Symbiogenesis: the holobiont as a unit of evolution

Symbiogenesis is the result of the permanent coexistence of various bionts to form the holobiont (namely, the host and its microbiota). The holobiome is the sum total of the component genomes in a eukaryotic organism; it comprises the genome of an individual member of a given taxon (the host genome) and the microbiome (the genomes of the symbiotic microbiota). The latter is made up of the genes of a variety of microbial communities that persist over time and are not eliminated by natural selection. Therefore, the holobiome can also be considered as the genomic reflection of the complex network of symbiotic interactions that link an individual member of a given taxon with its associated microbiome. Eukaryotic individuals can be analyzed as coevolved, tightly integrated, prokaryotic communities; in this view, natural selection acts on the holobiont as if it were an integrated unit. The best studied holobionts are those that emerged from symbioses involving insects. The presence of symbiotic associations throughout most of the evolutionary history of insects suggests that they were a driving force in the diversification of this group. Support for the evolutionary importance of symbiogenesis comes from the observation that the gradual passage from an ancestral to a descendant species by the accumulation of random mutations has not been demonstrated in the field, nor in the laboratory, nor in the fossil record. Instead, symbiogenesis expands the view of the point-mutation-only as the unique mechanisms of evolution and offers an explanation for the discontinuities in the fossil record («punctuated equilibrium»). As such, it challenges conventional paradigms in biology. This review describes the relationships between xylophagous insects and their microbiota in an attempt to understand the characteristics that have determined bacterial fidelity over generations and throughout evolutionary history (AU)

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Symbiogenesis: the holobiont as a unit of evolution.

Symbiogenesis is the result of the permanent coexistence of various bionts to form the holobiont (namely, the host and its microbiota). The holobiome is the sum total of the component genomes in a eukaryotic organism; it comprises the genome of an individual member of a given taxon (the host genome) and the microbiome (the genomes of the symbiotic microbiota). The latter is made up of the genes of a variety of microbial communities that persist over time and are not eliminated by natural selection. Therefore, the holobiome can also be considered as the genomic reflection of the complex network of symbiotic interactions that link an individual member of a given taxon with its associated microbiome. Eukaryotic individuals can be analyzed as coevolved, tightly integrated, prokaryotic communities; in this view, natural selection acts on the holobiont as if it were an integrated unit. The best studied holobionts are those that emerged from symbioses involving insects. The presence of symbiotic associations throughout most of the evolutionary history of insects suggests that they were a driving force in the diversification of this group. Support for the evolutionary importance of symbiogenesis comes from the observation that the gradual passage from an ancestral to a descendant species by the accumulation of random mutations has not been demonstrated in the field, nor in the laboratory, nor in the fossil record. Instead, symbiogenesis expands the view of the point-mutation-only as the unique mechanisms of evolution and offers an explanation for the discontinuities in the fossil record ("punctuated equilibrium"). As such, it challenges conventional paradigms in biology. This review describes the relationships between xylophagous insects and their microbiota in an attempt to understand the characteristics that have determined bacterial fidelity over generations and throughout evolutionary history.

Spirochete attachment ultrastructure: Implications for the origin and evolution of cilia.

The fine structure of spirochete attachments to the plasma membrane of anaerobic protists displays variations here interpreted as legacies of an evolutionary sequence analogous to that from free-living spirochetes to undulipodia (eukaryotic "flagella" and homologous structures). Attached spirochetes form a vestment, a wriggling fringe of motile cells at the edge of the plasma membrane of unidentified cellulolytic protist cells in the hypertrophied hindgut of the digestive system of Mastotermes darwiniensis, the large wood-feeding termite from northern Australia. From the membrane extend both undulipodia and a complex of comparably sized (10-12 microm x 0.2-0.3 microm) ectosymbiotic spirochetes that resembles unruly ciliated epithelium. In the intestines are helical (swimming) and round-body morphotypes. Round bodies (RBs) are slow or immotile spirochetes, propagules known to revert to typical swimming helices under culture conditions favorable for growth. The surfaces of both the spirochete gram-negative eubacteria and the parabasalid protists display distinctive attachment structures. The attached hypertrophied structures, some of which resemble ciliate kinetids, are found consistently at sites where the spirochete termini contact the protist plasma membranes.

Destruction of spirochete Borrelia burgdorferi round-body propagules (RBs) by the antibiotic tigecycline.

Persistence of tissue spirochetes of Borrelia burgdorferi as helices and round bodies (RBs) explains many erythema-Lyme disease symptoms. Spirochete RBs (reproductive propagules also called coccoid bodies, globular bodies, spherical bodies, granules, cysts, L-forms, sphaeroplasts, or vesicles) are induced by environmental conditions unfavorable for growth. Viable, they grow, move and reversibly convert into motile helices. Reversible pleiomorphy was recorded in at least six spirochete genera (>12 species). Penicillin solution is one unfavorable condition that induces RBs. This antibiotic that inhibits bacterial cell wall synthesis cures neither the second "Great Imitator" (Lyme borreliosis) nor the first: syphilis. Molecular-microscopic techniques, in principle, can detect in animals (insects, ticks, and mammals, including patients) helices and RBs of live spirochetes. Genome sequences of B. burgdorferi and Treponema pallidum spirochetes show absence of >75% of genes in comparison with their free-living relatives. Irreversible integration of spirochetes at behavioral, metabolic, gene product and genetic levels into animal tissue has been documented. Irreversible integration of spirochetes may severely impair immunological response such that they persist undetected in tissue. We report in vitro inhibition and destruction of B. burgdorferi (helices, RBs = "cysts") by the antibiotic Tigecycline (TG; Wyeth), a glycylcycline protein-synthesis inhibitor (of both 30S and 70S ribosome subunits). Studies of the pleiomorphic life history stages in response to TG of both B. burgdorferi and Treponema pallidum in vivo and in vitro are strongly encouraged.

Genome acquisition in horizontal gene transfer: symbiogenesis and macromolecular sequence analysis.

Phylogenetic diagrams ("trees of life") based on computer-generated analyses of nucleic acid (DNA, RNA) or protein (amino acid residues) sequences are purported to reconstruct evolutionary history of the living organisms from which the macromolecules were isolated (1). "Horizontal gene transfer", an expression that refers to the ad hoc explanation of anomalous distribution of these macromolecular sequences, is an inferred past event to explain evolution that, even in principle, is not documentable. Although the diagrams ("phylogenies") help establish the details of relationships among important and widely distributed essential components of living systems (e.g., DNA of large and small replicons such as plasmids, viruses, genophores), chromatin, or protein enzymes that have conserved their function throughout the history of the evolutionary lineage (e.g., DNA that codes for polymerases or 16/18S ribosomal RNA), the HGT concept is an Alfred North Whiteheadian fallacy of misplaced concreteness (2). It is deeply flawed because of sets of unstated, unwarranted assumptions accepted as fact by practitioners: genomics and proteomic experts. They tend to be zoocentric and in particular anthropocentric computer scientists. Their relative lack of familiarity with the fossil record, hard-won life histories and transmission-genetics, taxonomy, physiology, metabolism, and ecology of the communities in which the organisms invariably reside, and many other aspects of life have led to codification of systematic errors in analysis of their, often superb, molecular data. Here we point to a prodigious but little-known symbiogenesis literature that contrasts the transfer of sets of genes with HGT taken to mean one or a-very-few-genes at a time.

The last eukaryotic common ancestor (LECA): acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon.

We develop a symbiogenetic concept of the origin of eukaryotic intracellular motility systems from anaerobic but aerotolerant spirochetes in sulfide-rich environments. The last eukaryotic common ancestors (LECAs) have extant archaeprotist descendants: motile nucleated cells with Embden-Meyerhof glycolysis and substrate-level phosphorylation that lack the alpha-proteobacterial symbiont that became the mitochondrion. Swimming and regulated O(2)-tolerance via sulfide oxidation already had been acquired by sulfidogenic wall-less archaebacteria (thermoplasmas) after aerotolerant cytoplasmic-tubule-containing spirochetes (eubacteria) attached to them. Increasing stability of sulfide-oxidizing/sulfur-reducing consortia analogous to extant sulfur syntrophies (Thiodendron) led to fusion. The eubacteria-archaebacteria symbiosis became permanent as the nucleus evolved by prokaryotic recombination with membrane hypertrophy, analogous to Gemmata obscuriglobus and other delta-proteobacteria with membrane-bounded nucleoids. Histone-coated DNA, protein-synthetic RNAs, amino-acylating, and other enzymes were contributed by the sulfidogen whereas most intracellular motility derives from the spirochete. From this redox syntrophy in anoxic and microoxic Proterozoic habitats LECA evolved. The nucleus originated by recombination of eu- and archaebacterial DNA that remained attached to eubacterial motility structures and became the microtubular cytoskeleton, including the mitotic apparatus. Direct LECA descendants include free-living archaeprotists in anoxic environments: archamoebae, metamonads, parabasalids, and some mammalian symbionts with mitosomes. LECA later acquired the fully aerobic Krebs cycle-oxidative phosphorylation-mitochondrial metabolism by integration of the protomitochondrion, a third alpha-proteobacterial symbiont from which the ancestors to most protoctists, all fungi, plants, and animals evolved. Secondarily anaerobic eukaryotes descended from LECA after integration of this oxygen-respiring eubacterium. Explanatory power and experimental predictions for molecular biology of the LECA concept are stated.

Motility proteins and the origin of the nucleus.

Hypotheses on the origin of eukaryotic cells must account for the origin of the microtubular cytoskeletal structures (including the mitotic spindle, undulipodium/cilium (so-called flagellum) and other structures underlain by the 9(2)+2 microtubular axoneme) in addition to the membrane-bounded nucleus. Whereas bacteria with membrane-bounded nucleoids have been described, no precedent for mitotic, cytoskeletal, or axonemal microtubular structures are known in prokaryotes. Molecular phylogenetic analyses indicate that the cells of the earliest-branching lineages of eukaryotes contain the karyomastigont cytoskeletal system. These protist cells divide via an extranuclear spindle and a persistent nuclear membrane. We suggest that this association between the centriole/kinetosome axoneme (undulipodium) and the nucleus existed from the earliest stage of eukaryotic cell evolution. We interpret the karyomastigont to be a legacy of the symbiosis between thermoacidophilic archaebacteria and motile eubacteria from which the first eukaryote evolved. Mutually inconsistent hypotheses for the origin of the nucleus are reviewed and sequenced proteins of cell motility are discussed because of their potential value in resolving this problem. A correlation of fossil evidence with modern cell and microbiological studies leads us to the karyomastigont theory of the origin of the nucleus.

Spirochete and protist symbionts of a termite (Mastotermes electrodominicus) in Miocene amber.

Extraordinary preservation in amber of the Miocene termite Mastotermes electrodominicus has led to the discovery of fossil symbiotic microbes. Spirochete bacteria and wood-digesting protists were identified in the intestinal tissue of the insect. Fossil wood (xylem: developing vessel-element cells, fibers, pit connections), protists (most likely xylophagic amitochondriates), an endospore (probably of the filamentous intestinal bacterium Arthromitus = Bacillus), and large spirochetes were seen in thin section by light and transmission electron microscopy. The intestinal microbiota of the living termite Mastotermes darwiniensis, a genus now restricted to northern Australia, markedly resembles that preserved in amber. This is a direct observation of a 20-million-year-old xylophagus termite fossil microbial community.