodopsins, including optogenetics application and engineering of novel rhodopsins. (shrink)

Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit (...) variants during stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general. (shrink)

Microbiologists are transitioning from the study and characterization of individual strains or species to the profiling of whole microbiomes and microbial ecology. Equipped with high-throughput methods for studying the taxonomic and functional characteristics of diverse samples, they are just beginning to encounter the conceptual, theoretical, and experimental problems of comparing taxonomy to function, and extracting useful measures from such comparisons. Although still unresolved, these problems are well studied in macro-ecology and are reiterated here as an historical precautionary for (...) class='Hi'>microbial ecologists. Beyond expected and unresolved terminological vagueness, we argue that assessments and comparisons of taxonomic and functional profiles in micro-ecology suffer from theoretically unresolvable arbitrariness and ambiguities. We divide these into problems of scale, individuation, and commensurability. We argue that there is no technically/theoretically “correct” scale, individuation, or comparison of taxonomy and function, but there are nonetheless better and worse methodologies for profiling. (shrink)

In this article, we question to what extent origin-food labels, namely Geographical Indications and Slow Food Presidia, may effectively account for cultural biodiversity. Building on Foucault’s discourse theory, we question how the Slow Food movement and GI promoters have developed their own discourse and practice on CB, how these discourses contrast, and how they inform projects. Focusing on the practices to cultivate the microbiological life of three origin labeled cheeses, we have revealed the gap between these institutional discourses and what (...) happens on the ground. We argue that how actors’ relationships in the marketplace unfold, from public authorities to the collectives of producers to consumers, may threaten the effects that these experiences of alternative food productions may have in the defense of biodiversity, causing, for instance, the loss of diversity of the invisible microbial ecosystems of artisan raw milk cheese. However, we conclude that, despite limitations, the mediatized institutional narrative on CB can amplify the political voice of local actors by fostering community and social relationships between the farmers. (shrink)

There is an urgent need for novel protection strategies to sustainably secure crop production under changing climates. Studying microbial effectors, defined as microbe‐derived proteins that alter signalling inside plant cells, has advanced our understanding of plant immunity and microbial plant colonisation strategies. Our understanding of effectors in the establishment and beneficial outcome of plant symbioses is less well known. Combining functional and comparative interaction assays uncovered specific symbiont effector targets in highly interconnected plant signalling networks and revealed the (...) potential of effectors in beneficially modulating plant traits. The diverse functionality of symbiont effectors differs from the paradigmatic immuno‐suppressive function of pathogen effectors. These effectors provide solutions for improving crop resilience against climate stress by their evolution‐driven specification in host protein targeting and modulation. Symbiont effectors represent stringent tools not only to identify genetic targets for crop breeding, but to serve as applicable agents in crop management strategies under changing environments. (shrink)

Culture-independent high-throughput sequencing has provided unprecedented insights into microbial ecology, particularly for Earth’s most ubiquitous and diverse inhabitants – the viruses. A plethora of methods now exist for amplifying the vanishingly small amounts of nucleic acids in natural viral communities in order to sequence them, and sequencing depth is now so great that viral genomes can be detected and assembled even amid large concentrations of non-viral DNA. Complementing these advances in amplification and sequencing is the ability to physically link (...) fluorescently labeled viruses to their host cells via high-throughput flow sorting. Sequencing of such isolated virus–host pairs facilitates cultivation-independent exploration of the natural host range of viruses. Within the next decade, as these technologies become widespread, we can expect to see a systematic expansion of our knowledge of viruses and their hosts. (shrink)

Pluralism is popular among philosophers of biology. This essay argues that negative judgments about universal biology, while understandable, are very premature. Familiar life on Earth represents a single example of life and, most importantly, there are empirical as well as theoretical reasons for suspecting that it may be unrepresentative. Scientifically compelling generalizations about the unity of life must await the discovery of forms of life descended from an alternative origin, the most promising candidate being the discovery of extraterrestrial life. Nonetheless, (...) in the absence of additional examples of life, we are best off exploring the microbial world for promising explanatory concepts, principles, and mechanisms rather than prematurely giving up on universal biology. Unicellular microbes are by far the oldest, metabolically most diverse, and environmentally tolerant form of life on our planet. Yet somewhat ironically, much of our theorizing about life still implicitly privileges complex multicellular eukaryotes, which are now understood to be highly specialized, fragile latecomers to Earth. The problem with pursuing a pluralist approach to understanding life is that it is likely to blind us to the significance of just those entities and causal processes most likely to shed light on the underlying nature of life. (shrink)

Cognitive biases can lead to misinterpretations of human and non-human biology and behavior. The concept of the Umwelt describes phylogenetic contrasts in the sensory realms of different species and has important implications for evolutionary studies of cognition (including biases) and social behavior. It has recently been suggested that the microbiome (the diverse network of microorganisms in a given environment, including those within a host organism such as humans) has an influential role in host behavior and health. In this paper, we (...) discuss the host’s microbiome in relation to cognitive biases and the concept of the Umwelt. Failing to consider the role of host–microbiome (collectively termed a “holobiont”) interactions in a given behavior, may underpin a potentially important cognitive bias – which we refer to as the Holobiont Blindspot. We also suggest that microbially mediated behavioral responses could augment our understanding of the Umwelt. For example, the potential role of the microbiome in perception and action could be an important component of the system that gives rise to the Umwelt. We also discuss whether microbial symbionts could be considered in System 1 thinking – that is, decisions driven by perception, intuition and associative memory. Recognizing Holobiont Blindspots and considering the microbiome as a key factor in the Umwelt and System 1 thinking has the potential to advance studies of cognition. Furthermore, investigating Holobiont Blindspots could have important implications for our understanding of social behaviors and mental health. Indeed, the way we think about how we think may need to be revisited. (shrink)

Resistance to the drugs used in the treatment of many infectious diseases is increasing, while microbial infections are being found to be responsible for more life‐threatening diseases than previously thought. Despite a large investment in the invention and application of high‐throughput screening techniques involving miniaturization and automation, and a diverse array of strategies for designing and constructing various chemical libraries, relatively few new drugs have resulted. Natural products, however, have been a major source of drugs for centuries. Since some (...) of them are produced by organisms as a result of selection in favour of improved defense against competing deleterious microorganisms, in principle they would be less likely to incur resistance. Furthermore, the production of those defensive secondary metabolites is inducible because their original function is a response to environmental challenges. Moreover, symbioses, co‐habitation associations between two or more different species of organisms, are universal in nature, and the production of secondary metabolites by symbiotic microbes may be an important adaptation allowing microbes to affect their hosts. Therefore, co‐culture strategies, using combinations of plant cell–pathogenic microbes, plant cell–endophytes (or symbionts), and symbiont–pathogenic microbes, based on the principles of chemical defense and the known mechanisms of organism interactions, may be an efficient general approach in the search for new anti‐microbial drugs. BioEssays 26:808–813, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

The de‐repression of transposable elements (TEs) in mammalian genomes is thought to contribute to genome instability, inflammation, and ageing, yet is viewed as a cell‐autonomous event. In contrast to mammalian cells, prokaryotes constantly exchange genetic material through TEs, crossing both cell and species barriers, contributing to rapid microbial evolution and diversity in complex communities such as the mammalian gut. Here, it is proposed that TEs released from prokaryotes in the microbiome or from pathogenic infections regularly cross the kingdom (...) barrier to the somatic cells of their eukaryotic hosts. It is proposed this horizontal transfer of TEs from microbe to host is a stochastic, ongoing catalyst of genome destabilization, resulting in structural and epigenetic variations, and activation of well‐evolved host defense mechanisms contributing to inflammation, senescence, and biological ageing. It is proposed that innate immunity pathways defend against the horizontal acquisition of microbial TEs, and that activation of this pathway during horizontal transposon transfer promotes chronic inflammation during ageing. Finally, it is suggested that horizontal acquisition of prokaryotic TEs into mammalian genomes has been masked and subsequently under‐reported due to flaws in current sequencing pipelines, and new strategies to uncover these events are proposed. (shrink)

The book integrates humans’ biological lives as animals with acculturation and interaction within diverse social worlds. Recent work in evolutionary biology, the social theory of practices, and cognition as embodied and enactive shows how aspects of human life often treated as social or cognitive are integrated “naturecultural” phenomena. Human evolution enables people’s varied biological development in practice-differentiated environments sustained by ongoing niche reconstruction. These naturecultural aspects of human life include language and other expressive repertoires; cultivated bodily skills; differentiated practical and (...) cultural domains and their associated settings and equipmental complexes; critical assessment of lives and practices; and power and resistance. This interdependent, practice-differentiated way of life explains how humans are accountable and responsive to diverse normative concerns. Our moral, social, practical, skillful, epistemic, conceptual, aesthetic, and other normative concerns are evolved, “two-dimensional” transformations of other animals’ one-dimensional biological success or failure in sustaining their lineages. These diverse normative concerns are not already-determinate norms, however. They indicate what is at issue and at stake in the ongoing development of various practices and their mutual interdependence, including how people express and reason about those issues discursively. Social power is thereby also a normative phenomenon, expressing how causal capacities and actions reconfigure the normative significance of other people’s situations. The book primarily addresses the biological significance of people’s situated involvement with one another. It nevertheless also highlights the social-ecological interdependence of people’s practice-differentiated ways of life with many non-human companion species, from microbial symbionts and pathogens to domesticated or commensal plants and animals. (shrink)

The US National Institute of Health’s Human Microbiome Project aims to use genomic techniques to understand the microbial communities that live on the human body. The emergent field of microbiome science brought together diverse disciplinary perspectives and technologies, thus facilitating the negotiation of differing values. Here, we describe how values are conceptualized and negotiated within microbiome research. Analyzing discussions from a series of interdisciplinary workshops conducted with microbiome researchers, we argue that negotiations of epistemic, social, and institutional values were (...) inextricable from the reflective and strategic category work that defined and organized the microbiome as an object of study and a potential future site of biomedical intervention. Negotiating the divergence or tension between emerging scientific and regulatory classifications also activated “values levers” and opened up reflective discussions of how classifications embody values and how these values might differ across domains. These data suggest that scholars at the intersections of science and technology studies, ethics, and policy could leverage such openings to identify and intervene in the ways that ethical/regulatory and scientific/technical practices are coproduced within unfolding research. (shrink)

Recent biological studies have wrought a sea-change in our understanding of our intimate relations with the microbiota dwelling within or upon the human body. Since these microorganisms are imperceptible, we have access to them only indirectly, through data analysis, rather than through experiments or tools that enhance human observation. Merleau-Ponty’s understanding of the human subject and our relations with animals depends upon perception in a dynamic of reversibility. Thus both the scientific method of approach and the extension of subjectivity to (...) microbiota challenge his views. Yet, with Merleau-Ponty’s concepts of intertwining and the anonymous visibility that subtends it, we can redefine the human being as a community in kinship with multiple microbial species, sharing space, metabolic functions, and future.Des études biologiques récentes ont provoqué un bouleversement dans notre compréhension de nos relations intimes avec les microbiotes habitant dans ou à la surface du corps humain. Puisque ces micro-organismes sont imperceptibles, nous n’accédons à eux qu’indirectement, par l’analyses des données, plutôt que par l’expérience ou les outils qui renforcent l’observation humaine. La compréhension merleau-pontienne du sujet humain et de nos relations avec les animaux dépend de la dynamique de la réversibilité. Par conséquent, la méthode de saisie scientifique et l’extension de la subjectivité aux microbiotes interrogent et défient sa conception. Cependant, à partir des concepts d’entrelacement et de visibilité anonyme qui le sous-tend, nous pouvons redéfinir l’être humain comme une communauté d’affinités avec de multiples espèces microbiennes, qui partage un espace, des fonctions métaboliques et même un futur.Studi biologici recenti hanno introdotto una profonda trasformazione nella nostra comprensione dell’intima relazione che intratteniamo con i microbiota che dimorano all’interno o sulla superficie del corpo umano. Poiché questi micro-organismi sono impercettibili, abbiamo accesso ad essi solo indirettamente, attraverso l’analisi di dati, oppure attraverso esperimenti o strumenti che accrescano l’osservazione umana. La comprensione di Merleau-Ponty del soggetto umano e della nostra relazione con gli animali si basa sulla percezione in una dinamica di reversibilità. Una simile prospettiva è messa alla prova se confrontata sia con il metodo dell’approccio scientifico, che con una possibile estensione della soggettività ai microbiota. Allo stesso tempo, attraverso il concetto merleau-pontiano di intreccio, e a partire dall’idea di una visibilità anonima che lo sottende, diviene possibile ridefinire la natura umana come una comunità condivisa dalle diverse specie microbiche, in quanto compartecipano degli stessi spazi, funzioni metaboliche e avvenire. (shrink)

The Hawaiian Drosophila have been a model system for evolutionary, ecological, and ethological studies since the inception of the Hawaiian Drosophila Project in the 1960s. Here we review the past and present research on this incredible lineage and provide a prospectus for future directions on genomics and microbial interactions. While the number of publications on this group has waxed and waned over the years, we assert that recent systematic, biogeographic, and ecological studies have reinvigorated Hawaiian Drosophila as an evolutionary (...) model system. The characteristics that distinguish good model clades from good model organisms (e.g., Drosophila melanogaster) are somewhat different so we first define what constitutes a good evolutionary model. We argue that the Hawaiian Drosophila possess many desired aspects of a good evolutionary model, describe how this group of geographically isolated flies have been used in the past, and propose some exciting avenues for future evolutionary research on this diverse, dynamic clade of Drosophila. (shrink)

Experts identified water quality, manure, good handling practices (including personal hygiene and equipment sanitation), and traceability as critical farm problem areas that, if addressed, are likely to decrease risk associated with microbial contamination of fresh produce from all scales of agriculture. However, the diverse nature of production strategies used by produce farmers presents multiple options for addressing foodborne illness issues while simultaneously creating potential complications. We use a mental models methodology to enhance our understanding of the underlying factors and (...) assumptions of small, medium, and large produce growers that influence their decision-making processes for contamination prevention and control. This empirical evidence demonstrates how challenges and opportunities to food safety are related to the scale of production and marketing strategies. We believe that refining the development of standards and existing extension and outreach food safety programs are important to both consumer protection and supporting agricultural communities. Additionally, this approach will help develop and refine food safety programs that will result in empirically grounded recommendations based on identified grower information needs. (shrink)

For twenty years, _Teaching for Diversity and Social Justice_ has been the definitive sourcebook of theoretical foundations, pedagogical and design frameworks, and curricular models for social justice teaching practice. Thoroughly revised and updated, this third edition continues in the tradition of its predecessors to cover the most relevant issues and controversies in social justice education in a practical, hands-on format. Filled with ready-to-apply activities and discussion questions, this book provides teachers and facilitators with an accessible pedagogical approach to issues (...) of oppression in classrooms. The revised edition also focuses on providing students the tools needed to apply their learning about these issues. Features new to this edition include: A new bridging chapter focusing on the core concepts that need to be included in _all_ SJE practice and illustrating ways of "getting started" teaching foundational core concepts and processes. A new chapter addressing the possibilities for adapting social justice education to online and blended courses. Expanded overview sections that highlight the historical contexts and legacies of oppression, opportunities for action and change, and the intersections among forms of oppression. Added coverage of key topics for teaching social justice issues, such as establishing a positive classroom climate, institutional and social manifestations of oppression, the global implications of contemporary SJE work, and action steps for addressing injustice. New and revised material for each of the core chapters in the book complemented by fully-developed online teaching designs, including over 150 downloadables, activities, and handouts on the book’s Companion Website. A classic for teachers across disciplines, _Teaching for Diversity and Social Justice_ presents a thoughtful, well-constructed, and inclusive foundation for engaging students in the complex and often daunting problems of discrimination and inequality in American society. (shrink)

Frequency effects are pervasive in studies of language, with higher frequency words being recognized faster than lower frequency words. However, the exact nature of frequency effects has recently been questioned, with some studies finding that contextual information provides a better fit to lexical decision and naming data than word frequency ( Adelman et al., 2006 ). Recent work has cemented the importance of these results by demonstrating that a measure of the semantic diversity of the contexts that a word (...) occurs in provides a powerful measure to account for variability in word recognition latency ( Johns et al., 2012, 2015 ; Jones et al., 2012 ). The goal of the current study is to extend this measure to examine bilingualism and aging, where multiple theories use frequency of occurrence of linguistic constructs as central to accounting for empirical results ( Gollan et al., 2008 ; Ramscar et al., 2014 ). A lexical decision experiment was conducted with four groups of subjects: younger and older monolinguals and bilinguals. Consistent with past results, a semantic diversity variable accounted for the greatest amount of variance in the latency data. In addition, the pattern of fits of semantic diversity across multiple corpora suggests that bilinguals and older adults are more sensitive to semantic diversity information than younger monolinguals. (shrink)

Originally presented as the author's thesis (doctoral--Gregorian University).

How can liberal democracy best be realized in a world fraught with conflicting new forms of identity politics and intensifying conflicts over culture? This book brings unparalleled clarity to the contemporary debate over this question. Maintaining that cultures are themselves torn by conflicts about their own boundaries, Seyla Benhabib challenges the assumption shared by many theorists and activists that cultures are clearly defined wholes. She argues that much debate--including that of "strong" multiculturalism, which sees cultures as distinct pieces of a (...) mosaic--is dominated by this faulty belief, one with grave consequences for how we think injustices among groups should be redressed and human diversity achieved. Benhabib masterfully presents an alternative approach, developing an understanding of cultures as continually creating, re-creating, and renegotiating the imagined boundaries between "us" and "them." Drawing on contemporary cultural politics from Western Europe, Canada, and the United States, Benhabib develops a double-track model of deliberative democracy that permits maximum cultural contestation within the official public sphere as well as in and through social movements and the institutions of civil society. Agreeing with political liberals that constitutional and legal universalism should be preserved at the level of polity, she nonetheless contends that such a model is necessary to resolve multicultural conflicts. Analyzing in detail the transformation of citizenship practices in European Union countries, Benhabib concludes that flexible citizenship, certain kinds of legal pluralism and models of institutional powersharing are quite compatible with deliberative democracy, as long as they are in accord with egalitarian reciprocity, voluntary self-ascription, and freedom of exit and association. The Claims of Culture offers invaluable insight to all those, whether students or scholars, lawyers or policymakers, who strive to bridge the gap between the theory and practice of cultural politics in the twenty-first century. (shrink)