Appendix E — Appendix E: Dramatis Personae
A field guide to the organisms that appear in this book.
Ferroplasma acidiphilum - Habitat: Acidic, iron-rich environments; originally discovered in a bioreactor at a metallurgical plant in Tula, Russia - Metabolism: Iron oxidation (Fe\(^{2+}\) to Fe\(^{3+}\)); no cell wall, just a membrane - Claim to fame: Sometimes cited as a possible analog for early iron-based metabolism. Its proteins are unusually iron-rich and its metabolic pathways are centered on iron chemistry. Whether this reflects ancient features or convergent adaptation to modern acidic iron-rich environments is unresolved. - Key citation: Golyshina et al. (2000) (Golyshina et al. 2000); Ferrer et al. (2007) (Ferrer et al. 2007) - Appears in: Appendix C
Candidatus Desulforudis audaxviator - Habitat: Fracture water in deep gold mines, South Africa, 2.8 kilometers below the surface - Metabolism: Sulfate reduction with H\(_2\) (from radiolysis); fixes CO\(_2\) and N\(_2\) - Claim to fame: Among the most isolated organisms known – dominant member of a community (with ~25 other species) in fracture water sealed from the surface for millions of years. Carries minimal genes for oxygen defense (a lone superoxide dismutase but no catalase or peroxidase). - Key citation: Chivian et al. (2008), Science (Chivian et al. 2008) - Appears in: Chapter 9
Synechococcus (and cyanobacteria generally) - Habitat: Oceans, freshwater, soil, hot springs – nearly everywhere light reaches - Metabolism: Oxygenic photosynthesis (H\(_2\)O as electron donor, CO\(_2\) fixation via Calvin cycle) - Claim to fame: Ancestors of all cyanobacteria caused the Great Oxidation Event ~2.4 Ga, the largest atmospheric transformation in Earth’s history. Every chloroplast descends from a captured cyanobacterium. - Key citation: Blankenship (2010), Plant Physiology (Blankenship 2010) - Appears in: Chapters 4, 5, 7
Bacillus subtilis - Habitat: Soil, plant roots, biofilms - Metabolism: Aerobic heterotroph (versatile; also ferments) - Claim to fame: Among the most socially complex bacteria documented. Communicates via quorum sensing, forms biofilms, and under starvation activates a cannibalism circuit (SdpC toxin) that kills a fraction of the population to feed the survivors, delaying sporulation. - Key citation: Ellermeier et al. (2006), Journal of Bacteriology (Ellermeier et al. 2006) - Appears in: Chapter 6
Myxococcus xanthus - Habitat: Soil - Metabolism: Aerobic heterotroph (predatory) - Claim to fame: Hunts cooperatively in swarms, secreting lytic enzymes that kill prey. Under starvation, aggregates into multicellular fruiting bodies where most cells sacrifice themselves so a minority can sporulate. The most wolf-like bacterium known. - Key citation: Fiegna et al. (2006) (Fiegna et al. 2006) - Appears in: Chapter 6
Ruthia magnifica - Habitat: Gill cells of the giant clam Calyptogena magnifica, at hydrothermal vents - Metabolism: Chemoautotrophy – oxidizes H\(_2\)S, fixes CO\(_2\) via Calvin cycle - Claim to fame: An intracellular symbiont that still retains a complete genome for independent chemoautotrophic life. Represents an early stage on the spectrum from free-living bacterium to organelle. - Key citation: Newton et al. (2007), Science (Newton et al. 2007) - Appears in: Chapter 7
Candidatus Carsonella ruddii - Habitat: Specialized cells (bacteriocytes) inside psyllid insects - Metabolism: Amino acid biosynthesis for the host (cannot replicate independently) - Claim to fame: Possesses the smallest genome of any known cellular organism (160 kb) – so reduced that some biologists question whether it is still a living organism or has become an organelle. Represents a late stage of symbiont-to-organelle evolution. - Key citation: Nakabachi et al. (2006), Science (Nakabachi et al. 2006) - Appears in: Chapter 7
Lokiarchaeota (Asgard archaea) - Habitat: Deep-sea sediments near Loki’s Castle hydrothermal vent field, Mid-Atlantic Ridge, 3,283 m depth - Metabolism: Not yet cultured; predicted from genomic data - Claim to fame: One of the Asgard archaea, the broader clade that phylogenetic analyses place as the closest prokaryotic relatives of eukaryotes. Its genome encodes actin-like cytoskeletal proteins and membrane-remodeling machinery – capabilities once thought exclusive to eukaryotes. Most analyses place eukaryotes within the Asgard archaea, not as their sister group, though the exact branching order among Asgard lineages is still being resolved. - Key citation: Spang et al. (2015), Nature (Spang et al. 2015) - Appears in: Chapter 7
Riftia pachyptila - Habitat: Hydrothermal vents, East Pacific Rise - Metabolism: Entirely dependent on chemoautotrophic endosymbionts (has no mouth, gut, or anus) - Claim to fame: The iconic tube worm of deep-sea vents. Its trophosome organ is packed with sulfur-oxidizing bacteria that fix carbon, fed by a specialized hemoglobin that transports both O\(_2\) and H\(_2\)S simultaneously. - Key citation: Arp et al. (1987), Journal of Experimental Biology (Arp et al. 1987) - Appears in: Chapter 7
Elysia chlorotica - Habitat: Tidal marshes and shallow coastal waters of eastern North America; feeds on algae - Metabolism: Steals functional chloroplasts from the alga Vaucheria litorea and retains them in its own digestive cells – a temporary, non-heritable photosynthesis (kleptoplasty) - Claim to fame: A living thought experiment for how chloroplast acquisition might have begun. Each generation must acquire chloroplasts anew by feeding. The chloroplasts likely persist on their own long-lived proteins and mRNAs rather than on transferred genes. - Key citation: Rumpho et al. (2008) (Rumpho et al. 2008) - Appears in: Chapter 7