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: May represent an accidentally preserved remnant of Earth’s earliest iron-based metabolism. Its proteins are unusually iron-rich, its metabolic pathways simple and centered on iron chemistry, and its lifestyle closely matches conditions in the microcavities of pyrite crystals on the early Earth. The metallurgical plant in Tula accidentally recreated iron-age conditions – and Ferroplasma was still there, running the same ancient chemistry. - Key citation: Golyshina et al. (2000) (Golyshina et al. 2000); Ferrer et al. (2007) (Ferrer et al. 2007) - Appears in: Chapter 3
Candidatus Desulforudis audaxviator - Habitat: Fracture water in deep gold mines, South Africa, 2.8 km below the surface - Metabolism: Sulfate reduction with H\(_2\) (from radiolysis); fixes CO\(_2\) and N\(_2\) - Claim to fame: The most isolated organism known – dominant member of a single-species ecosystem sealed from the surface for at least 20 million years. Has no genes for oxygen use or defense. - 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: The most socially complex bacterium documented. Communicates via quorum sensing, forms biofilms, and under starvation activates a cannibalism circuit (SdpC toxin) that kills half 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: The closest known prokaryotic relative of eukaryotes. Carries genes for actin-like cytoskeletal proteins and membrane remodeling – capabilities once thought exclusive to eukaryotes. Phylogenetic evidence places eukaryotes within the Asgard archaea, not as their sister group. - 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: Discussed in multiple vent ecology reviews - Appears in: Chapter 7
Elysia viridis - Habitat: Shallow coastal waters of Europe; feeds on algae - Metabolism: Steals functional chloroplasts from algae and incorporates them into its own digestive cells – a temporary, non-heritable photosynthesis - Claim to fame: A living thought experiment for how chloroplast acquisition might have begun. Each generation must acquire chloroplasts anew by feeding. Demonstrates that the boundary between predation and symbiosis can be crossed in a single meal. - Key citation: Provorov & Dolgikh (2005) (Provorov and Dolgikh 2005) - Appears in: Chapter 7