Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life

Reconstructing the last common ancestor of all eukaryotes

Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.

How Does Cancer Occur? How Should It Be Treated? Treatment from the Perspective of Alkalization Therapy Based on Science-Based Medicine

This review article investigates the relationship between mitochondrial dysfunction and cancer progression, emphasizing the metabolic shifts that promote tumor growth. Mitochondria are crucial for cellular energy production, but they also play a significant role in cancer progression by promoting glycolysis even under oxygen-rich conditions, a phenomenon known as the Warburg effect. This metabolic reprogramming enables cancer cells to maintain an alkaline internal pH and an acidic external environment, which are critical for their proliferation and survival in hypoxic conditions. The article also explores the acidic tumor microenvironment (TME), a consequence of intensive glycolytic activity and proton production by cancer cells. This acidic milieu enhances the invasiveness and metastatic potential of cancer cells and contributes to increased resistance to chemotherapy. Alkalization therapy, which involves neutralizing this acidity through dietary modifications and the administration of alkalizing agents such as sodium bicarbonate, is highlighted as an effective strategy to counteract these adverse conditions and impede cancer progression. Integrating insights from science-based medicine, the review evaluates the effectiveness of alkalization therapy across various cancer types through clinical assessments. Science-based medicine, which utilizes inductive reasoning from observed clinical outcomes, lends support to the hypothesis of metabolic reprogramming in cancer treatment. By addressing both metabolic and environmental disruptions, this review suggests that considering cancer as primarily a metabolic disorder could lead to more targeted and effective treatment strategies, potentially improving outcomes for patients with advanced-stage cancers.

The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree

Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn's terminology, this discovery of a major biological entity was made during a 'normal science' project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese's project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.

The symbiotic origin of the eukaryotic cell

Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.

Is an archaeon the ancestor of eukaryotes?

The origin of complex cellular life is a key puzzle in evolutionary research, which has broad implications for various neighbouring scientific disciplines. Naturally, views on this topic vary widely depending on the world view and context from which this topic is approached. In the following, I will share my perspective about our current scientific knowledge on the origin of eukaryotic cells, that is, eukaryogenesis, from a biological point of view focusing on the question as to whether an archaeon was the ancestor of eukaryotes.

Sex in protists: A new perspective on the reproduction mechanisms of trypanosomatids

The Protist kingdom individuals are the most ancestral representatives of eukaryotes. They have inhabited Earth since ancient times and are currently found in the most diverse environments presenting a great heterogeneity of life forms. The unicellular and multicellular algae, photosynthetic and heterotrophic organisms, as well as free-living and pathogenic protozoa represents the protist group. The evolution of sex is directly associated with the origin of eukaryotes being protists the earliest protagonists of sexual reproduction on earth. In eukaryotes, the recombination through genetic exchange is a ubiquitous mechanism that can be stimulated by DNA damage. Scientific evidences support the hypothesis that reactive oxygen species (ROS) induced DNA damage can promote sexual recombination in eukaryotes which might have been a decisive factor for the origin of sex. The fact that some recombination enzymes also participate in meiotic sex in modern eukaryotes reinforces the idea that sexual reproduction emerged as consequence of specific mechanisms to cope with mutations and alterations in genetic material. In this review we will discuss about origin of sex and different strategies of evolve sexual reproduction in some protists such that cause human diseases like malaria, toxoplasmosis, sleeping sickness, Chagas disease, and leishmaniasis.

Meaning and Significance of “Alkalization Therapy for Cancer”

Objectives of the Study

Our research aims to answer the following questions. Can cancer progression be stopped by changing the body condition of person with cancer? Can cancer be cured?If cancer progression can be stopped, what is the underlying mechanism?

Theoretical Rationale for Alkalization Therapy

Almost 70 years ago, Goldblatt H. & Cameron G. reported on the idea of alkalization therapy. Before that, Otto Warburg had been studying the metabolism of cancer and had discovered the essential nature of cancer. He published a review in Science in 1956 under the title “On the origin of cancer cells”. From his phenomena described above, we established the theoretical rationale for alkalization therapy, based on the question of “How does cancer form and what is its nature”?

Limitations of Deductive Methods and Inductive Approaches

In this paper, we describe a method to reconstruct the limitations and weaknesses of modern cancer medicine as Science-based Medicine using an inductive method, and to present a new vision of cancer therapy. How should we treat cancer? (Case presentation): Using a specific clinical case, we present patients in whom were successfully treated with no or few anticancer drugs.

Summary

The biggest weakness of current cancer treatments is that they only treat the cancer and not the actual patient. The “alkalization therapy” that we advocate does not compete with any of the current standard treatments, but improves the effectiveness of standard treatments, reduces side effects, and lowers medical costs.

The Continuity Principle and the Evolution of Replication Fidelity

Evolution in modern life requires high replication fidelity to allow for natural selection. A simulation model utilizing simulated phenotype data on cellular probability of survival was developed to determine how self-replication fidelity could evolve in early life. The results indicate that initial survivability and replication fidelity both contribute to overall fitness as measured by growth rates of the cell population. Survival probability was the more dominant feature, and evolution was possible even with zero replication fidelity. A derived formula for the relationship of survival probability and replication fidelity with growth rate was consistent with the simulated empirical data. Quantitative assessment of continuity and other evidence was obtained for a saltation (non-continuous) evolutionary process starting from low to moderate levels of survival probability and self-replication fidelity to reach the high levels seen in modern life forms.

Friends or Foes-Microbial Interactions in Nature

Simple Summary

Microorganisms like bacteria, archaea, fungi, microalgae, and viruses mostly form complex interactive networks within the ecosystem rather than existing as single planktonic cells. Interactions among microorganisms occur between the same species, with different species, or even among entirely different genera, families, or even domains. These interactions occur after environmental sensing, followed by converting those signals to molecular and genetic information, including many mechanisms and classes of molecules. Comprehensive studies on microbial interactions disclose key strategies of microbes to colonize and establish in a variety of different environments. Knowledge of the mechanisms involved in the microbial interactions is essential to understand the ecological impact of microbes and the development of dysbioses. It might be the key to exploit strategies and specific agents against different facing challenges, such as chronic and infectious diseases, hunger crisis, pollution, and sustainability.

Abstract

Microorganisms are present in nearly every niche on Earth and mainly do not exist solely but form communities of single or mixed species. Within such microbial populations and between the microbes and a eukaryotic host, various microbial interactions take place in an ever-changing environment. Those microbial interactions are crucial for a successful establishment and maintenance of a microbial population. The basic unit of interaction is the gene expression of each organism in this community in response to biotic or abiotic stimuli. Differential gene expression is responsible for producing exchangeable molecules involved in the interactions, ultimately leading to community behavior. Cooperative and competitive interactions within bacterial communities and between the associated bacteria and the host are the focus of this review, emphasizing microbial cell–cell communication (quorum sensing). Further, metagenomics is discussed as a helpful tool to analyze the complex genomic information of microbial communities and the functional role of different microbes within a community and to identify novel biomolecules for biotechnological applications.

Prokaryotic symbiotic consortia and the origin of nucleated cells: A critical review of Lynn Margulis hypothesis

The publication in the late 1960s of Lynn Margulis endosymbiotic proposal is a scientific milestone that brought to the fore of evolutionary discussions the issue of the origin of nucleated cells. Although it is true that the times were ripe, the timely publication of Lynn Margulis' original paper was the product of an intellectually bold 29-years old scientist, who based on the critical analysis of the available scientific information produced an all-encompassing, sophisticated narrative scheme on the origin of eukaryotic cells as a result of the evolution of prokaryotic consortia and, in bold intellectual stroke, put it all in the context of planetary evolution. A critical historical reassessment of her original proposal demonstrates that her hypothesis was not a simple archival outline of past schemes, but a renewed historical narrative of prokaryotic evolution and the role of endosymbiosis in the origin of eukaryotes. Although it is now accepted that the closest bacterial relatives of mitochondria and plastids are α-proteobacteria and cyanobacteria, respectively, comparative genomics demonstrates the mosaic character of the organelle genomes. The available evidence has completely refuted Margulis' proposal of an exogenous origin for eukaryotic flagella, the (9 + 2) basal bodies, and centromeres, but we discuss in detail the reasons that led her to devote considerable efforts to argue for a symbiotic origin of the eukaryotic motility. An analysis of the arguments successfully employed by Margulis in her persuasive advocacy of endosymbiosis, combined with the discussions of her flaws and the scientific atmosphere during the period in which she formulated her proposals, are critical for a proper appraisal of the historical conditions that shaped her theory and its acceptance.

Are Reactive Sulfur Species the New Reactive Oxygen Species?

Significance: Oxidative stress in moderation positively affects homeostasis through signaling, while in excess it is associated with adverse health outcomes. Both activities are generally attributed to reactive oxygen species (ROS); hydrogen peroxide as the signal, and cysteines on regulatory proteins as the target. However, using antioxidants to affect signaling or benefit health has not consistently translated into expected outcomes, or when it does, the mechanism is often unclear. Recent Advances: Reactive sulfur species (RSS) were integral in the origin of life and throughout much of evolution. Sophisticated metabolic pathways that evolved to regulate RSS were easily "tweaked" to deal with ROS due to the remarkable similarities between the two. However, unlike ROS, RSS are stored, recycled, and chemically more versatile. Despite these observations, the relevance and regulatory functions of RSS in extant organisms are generally underappreciated. Critical Issues: A number of factors bias observations in favor of ROS over RSS. Research conducted in room air is hyperoxic to cells, and promotes ROS production and RSS oxidation. Metabolic rates of rodent models greatly exceed those of humans; does this favor ROS? Analytical methods designed to detect ROS also respond to RSS. Do these disguise the contributions of RSS? Future Directions: Resolving the ROS/RSS issue is vital to understand biology in general and human health in particular. Improvements in experimental design and analytical methods are crucial. Perhaps the most important is an appreciation of all the attributes of RSS and keeping an open mind.

A need to consider the evolutionary genetics of host-symbiont mutualisms

Despite the ubiquity and importance of mutualistic interactions, we know little about the evolutionary genetics underlying their long-term persistence. As in antagonistic interactions, mutualistic symbioses are characterized by substantial levels of phenotypic and genetic diversity. In contrast to antagonistic interactions, however, we, by and large, do not understand how this variation arises, how it is maintained, nor its implications for future evolutionary change. Currently, we rely on phenotypic models to address the persistence of mutualistic symbioses, but the success of an interaction almost certainly depends heavily on genetic interactions. In this review, we argue that evolutionary genetic models could provide a framework for understanding the causes and consequences of diversity and why selection may favour processes that maintain variation in mutualistic interactions.

Mitochondrial metabolic substrate utilization in granulosa cells reflects body mass index and total follicle stimulating hormone dosage in in vitro fertilization patients

PURPOSE

To utilize a novel mitochondrial function assay with pooled granulosa cells to determine whether mitochondrial function would differ by patient demographics and embryo development.

METHODS

This was a prospective pilot study in a hospital-based assisted reproductive program and public university. Mitochondrial metabolic substrate utilization was assessed in pooled granulosa cells from 40 women undergoing in vitro fertilization during 2018 and 2019.

RESULTS

Assessment of mitochondrial substrate metabolism in pooled granulosa cells revealed higher citric acid, L-malic acid, and octanoyl-L-carnitine utilization with higher body mass index (BMI). Utilization of citric acid, cis-aconitic acid, D-alpha-keto-glutaric acid, L-glutamine, and alanine plus glycine was significantly lower as total dosage of FSH administered increased. Utilization of glycogen was significantly higher in patients with a higher percentage of fertilized oocytes. D-alpha-keto-glutaric acid utilization was significantly lower in patients with a higher percentage of good 8-cell embryos. L-glutamine utilization was significantly lower, with a higher percentage of blastocyst formation. Mitochondrial metabolic scores (MMS), which reflect overall mitochondrial activity of the granulosa pool, were significantly higher in patients with higher BMI and with greater numbers of mature oocytes retrieved. MMS in granulosa decreased as total FSH dose administered increased.

CONCLUSIONS

Granulosa cell utilization of substrates feeding into the citric acid cycle changed with total FSH dosage and BMI. Fertilization rate, 8-cell embryo quality, and blastocyst formation also associated with different energy substrate usage. Mitochondrial substrate utilization by granulosa cells from individual follicles could be further developed into a useful diagnostic tool.

Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling

In this study we analyze the growth-phase dependent metabolic states of Bdellovibrio bacteriovorus by constructing a fully compartmented, mass and charge-balanced genome-scale metabolic model of this predatory bacterium (iCH457). Considering the differences between life cycle phases driving the growth of this predator, growth-phase condition-specific models have been generated allowing the systematic study of its metabolic capabilities. Using these computational tools, we have been able to analyze, from a system level, the dynamic metabolism of the predatory bacteria as the life cycle progresses. We provide computational evidences supporting potential axenic growth of B. bacteriovorus's in a rich medium based on its encoded metabolic capabilities. Our systems-level analysis confirms the presence of "energy-saving" mechanisms in this predator as well as an abrupt metabolic shift between the attack and intraperiplasmic growth phases. Our results strongly suggest that predatory bacteria's metabolic networks have low robustness, likely hampering their ability to tackle drastic environmental fluctuations, thus being confined to stable and predictable habitats. Overall, we present here a valuable computational testbed based on predatory bacteria activity for rational design of novel and controlled biocatalysts in biotechnological/clinical applications.

Insight into the Possible Use of the Predator Bdellovibrio bacteriovorus as a Probiotic

The gut microbiota is a complex microbial ecosystem that coexists with the human organism in the intestinal tract. The members of this ecosystem live together in a balance between them and the host, contributing to its healthy state. Stress, aging, and antibiotic therapies are the principal factors affecting the gut microbiota composition, breaking the mutualistic relationship among microbes and resulting in the overgrowth of potential pathogens. This condition, called dysbiosis, has been linked to several chronic pathologies. In this review, we propose the use of the predator Bdellovibrio bacteriovorus as a possible probiotic to prevent or counteract dysbiotic outcomes and look at the findings of previous research.

Simulations of sea urchin early development delineate the role of oriented cell division in the morula-to-blastula transition

The sea urchin morula to blastula transition has long been thought to require oriented cell divisions and blastomere adherence to the enveloping hyaline layer. In a computer simulation model, cell divisions constrained by a surface plane division rule are adequate to effect morphological transition. The hyaline membrane acts as an enhancer but is not essential. The model is consistent with the orientation of micromere divisions and the open blastulae of direct developing species. The surface plane division rule precedes overt epithelization of surface cells and acts to organize the developing epithelium. It is a universal feature of early metazoan development and simulations of non-echinoid cleavage patterns support its role throughout Metazoa. The surface plane division rule requires only local cues and cells need not reference global positional information or embryonic axes.

Cyclic GMP-AMP signalling protects bacteria against viral infection

The cyclic GMP-AMP synthase (cGAS)-STING pathway is a central component of the cell-autonomous innate immune system in animals^1,2. The cGAS protein is a sensor of cytosolic viral DNA and, upon sensing DNA, it produces a cyclic GMP-AMP (cGAMP) signalling molecule that binds to the STING protein and activates the immune response^3-5. The production of cGAMP has also been detected in bacteria⁶, and has been shown, in Vibrio cholerae, to activate a phospholipase that degrades the inner bacterial membrane⁷. However, the biological role of cGAMP signalling in bacteria remains unknown. Here we show that cGAMP signalling is part of an antiphage defence system that is common in bacteria. This system is composed of a four-gene operon that encodes the bacterial cGAS and the associated phospholipase, as well as two enzymes with the eukaryotic-like domains E1, E2 and JAB. We show that this operon confers resistance against a wide variety of phages. Phage infection triggers the production of cGAMP, which-in turn-activates the phospholipase, leading to a loss of membrane integrity and to cell death before completion of phage reproduction. Diverged versions of this system appear in more than 10% of prokaryotic genomes, and we show that variants with effectors other than phospholipase also protect against phage infection. Our results suggest that the eukaryotic cGAS-STING antiviral pathway has ancient evolutionary roots that stem from microbial defences against phages.

Hydrogen sulfide, reactive sulfur species and coping with reactive oxygen species

Life began in a ferruginous (anoxic and Fe²⁺ dominated) world around 3.8 billion years ago (bya). Hydrogen sulfide (H₂S) and other sulfur molecules from hydrothermal vents and other fissures provided many key necessities for life's origin including catalytic platforms (primordial enzymes) that also served as primitive boundaries (cell walls), substrates for organic synthesis and a continuous source of energy in the form of reducing equivalents. Anoxigenic photosynthesis oxidizing H₂S followed within a few hundred million years and laid the metabolic groundwork for oxidative photosynthesis some half-billion years later that slightly and episodically increased atmospheric oxygen around 2.3 bya. This oxidized terrestrial sulfur to sulfate which was washed to the sea where it was reduced creating vast euxinic (anoxic and sulfidic) areas. It was in this environment that eukaryotic cells appeared around 1.5 bya and where they evolved for nearly 1 billion additional years. Oxidative photosynthesis finally oxidized the oceans and around 0.6 bya oxygen levels in the atmosphere and oceans began to rise toward present day levels. This is purported to have been a life-threatening event due to the prevalence of reactive oxygen species (ROS) and thus necessitated the elaboration of chemical and enzymatic antioxidant mechanisms. However, these antioxidants initially appeared around the time of anoxigenic photosynthesis suggesting a commitment to metabolism of reactive sulfur species (RSS). This review examines these events and suggests that many of the biological attributes assigned to ROS may, in fact, be due to RSS. This is underscored by observations that ROS and RSS are chemically similar, often indistinguishable by analytical methods and the fact that the bulk of biochemical and physiological experiments are performed in unphysiologically oxic environments where ROS are artifactually favored over RSS.

Energide-cell body as smallest unit of eukaryotic life

Background

The evolutionary origin of the eukaryotic nucleus is obscure and controversial. Currently preferred are autogenic concepts; ideas of a symbiotic origin are mostly discarded and forgotten. Here we briefly discuss these issues and propose a new version of the symbiotic and archaeal origin of the eukaryotic nucleus.

Scope and Conclusions

The nucleus of eukaryotic cells forms via its perinuclear microtubules, the primary eukaryotic unit known also as the Energide-cell body. As for all other endosymbiotic organelles, new Energides are generated only from other Energides. While the Energide cannot be generated de novo, it can use its secretory apparatus to generate de novo the cell periphery apparatus. We suggest that Virchow's tenet Omnis cellula e cellula should be updated as Omnis Energide e Energide to reflect the status of the Energide as the primary unit of the eukaryotic cell, and life. In addition, the plasma membrane provides feedback to the Energide and renders it protection via the plasma membrane-derived endosomal network. New discoveries suggest archaeal origins of both the Energide and its host cell.

Role of Epichloë Endophytes in Defense Responses of Cool-Season Grasses to Pathogens: A Review

Various cool-season grasses are infected by Epichloë endophyte, and this symbiotic relationship is always of benefit to the host grass due to an increased resistance to abiotic and biotic stresses. Fungal diseases adversely affect the yield, quality, and economic benefits of rangelands, which affects the production of animal husbandry. Therefore, it is imperative to breed resistant cultivars and to better understand the role of fungal endophytes in order to protect grasses against pathogens. The present review introduces research regarding how these endophytes affect the growth of pathogens in vitro and how they change the resistance of host plants to plant diseases. From the perspective of physical defense, changes in physiological indexes, and secretion of chemical compounds, we summarize the potential mechanisms by which endophytes are able to enhance the disease resistance of a host grass. Through these, we aim to establish a solid theoretical foundation for plant disease control and disease resistance breeding by application of fungal endophytes. A broader understanding of fungal endophyte effects on hosts could create a new opportunity for managing or introducing fungal symbioses in both agronomic or non-agronomic ecosystems.

LEA Proteins and the Evolution of the WHy Domain

The late embryogenesis abundant (LEA) family is composed of a diverse collection of multidomain and multifunctional proteins found in all three domains of the tree of life, but they are particularly common in plants. Most members of the family are known to play an important role in abiotic stress response and stress tolerance in plants but are also part of the plant hypersensitive response to pathogen infection. The mechanistic basis for LEA protein functionality is still poorly understood. The group of LEA 2 proteins harbor one or more copies of a unique domain, the water stress and hypersensitive response (WHy) domain. This domain sequence has recently been identified as a unique open reading frame (ORF) in some bacterial genomes (mostly in the phylum Firmicutes), and the recombinant bacterial WHy protein has been shown to exhibit a stress tolerance phenotype in Escherichia coli and an in vitro protein denaturation protective function. Multidomain phylogenetic analyses suggest that the WHy protein gene sequence may have ancestral origins in the domain Archaea, with subsequent acquisition in Bacteria and eukaryotes via endosymbiont or horizontal gene transfer mechanisms. Here, we review the structure, function, and nomenclature of LEA proteins, with a focus on the WHy domain as an integral component of the LEA constructs and as an independent protein.

Mitochondrial DNA as a biomarker for in-vitro fertilization outcome

PURPOSE OF REVIEW

This article discusses the use of mitochondrial DNA (mtDNA) copy number as a potential biomarker for embryo viability in assisted reproduction.

RECENT FINDINGS

Mitochondria have a well-established role in regulating embryo energy metabolism, and their efficiency has significant implications for reproductive success. Two recent studies suggested that elevated mtDNA copy number is associated with decreased implantation potential in human embryos generated by IVF. In the first study, Fragouli et al. reported that blastocysts that are aneuploid and those obtained from older reproductive age women have a higher mtDNA copy number. In addition, euploid blastocysts that failed to implant had a higher mtDNA copy number; and pregnancy did not occur when mtDNA copy number was above a threshold. In a subsequent study, Diez-Juan et al. found that mtDNA copy number inversely correlates with implantation potential of euploid embryos, not only for blastocysts but also for cleavage stage embryos. Instead of a threshold model, they proposed a score for embryos based on mtDNA copy number, which would be indicative of implantation potential. Unlike the previous study, Diez-Juan et al. did not find an age-associated decrease in mtDNA copy number in day 3 or day 5 embryos.

SUMMARY

Recent reports suggest that mtDNA copy number may be used as a biomarker for embryo viability. Further studies are necessary to determine whether mtDNA copy number constitutes a parameter independent of morphology and preimplantation genetic screening and whether its use may result in higher IVF pregnancy rates.

Aerobic function in mitochondria persists beyond death by heat stress in insects

The critical thermal maximum (CT_max) of insects can be determined using flow-through thermolimit respirometry. It has been demonstrated that respiratory patterns cease and insects do not recover once the CT_max temperature has been reached. However, if high temperatures are maintained following the CT_max, researchers have observed a curious phenomenon whereby the insect body releases a large burst of carbon dioxide at a rate and magnitude that often exceed that of the live insect. This carbon dioxide release has been termed the post-mortal peak (PMP). We demonstrate here that the PMP is observed only at high temperatures, is oxygen-dependent, is prevented by cyanide exposure, and is associated with concomitant consumption of oxygen. We conclude that the PMP derives from highly active, aerobic metabolism in the mitochondria. The insect tracheal system contains air-filled tubes that reach deep into the tissues and allow mitochondria access to oxygen even upon organismal death. This unique condition permits the investigation of mitochondrial function during thermal failure in a manner that cannot be achieved using vertebrate organisms or in vitro preparations.

The Physiology of Phagocytosis in the Context of Mitochondrial Origin

How mitochondria came to reside within the cytosol of their host has been debated for 50 years. Though current data indicate that the last eukaryote common ancestor possessed mitochondria and was a complex cell, whether mitochondria or complexity came first in eukaryotic evolution is still discussed. In autogenous models (complexity first), the origin of phagocytosis poses the limiting step at eukaryote origin, with mitochondria coming late as an undigested growth substrate. In symbiosis-based models (mitochondria first), the host was an archaeon, and the origin of mitochondria was the limiting step at eukaryote origin, with mitochondria providing bacterial genes, ATP synthesis on internalized bioenergetic membranes, and mitochondrion-derived vesicles as the seed of the eukaryote endomembrane system. Metagenomic studies are uncovering new host-related archaeal lineages that are reported as complex or phagocytosing, although images of such cells are lacking. Here we review the physiology and components of phagocytosis in eukaryotes, critically inspecting the concept of a phagotrophic host. From ATP supply and demand, a mitochondrion-lacking phagotrophic archaeal fermenter would have to ingest about 34 times its body weight in prokaryotic prey to obtain enough ATP to support one cell division. It would lack chemiosmotic ATP synthesis at the plasma membrane, because phagocytosis and chemiosmosis in the same membrane are incompatible. It would have lived from amino acid fermentations, because prokaryotes are mainly protein. Its ATP yield would have been impaired relative to typical archaeal amino acid fermentations, which involve chemiosmosis. In contrast, phagocytosis would have had great physiological benefit for a mitochondrion-bearing cell.

From endosymbiosis to holobionts: Evaluating a conceptual legacy

In her influential 1967 paper, Lynn Margulis synthesized a range of data to support the idea of endosymbiosis. Building on the success of this work, she applied the same methodology to promote the role of symbiosis more generally in evolution. As part of this broader project, she coined the term 'holobiont' to refer to a unified entity of symbiont and host. This concept is now applied with great gusto in microbiome research, and often implies not just a physiological unit but also various senses of an evolving system. My analysis will track how Margulis came to propose the term, its current use in microbiome research, and how those applications link back to Margulis. I then evaluate what contemporary use says about Margulis's legacy for microbiome research.

Symbiosis in eukaryotic evolution

Fifty years ago, Lynn Margulis, inspiring in early twentieth-century ideas that put forward a symbiotic origin for some eukaryotic organelles, proposed a unified theory for the origin of the eukaryotic cell based on symbiosis as evolutionary mechanism. Margulis was profoundly aware of the importance of symbiosis in the natural microbial world and anticipated the evolutionary significance that integrated cooperative interactions might have as mechanism to increase cellular complexity. Today, we have started fully appreciating the vast extent of microbial diversity and the importance of syntrophic metabolic cooperation in natural ecosystems, especially in sediments and microbial mats. Also, not only the symbiogenetic origin of mitochondria and chloroplasts has been clearly demonstrated, but improvement in phylogenomic methods combined with recent discoveries of archaeal lineages more closely related to eukaryotes further support the symbiogenetic origin of the eukaryotic cell. Margulis left us in legacy the idea of 'eukaryogenesis by symbiogenesis'. Although this has been largely verified, when, where, and specifically how eukaryotic cells evolved are yet unclear. Here, we shortly review current knowledge about symbiotic interactions in the microbial world and their evolutionary impact, the status of eukaryogenetic models and the current challenges and perspectives ahead to reconstruct the evolutionary path to eukaryotes.

Alien Mindscapes-A Perspective on the Search for Extraterrestrial Intelligence

Advances in planetary and space sciences, astrobiology, and life and cognitive sciences, combined with developments in communication theory, bioneural computing, machine learning, and big data analysis, create new opportunities to explore the probabilistic nature of alien life. Brought together in a multidisciplinary approach, they have the potential to support an integrated and expanded Search for Extraterrestrial Intelligence (SETI (1) ), a search that includes looking for life as we do not know it. This approach will augment the odds of detecting a signal by broadening our understanding of the evolutionary and systemic components in the search for extraterrestrial intelligence (ETI), provide more targets for radio and optical SETI, and identify new ways of decoding and coding messages using universal markers.

KEY WORDS

SETI-Astrobiology-Coevolution of Earth and life-Planetary habitability and biosignatures. Astrobiology 16, 661-676.

Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?

The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this ‘dispersed eukaryome’ implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently.

Long-term ungulate exclusion reduces fungal symbiont prevalence in native grasslands

When symbionts are inherited by offspring, they can have substantial ecological and evolutionary consequences because they occur in all host life stages. Although natural frequencies of inherited symbionts are commonly <100 %, few studies investigate the ecological drivers of variation in symbiont prevalence. In plants, inherited fungal endophytes can improve resistance to herbivory, growth under drought, and competitive ability. We evaluated whether native ungulate herbivory increased the prevalence of a fungal endophyte in the common, native bunchgrass, Festuca campestris (rough fescue, Poaceae). We used large-scale (1 ha) and long-term (7-10 year) fencing treatments to exclude native ungulates and recorded shifts in endophyte prevalence at the scale of plant populations and for individual plants. We characterized the fungal endophyte in F. campestris, Epichloë species FcaTG-1 (F. campestris taxonomic group 1) for the first time. Under ungulate exclusion, endophyte prevalence was 19 % lower in plant populations, 25 % lower within plant individuals, and 39 % lower in offspring (seeds) than in ungulate-exposed controls. Population-level endophyte frequencies were also negatively correlated with soil moisture across geographic sites. Observations of high within-plant variability in symbiont prevalence are novel for the Epichloë species, and contribute to a small, but growing, literature that documents phenotypic plasticity in plant-endophyte symbiota. Altogether, we show that native ungulates can be an important driver of symbiont prevalence in native plant populations, even in the absence of evidence for direct mechanisms of mammal deterrence. Understanding the ecological controls on symbiont prevalence could help to predict future shifts in grasslands that are dominated by Epichloë host plants.

Antibacterial Peptides: Opportunities for the Prevention and Treatment of Dental Caries

Dental caries is a multifactorial disease that is a growing and costly global health concern. The onset of disease is a consequence of an ecological imbalance within the dental plaque biofilm that favors specific acidogenic and aciduric caries pathogens, namely Streptococcus mutans and Streptococcus sobrinus. It is now recognized by the scientific and medical community that it is neither possible nor desirable to totally eliminate dental plaque. Conversely, the chemical biocides most commonly used for caries prevention and treatment indiscriminately attack all plaque microorganisms. These treatments also suffer from other drawbacks such as bad taste, irritability, and staining. Furthermore, the public demand for safe and natural personal hygiene products continues to rise. Therefore, there are opportunities that exist to develop new strategies for the treatment of this disease. As an alternative to conventional antibiotics, antibacterial peptides have been explored greatly over the last three decades for many different therapeutic uses. There are currently tens of hundreds of antibacterial peptides characterized across the evolutionary spectrum, and among these, many demonstrate physical and/or biological properties that may be suitable for a more targeted approach to the selective control or elimination of putative caries pathogens. Additionally, many peptides, such as nisin, are odorless, colorless, and tasteless and do not cause irritation or staining. This review focuses on antibacterial peptides for their potential role in the treatment and prevention of dental caries and suggests candidates that need to be explored further. Practical considerations for the development of antibacterial peptides as oral treatments are also discussed.

The Role of Hydrogen Sulfide in Evolution and the Evolution of Hydrogen Sulfide in Metabolism and Signaling

The chemical versatility of sulfur and its abundance in the prebiotic Earth as reduced sulfide (H2S) implicate this molecule in the origin of life 3.8 billion years ago and also as a major source of energy in the first seven-eighths of evolution. The tremendous increase in ambient oxygen ∼600 million years ago brought an end to H2S as an energy source, and H2S-dependent animals either became extinct, retreated to isolated sulfide niches, or adapted. The first 3 billion years of molecular tinkering were not lost, however, and much of this biochemical armamentarium easily adapted to an oxic environment where it contributes to metabolism and signaling even in humans. This review examines the role of H2S in evolution and the evolution of H2S metabolism and signaling.

Open Questions on the Origin of Eukaryotes

Despite recent progress, the origin of the eukaryotic cell remains enigmatic. It is now known that the last eukaryotic common ancestor was complex and that endosymbiosis played a crucial role in eukaryogenesis at least via the acquisition of the alphaproteobacterial ancestor of mitochondria. However, the nature of the mitochondrial host is controversial, although the recent discovery of an archaeal lineage phylogenetically close to eukaryotes reinforces models proposing archaea-derived hosts. We argue that, in addition to improved phylogenomic analyses with more comprehensive taxon sampling to pinpoint the closest prokaryotic relatives of eukaryotes, determining plausible mechanisms and selective forces at the origin of key eukaryotic features, such as the nucleus or the bacterial-like eukaryotic membrane system, is essential to constrain existing models.

Origin and evolution of metabolic sub-cellular compartmentalization in eukaryotes

A high level of subcellular compartmentalization is a hallmark of eukaryotic cells. This intricate internal organization was present already in the common ancestor of all extant eukaryotes, and the determination of the origins and early evolution of the different organelles remains largely elusive. Organellar proteomes are determined through regulated pathways that target proteins produced in the cytosol to their final subcellular destinations. This internal sorting of proteins can vary across different physiological conditions, cell types and lineages. Evolutionary retargeting - the alteration of a subcellular localization of a protein in the course of evolution - has been rampant in eukaryotes and involves any possible combination of organelles. This fact adds another layer of difficulty to the reconstruction of the origins and evolution of organelles. In this review we discuss current themes in relation to the origin and evolution of organellar proteomes. Throughout the text, a special focus is set on the evolution of mitochondrial and peroxisomal proteomes, which are two organelles for which extensive proteomic and evolutionary studies have been performed.

Bioenergetic evolution in proteobacteria and mitochondria

Mitochondria are the energy-producing organelles of our cells and derive from bacterial ancestors that became endosymbionts of microorganisms from a different lineage, together with which they formed eukaryotic cells. For a long time it has remained unclear from which bacteria mitochondria actually evolved, even if these organisms in all likelihood originated from the α lineage of proteobacteria. A recent article (Degli Esposti M, et al. 2014. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One 9:e96566) has presented novel evidence indicating that methylotrophic bacteria could be among the closest living relatives of mitochondrial ancestors. Methylotrophs are ubiquitous bacteria that live on single carbon sources such as methanol and methane; in the latter case they are called methanotrophs. In this review, I examine their possible ancestry to mitochondria within a survey of the common features that can be found in the central and terminal bioenergetic systems of proteobacteria and mitochondria. I also discuss previously overlooked information on methanotrophic bacteria, in particular their intracytoplasmic membranes resembling mitochondrial cristae and their capacity of establishing endosymbiotic relationships with invertebrate animals and archaic plants. This information appears to sustain the new idea that mitochondrial ancestors could be related to extant methanotrophic proteobacteria, a possibility that the genomes of methanotrophic endosymbionts will hopefully clarify.

Bacterial influences on animal origins

Animals evolved in seas teeming with bacteria, yet the influences of bacteria on animal origins are poorly understood. Comparisons among modern animals and their closest living relatives, the choanoflagellates, suggest that the first animals used flagellated collar cells to capture bacterial prey. The cell biology of prey capture, such as cell adhesion between predator and prey, involves mechanisms that may have been co-opted to mediate intercellular interactions during the evolution of animal multicellularity. Moreover, a history of bacterivory may have influenced the evolution of animal genomes by driving the evolution of genetic pathways for immunity and facilitating lateral gene transfer. Understanding the interactions between bacteria and the progenitors of animals may help to explain the myriad ways in which bacteria shape the biology of modern animals, including ourselves.

Evolution of mitochondria reconstructed from the energy metabolism of living bacteria

The ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. However, the identity and relatives of proto-mitochondria remain elusive. Here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. We reached this conclusion after reconstructing the possible evolutionary pathways of the bioenergy systems of proto-mitochondria with a genomic survey of extant α-proteobacteria. Results obtained with complementary molecular and genetic analyses of diverse bioenergetic proteins converge in indicating the pathway stemming from methylotrophic bacteria as the most probable route of mitochondrial evolution. Contrary to other α-proteobacteria, methylotrophs show transition forms for the bioenergetic systems analysed. Our approach of focusing on these bioenergetic systems overcomes the phylogenetic impasse that has previously complicated the search for mitochondrial ancestors. Moreover, our results provide a new perspective for experimentally re-evolving mitochondria from extant bacteria and in the future produce synthetic mitochondria.

The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes

The ancestral set of eukaryotic genes is a chimera composed of genes of archaeal and bacterial origins thanks to the endosymbiosis event that gave rise to the mitochondria and apparently antedated the last common ancestor of the extant eukaryotes. The proto-mitochondrial endosymbiont is confidently identified as an α-proteobacterium. In contrast, the archaeal ancestor of eukaryotes remains elusive, although evidence is accumulating that it could have belonged to a deep lineage within the TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) superphylum of the Archaea. Recent surveys of archaeal genomes show that the apparent ancestors of several key functional systems of eukaryotes, the components of the archaeal "eukaryome," such as ubiquitin signaling, RNA interference, and actin-based and tubulin-based cytoskeleton structures, are identifiable in different archaeal groups. We suggest that the archaeal ancestor of eukaryotes was a complex form, rooted deeply within the TACK superphylum, that already possessed some quintessential eukaryotic features, in particular, a cytoskeleton, and perhaps was capable of a primitive form of phagocytosis that would facilitate the engulfment of potential symbionts. This putative group of Archaea could have existed for a relatively short time before going extinct or undergoing genome streamlining, resulting in the dispersion of the eukaryome. This scenario might explain the difficulty with the identification of the archaeal ancestor of eukaryotes despite the straightforward detection of apparent ancestors to many signature eukaryotic functional systems.

Effects of natural hybrid and non-hybrid Epichloë endophytes on the response of Hordelymus europaeus to drought stress

Interspecific hybrid endophytes of the genus Epichloë (Ascomycota, Clavicipitaceae) are prevalent in wild grass populations, possibly because of their larger gene variation, resulting in increased fitness benefits for host plants; however, the reasons are not yet known. We tested hypotheses regarding niche expansion mediated by hybrid endophytes, population-dependent interactions and local co-adaptation in the woodland grass Hordelymus europaeus, which naturally hosts both hybrid and non-hybrid endophyte taxa. Seedlings derived from seeds of four grass populations made endophyte free were re-inoculated with hybrid or non-hybrid endophyte strains, or left endophyte free. Plants were grown in the glasshouse with or without drought treatment. Endophyte infection increased plant biomass and tiller production by 10-15% in both treatments. Endophyte types had similar effects on growth, but opposite effects on reproduction: non-hybrid endophytes increased seed production, whereas hybrid endophytes reduced or prevented it completely. The results are consistent with the observation that non-hybrid endophytes in H. europaeus prevail at dry sites, but cannot explain the prevalence of hybrid endophytes. Thus, our results do not support the hypothesis of niche expansion of hybrid-infected plants. Moreover, plants inoculated with native relative to foreign endophytes yielded higher infections, but both showed similar growth and survival, suggesting weak co-adaptation.

Crystallization around solid-like nanosized docks can explain the specificity, diversity, and stability of membrane microdomains

To date, it is widely accepted that microdomains do form in the biological membranes of all eukaryotic cells, and quite possibly also in prokaryotes. Those sub-micrometric domains play crucial roles in signaling, in intracellular transport, and even in inter-cellular communications. Despite their ubiquitous distribution, and the broad and lasting interest invested in those microdomains, their actual nature and composition, and even the physical rules that regiment their assembly still remain elusive and hotly debated. One of the most often considered models is the raft hypothesis, i.e., the partition of lipids between liquid disordered and ordered phases (Ld and Lo, respectively), the latter being enriched in sphingolipids and cholesterol. Although it is experimentally possible to obtain the formation of microdomains in synthetic membranes through Ld/Lo phase separation, there is an ever increasing amount of evidence, obtained with a wide array of experimental approaches, that a partition between domains in Ld and Lo phases cannot account for many of the observations collected in real cells. In particular, it is now commonly perceived that the plasma membrane of cells is mostly in Lo phase and recent data support the existence of gel or solid ordered domains in a whole variety of live cells under physiological conditions. Here, we present a model whereby seeds comprised of oligomerised proteins and/or lipids would serve as crystal nucleation centers for the formation of diverse gel/crystalline nanodomains. This could confer the selectivity necessary for the formation of multiple types of membrane domains, as well as the stability required to match the time frames of cellular events, such as intra- or inter-cellular transport or assembly of signaling platforms. Testing of this model will, however, require the development of new methods allowing the clear-cut discrimination between Lo and solid nanoscopic phases in live cells.

Physiological implications of hydrogen sulfide: a whiff exploration that blossomed

The important life-supporting role of hydrogen sulfide (H(2)S) has evolved from bacteria to plants, invertebrates, vertebrates, and finally to mammals. Over the centuries, however, H(2)S had only been known for its toxicity and environmental hazard. Physiological importance of H(2)S has been appreciated for about a decade. It started by the discovery of endogenous H(2)S production in mammalian cells and gained momentum by typifying this gasotransmitter with a variety of physiological functions. The H(2)S-catalyzing enzymes are differentially expressed in cardiovascular, neuronal, immune, renal, respiratory, gastrointestinal, reproductive, liver, and endocrine systems and affect the functions of these systems through the production of H(2)S. The physiological functions of H(2)S are mediated by different molecular targets, such as different ion channels and signaling proteins. Alternations of H(2)S metabolism lead to an array of pathological disturbances in the form of hypertension, atherosclerosis, heart failure, diabetes, cirrhosis, inflammation, sepsis, neurodegenerative disease, erectile dysfunction, and asthma, to name a few. Many new technologies have been developed to detect endogenous H(2)S production, and novel H(2)S-delivery compounds have been invented to aid therapeutic intervention of diseases related to abnormal H(2)S metabolism. While acknowledging the challenges ahead, research on H(2)S physiology and medicine is entering an exponential exploration era.

For quite a few chromosomes more: the origin of eukaryotes…

The evolution of eukaryotes addresses an enigmatic question: what are the evolutionary advantages of having a nucleus? The nucleus is traditionally thought to act as protection for DNA, but eukaryotes are more fragile than bacteria. The compartmentalization of the eukaryotic cell might stem from invaginations of the plasma membrane, and I argue that this autogenous origin of the nucleus constituted a selective innovation caused by cellular constraints due to a large genome. The protoeukaryotic nucleus appears to be a physical and chemical solution to the problem of large amounts of DNA in the form of many linear chromosomes. The selective advantages of having a nuclear envelope are to house a large genome in a stabilized structure and to decouple gene translation from transcription. Supporting the karyogenic model, this new hypothesis opens an original perspective to help in understanding the very ancient origin of eukaryotes.

Origin and diversification of eukaryotes

The bulk of the diversity of eukaryotic life is microbial. Although the larger eukaryotes-namely plants, animals, and fungi-dominate our visual landscapes, microbial lineages compose the greater part of both genetic diversity and biomass, and contain many evolutionary innovations. Our understanding of the origin and diversification of eukaryotes has improved substantially with analyses of molecular data from diverse lineages. These data have provided insight into the nature of the genome of the last eukaryotic common ancestor (LECA). Yet, the origin of key eukaryotic features, namely the nucleus and cytoskeleton, remains poorly understood. In contrast, the past decades have seen considerable refinement in hypotheses on the major branching events in the evolution of eukaryotic diversity. New insights have also emerged, including evidence for the acquisition of mitochondria at the time of the origin of eukaryotes and data supporting the dynamic nature of genomes in LECA.

Antibiotic-induced bacterial cell death exhibits physiological and biochemical hallmarks of apoptosis

Programmed cell death is a gene-directed process involved in the development and homeostasis of multicellular organisms. The most common mode of programmed cell death is apoptosis, which is characterized by a stereotypical set of biochemical and morphological hallmarks. Here we report that Escherichia coli also exhibit characteristic markers of apoptosis-including phosphatidylserine exposure, chromosome condensation, and DNA fragmentation-when faced with cell death-triggering stress, namely bactericidal antibiotic treatment. Notably, we also provide proteomic and genetic evidence for the ability of multifunctional RecA to bind peptide sequences that serve as substrates for eukaryotic caspases, and regulation of this phenotype by the protease, ClpXP, under conditions of cell death. Our findings illustrate that prokaryotic organisms possess mechanisms to dismantle and mark dying cells in response to diverse noxious stimuli and suggest that elaborate, multilayered proteolytic regulation of these features may have evolved in eukaryotes to harness and exploit their deadly potential.

Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes

The prokaryotic organisms can be divided into two main groups depending upon whether their cell envelopes contain one membrane (monoderms) or two membranes (diderms). It is important to understand how these and other variations that are observed in the cell envelopes of prokaryotic organisms have originated. In 2009, James Lake proposed that cells with two membranes (primarily Gram-negative bacteria) originated from an ancient endosymbiotic event involving an Actinobacteria and a Clostridia (Lake 2009). However, this Perspective argues that this proposal is based on a number of incorrect assumptions and the data presented in support of this model are also of questionable nature. Thus, there is no reliable evidence to support the endosymbiotic origin of double membrane bacteria. In contrast, many observations suggest that antibiotic selection pressure was an important selective force in prokaryotic evolution and that it likely played a central role in the evolution of diderm (Gram-negative) bacteria. Some bacterial phyla, such as Deinococcus-Thermus, which lack lipopolysaccharide (LPS) and yet contain some characteristics of the diderm bacteria, are postulated as evolutionary intermediates (simple diderms) in the transition between the monoderm bacterial taxa and the bacterial groups that have the archetypal LPS-containing outer cell membrane found in Gram-negative bacteria. It is possible to distinguish the two stages in the evolution of diderm-LPS cells (viz. monoderm bacteria → simple diderms lacking LPS → LPS containing archetypal diderm bacteria) by means of conserved inserts in the Hsp70 and Hsp60 proteins. The insert in the Hsp60 protein also distinguishes the traditional Gram-negative diderm bacterial phyla from atypical taxa of diderm bacteria (viz. Negativicutes, Fusobacteria, Synergistetes and Elusimicrobia). The Gram-negative bacterial phyla with an LPS-diderm cell envelope, as defined by the presence of the Hsp60 insert, are indicated to form a monophyletic clade and no loss of the outer membrane from any species from this group seems to have occurred. This argues against the origin of monoderm prokaryotes from diderm bacteria by loss of outer membrane.

From the scala naturae to the symbiogenetic and dynamic tree of life

All living beings on Earth, from bacteria to humans, are connected through descent from common ancestors and represent the summation of their corresponding, ca. 3500 million year long evolutionary history. However, the evolution of phenotypic features is not predictable, and biologists no longer use terms such as "primitive" or "perfect organisms". Despite these insights, the Bible-based concept of the so-called "ladder of life" or Scala Naturae, i.e., the idea that all living beings can be viewed as representing various degrees of "perfection", with humans at the very top of this biological hierarchy, was popular among naturalists until ca. 1850 (Charles Bonnet, Jean Lamarck and others). Charles Darwin is usually credited with the establishment of a branched evolutionary "Tree of Life". This insight of 1859 was based on his now firmly corroborated proposals of common ancestry and natural selection. In this article I argue that Darwin was still influenced by "ladder thinking", a theological view that prevailed throughout the 19th century and is also part of Ernst Haeckel's famous Oak tree (of Life) of 1866, which is, like Darwin's scheme, static. In 1910, Constantin Mereschkowsky proposed an alternative, "anti-selectionist" concept of biological evolution, which became known as the symbiogenesis-theory. According to the symbiogenesis-scenario, eukaryotic cells evolved on a static Earth from archaic prokaryotes via the fusion and subsequent cooperation of certain microbes. In 1929, Alfred Wegener published his theory of continental drift, which was later corroborated, modified and extended. The resulting theory of plate tectonics is now the principal organizing concept of geology. Over millions of years, plate tectonics and hence the "dynamic Earth" has caused destructive volcanic eruptions and earthquakes. At the same time, it created mountain ranges, deep oceans, novel freshwater habitats, and deserts. As a result, these geologic processes destroyed numerous populations of organisms, and produced the environmental conditions for new species of animals, plants and microbes to adapt and evolve. In this article I propose a tree-like "symbiogenesis, natural selection, and dynamic Earth (synade)-model" of macroevolution that is based on these novel facts and data.