Origins and Evolution

Chapter Overview

• Origins of Life

  • Nature of the earliest cells

  • Divergence of microbes from common ancestors, modified by gene transfer and symbiosis

  • Mechanisms of microbial evolution in nature and the laboratory

• Forming the First Cells

• Evolution: Phylogeny and Gene Transfer

• Natural Selection and Adaptation

• Microbial Species and Taxonomy

• Symbiosis and the Origin of Mitochondria and Chloroplasts

17.1 Origins of Life

• Several fundamental conditions required before the first cells could evolve:

  • Essential elements: Required to compose organic molecules.

  • Continual source of energy: Mainly from nuclear fusion reactions within the Sun.

  • Temperature range: Must permit liquid water; otherwise, metabolic reactions cease.

• Prebiotic soup theory: Proposes that fundamental biomolecules of life arose spontaneously through condensation of reduced inorganic molecules.

• Early metabolism involved anaerobic oxidation-reduction reactions.

Evidence for Early Life

• Evidence includes:**

  • Stromatolites: Earliest forms of life with clear fossil evidence, consisting of bacterial communities. Bulbous sedimentary layers of limestone (CaCO3) dated to 3.4 billion years ago.

17.2 Elements of Life

• Major elements of biomolecules formed through nuclear reactions within stars that exploded into supernovas before the birth of our solar system.

• Formation of Earth involved:

  • Coalescence of individual planets from matter attracted by gravity.

  • Geological composition of Earth includes core (rich in iron), mantle, and thin outer crust that supports the biosphere.

• Biosphere: The total sum of all life forms on Earth generates oxidants, most notably O2.

• Volcanic activity released gases like carbon dioxide and nitrogen, forming the first atmosphere composed mainly of CO2.

• Development of living organisms led to the atmosphere being filled with N2 and O2.

Geological Evidence for Early Life

• Biosignature: Biological signature found in the geological record. Biosignatures exist even earlier than oldest fossils, but their significance is limited as nonbiogenic explanations can't be ruled out.

• The Hadean eon (4.6 to 4.0 Gyr ago):

  • Named after Hades, the Greek world of the dead.

  • Meteor bombardment may have extinguished early life forms multiple times before microbial life was established.

• Evidence of microbial life includes:

  • Isotope ratios,

  • Stromatolites,

  • Microfossils.

• Earliest generally accepted microfossils date to 2.0 Gyr ago, including filamentous prokaryotes and colonial cyanobacteria.

17.3 Carbon Isotope Deletion Confirms Microfossils

• Banded Iron Formations (BIFs): An event in Earth's history showing the evolution of the first oxygenic phototrophs, specifically cyanobacteria that split water to form O2.

• Evidence of O2 in the biosphere arises from mineral oxidation states, particularly iron.

• Layers of iron oxides (e.g., Fe2O3) suggest alternating oxygen-rich and anoxic conditions.

• Banded iron is widespread and major sources of iron ore today.

• Fluctuating O2 levels occurred in the Archaean and early Proterozoic eons, potentially leading to the formation of the bands based on microbial oxygen consumption.

17.4 Proposed Timeline for the Origin and Evolution of Life

• Earth formed about 4.5 Gyr ago during the Hadean eon, primarily in a reducing environment until cyanobacteria increased atmospheric O2.

• Multicellular animals and plants emerged when O2 levels were adequate (around 0.6 Gyr ago).

  • Question marks indicate periods of uncertain evidence for specific life forms.

17.5 Forming the First Cells

• Key questions for models of early life formation include:

  • What environment did the first cells form in?

  • What metabolism did the first cells use to generate energy?

  • What was their hereditary material?

• Prebiotic soup: Suggests small organic molecules formed from simple reduced chemicals activated by lightning, leading to complex macromolecules capable of self-replication and membrane compartmentalization.

Early Oxidation-Reduction Reactions

• Early life forms gained energy from:

  • Oxidized minerals reacting with hydrogen gas.

  • Photoferrotrophy, where light excites an electron from Fe2+, oxidation of the ion to Fe3+, generating energy through electron transport.

17.6 The RNA World

• Prebiotic soup theory does not account for a biomolecule that encodes complex information, leading to the RNA world concept.

• In the RNA world model, RNA accomplished both informational and catalytic roles compared to today’s DNA and proteins.

  • Genome sequences reveal many catalytic and structural RNAs.

  • RNA forms and degrades with less energy than DNA.

  • Ribozymes exhibit enzymatic properties analogous to proteins.

• Early cells possibly consisted of RNA enzymes (ribozymes), which evolved to incorporate protein subunits for catalytic functions.

Unresolved Questions About Early Life

• Compelling geological and biochemical evidence suggests cyanobacteria-like organisms existed 2.5 to 3.7 Gyr ago, and anaerobic bacteria evolved at least as early.

• Outstanding questions include:

  • Temperature of early Earth?

  • Role of CH4 in the early atmosphere?

  • Actual source of Earth's first cells?

Evolution: Phylogeny and Gene Transfer

• Clades: Branching groups of related organisms, with each clade representing a monophyletic group sharing a common ancestor not shared with organisms outside of that clade.

• Phylogeny: The full description of the branching divergence of a species.

• Fundamental mechanisms of evolution include:

  • Random mutations as chromosomes replicate,

  • Natural selection and adaptation favoring organisms producing more offspring,

  • Reductive evolution involving loss or mutation of unselected DNA traits.

Molecular Clocks

• Temporal information from macromolecular sequences based on new random mutations with each DNA replication round.

• Reliable molecular clocks involve genes that encode components of transcription and translation.

  • Common genes used: 16S rRNA (bacteria), 18S rRNA (eukaryotes).

• Molecular clock application requires alignment of homologous sequences across divergent species or strains.

Phylogenetic Trees

• Divergence estimates derived from homologous sequences inform the creation of phylogenetic trees, indicating relative evolutionary divergence.

• Phylogenetic trees rely on complex mathematical analysis to plot the most probable tree.

• Common approaches:

  • Maximum parsimony: Best fit tree needing fewest mutations.

  • Maximum likelihood: Probability that a tree produced observed DNA sequences.

• Phylogenetic trees may be rooted or unrooted:

  • Rooted trees indicate common ancestor position.

17.7 Microbial Species and Taxonomy

• Eukaryotic species defined by interbreeding capability, whereas prokaryotes reproduce asexually.

• Debate exists over the definition of prokaryotic species and their classification/taxonomy.

• Advances in genome sequencing sought to provide consistent measures of microbial species but yielded puzzling results.

Working Definitions of a Species

• Microbiologists often accept three criteria:

  • SSU rRNA similarity ≥ 95% indicates same genus,

  • Average nucleotide identity (ANI) of orthologs ≥ 95%,

  • Shared ecotype for organisms with ≥ 95% identity.

• Pangenome:

  • Core genome: Genes possessed by all isolates.

  • Accessory genes: Found in some isolates.

  • Pangenomes can be open (infinite genes) or closed (finite genes), with open predominating in nature.

Classification and Nomenclature

• Taxonomy: Recognition and organization of distinct life forms.

  • Involves classification, nomenclature (naming), and identification of pure culture microbes.

• Classification creates a hierarchical taxa structure.

• New microorganisms are often labeled as emerging, unclassified, or candidate species during discovery.

Nongenetic Categories for Medicine and Ecology

• Genetic relatedness serves as a primary standard for classification across biology.

• Other practical categorization systems include:

  • Phenotypic categories (e.g., Gram-positive rods),

  • Ecological categories (e.g., photosynthetic bacteria),

  • Disease categories (e.g., pulmonary pathogens).

Naming a Species

• Accepted naming rules established by the International Committee on Systematics of Prokaryotes (ICSP).

• To establish a new species, a previously unknown isolate must be cultured and its genetic/phenotypic traits published, designated as “Candidatus.”

• Upon publication in the respective journal, the candidate species can transition to recognized species.

Evolution of Endosymbiosis and the Origin of Mitochondria and Chloroplasts

• Symbiosis: Intimate association between two unrelated species, can be mutualistic or parasitic.

• Symbiosis results in coevolution, showcasing parallel phylogeny.

• Endosymbiosis involves one partner growing within another's body, such as the human intestinal microbiome.

• Some human parasites carry bacterial endosymbionts that are essential for their growth, opening avenues for targeted antibiotic treatments.

Role of Mitochondria and Chloroplasts

• Lynn Margulis demonstrated that endosymbiosis led to the evolution of mitochondria from alphaproteobacteria and chloroplasts from cyanobacteria.

• The genomes of these organelles show extreme reduction compared to known endosymbiotic bacteria, retaining only essential genes like rRNA, tRNA, and genes crucial for respective cellular functions (respiration and photosynthesis).