Chapter 8Chapter 8

From Single-Celled From Single-CelledOrganisms to KingdomsOrganisms to Kingdoms

Figure CO: Tree© Carlos Caetano/ShutterStock,Inc.

Overview• Based on fossil record

– Abiogenesis produces the early replicating molecular systems ~4.0 – 3.5 Bya; details uncertain

– Prokaryotic cells arose 3.5 to 3.8 Bya.– By about two billion years later (2.5–2.8 Bya)

some had diversified into eukaryotic cells.

Figure 01A: Generalized prokaryotic

Microfossils• Microbial life has now been

found in the rocks from the Barberton Formation in South Africa, of 3.5 bybp

• The example shown here is in a rock that was emplaced as a glassy lava before crystallizing

• It is postulated that this life form actually "fed" on the rock material itself (now recrystallized into a basaltic rock type)

Microfossils • Microscopic views of these

filamentous microorganisms (Primaevifilum amoenum) recovered from rocks in Apex Formation in Western Australia dated to about 3.5 billion years of age

Reproduced from Schopf, J.W., Science 260 (1993): 640-646. Reprinted with permission from AAAS. Courtesy of J. William Schopf, Professor of Paleobiology & Director of IGPP CSEOL.

Figure 07A: Filamentous unicellular fossil

Figure 07B: Fossil

Biogeochemistry:Early Organisms' Contributions

• Original anaerobic conditions supported heterotrophs

• Later, some of the early organisms became photosynthetic Autotrophs

– Cyanobacteria (stromatolites) • Possibly due to a shortage of raw

materials for energy • Photosynthesis became their

adaptive advantage • Oxygen was a toxic byproduct to

which other organisms had to adapt

Figure 07C: Phase-contrast microphotograph of a filament

of cells of an extant cyanobacterium

Fossil Evidence for Dating Early Life

• Methane– Chemical evidence for the existence of

prokaryotic life more than 3.5 Bya provides clues to their likely metabolic pathways

• Stromatolites– Prokaryotes already had diversified 3.4

Bya, and existed in a structured, biological ecosystem

Fossil Evidence for Dating Early Life• Stromatolites in carbonate sediments

– Cyanobacteria or blue-green algae – Oldest are 3.4 - 3.5 bybp (Archean) – Abundant in rocks 2.8 - 3 bybp (Proterozoic)

• Algal filament fossils found in chert – 3.5 bybp at North Pole, western Australia

• Spheroidal bacterial structures (Monera) – Prokaryotic cells; cell division? – 3.0 - 3.1 bybp – Fig Tree Group, South Africa

Stromatolites

Figure 04C: 2-By-old fossils from theHelena Formation in Glacier National Park, Montana

© Chung Ooi Tan/ShutterStock, Inc.

Figure 04B: Cross-sections of the Namibian stromatolites

Figure 04A: Living stromatolites from Namibia, Africa

© Marli Miller/Visuals Unlimited

© Sinclair Stammers/Photo Researchers, Inc.

Figure 04D: Cross-sections of Fossil Stromatolites

© Sinclair Stammers/Photo Researchers, Inc.

Early Fossilized Cells/Unicellular Organisms

• Cyanobacteria and Stromatolites– Archean, from 3.8 to 2.5 Bya

Figure 06B: Record of stromatolite deposits and microbial fossils

Courtesy of J. William Schopf, Professor of Paleobiology & Director of IGPP CSEOL

Figure 06A: Record of stromatolite deposits and microbial fossils

Cyanobacteria

• The oldest known fossils are cyanobacteria from Archaean rocks of western Australia, dated 3.5 billion years old

• This may be somewhat surprising, since the oldest rocks are only a little older: 3.8 billion years old

• Cyanobacteria are among the easiest microfossils to recognize

Cyanobacteria

• Cyanobacteria were dominant for at least 2 billion years and some forms still exist today

• They produce large amounts of oxygen by photosynthesis (using sunlight to convert CO2 and H2O to simple sugar and free oxygen

• They played a key role in the transition of the Earth's atmosphere from reducing to a gradual buildup of oxygen

~2 BYBP ~850 mybpextant Anabaena sp.

The Tree of Life• All organisms, no matter how we name,

classify or arrange them on The Tree of Life, are bound together by four essential facts:– 1. They share a common inheritance– 2. Their past has been long enough for

inherited changes to accumulate– 3. The relationships among organisms are

the result of evolution– 4. Evolutionary processes explain how

organisms arose and how they were modified through time

Kingdoms of Organisms• Two Kingdoms

– Aristotle and through the Renaissance• Plantae (L. planta, plant) and Animalia (L.

anima, breath, life)

Kingdoms of Organisms• Two Kingdoms

– 18th Century• Linnaeus (1735) clarified the Two Kingdoms of Life, and

also recognized a third Kingdom - Lapideum (minerals)

Three Kingdoms of Organisms: 19th Century• Several of Darwin’s contemporaries

described Three Kingdoms of Life, adding protistans, including John Hogg (1800–1869), Sir Richard Owen (1804–1892), and Ernst Haeckel (1834-1919)– Haeckel made the most extensive classification– Kingdoms Plantae, Protista, and Animalia

Bacterial Classification• By the 1830s, bacteria were being

characterized by their shapes• By the late 1800s, Ernst Haeckel and

others used this cell morphological classification in their definition of the Monerans

• By the early 20th century, colony morphology was also used

Bacterial Classification

• Danish bacteriologist Hans Christian Joachim Gram (1853 - 1938) developed his Gram stain method (positive, negative, and later variable and uneven (Archae) types) for differentiating bacterial cell wall in 1884

Figure 01B: Generalized eukaryotic - animal

Figure 01C: Generalized eukaryotic - plant

Prokaryotes and Eukaryotes

Figure 01A: Generalized prokaryotic

Two Empires or Domains of Organisms: 20th Century

• Single-celled organisms (prokaryotes) and multicellular organisms (eukaryotes) had been recognized as structurally different for decades

• In 1925, Édouard Chatton (1883-1947) defined the terms Prokaryota and Eukaryota, though the terms had little impact on classification for decades

Two Empires &Four Kingdoms

• In 1938, Herbert F. Copeland (1902-1968) proposed a four-kingdom classification, moving the two prokaryotic groups, bacteria and "blue-green algae", into a separate Kingdom Monera

(1956)

Two Domains Became Five Kingdoms• Robert Harding Whittaker

(1920–1980) elevated the fungi to their own Kingdom in 1969

• Whittaker’s Five Kingdoms, one for prokaryotes and four (protists, fungi, plants and animals) for eukaryotes, did not require, but fit, the two domains

• Neither of the domains of prokaryotes and eukaryotes are monophyletic branches of the tree of life; they are polyphyletic Figure 02: Monophyletic and polyphyletic schemes

Five Kingdoms Became Three Domains• Carl Woese (1928 - 2012) defined Archae and

proposed the Three Domain classification of Life• Eubacteria (Bacteria) includes the major forms of

bacteria and the cyanobacteria, the latter being the earliest organisms known as fossils

• Archaea (Archaebacteria) are unicells with cell walls made of different molecules than those found in Eubacteria. Archaea often live under more rigorous environmental conditions, as in hot sulfur springs or extreme salt concentrations

• Eukarya (Eukaryota), the kingdom that includes some unicellular organisms (slime molds, ciliates, trypanosomes, and others) and the three groups of multicellular organisms: fungi, plants and animals

5 or 6 nested Kingdoms

Figure 03: Three Domains of Life, Eubacteria, Archaea and Eukarya

Protistans

Why Are Archaebacteria More Closely Related to Eukaryotes Than Bacteria?

Eukaryotic Traits• DNA replication machinery • Histone proteins and

nucleosome-like structures • transcription machinery

– RNA polymerase – Transcription factor II B (TFIIB) – TATA-binding protein (TBP)

• translation machinery – initiation factors – ribosomal proteins – elongation factors – poisoned by diphtheria toxin

(Eu)Bacterial Traits• Prokaryotic organization – no nucleus

or organelles • single large circular DNA genome with

no intronsand small DNA plasmids • operon control systems • rotary flagella• “bacterial” membrane transport

channels • common metabolic processes

– carbohydrate metabolism– ATP energy production – nitrogen-fixation – polysaccharide synthesis

Unique Archaebacterial Traits• cell wall chemistry – no peptidoglycan• membrane lipid chemistry - branched hydrocarbon chains (many also

containing rings within the hydrocarbon chains) attached to glycerol by ether linkages

• rRNA and aminoacyl-tRNA synthetases (AARS)• major nutrient metabolic pathways – non O2-evolving phototrophs,

lithotrophs drawing energy from inorganic compounds, and organotrophs drawing energy from organic compounds

• some Archaebacteria are “extremophiles”: anaerobes that tolerate high heat (thermophiles) or high salt concentrations (thermophiles) or extreme pH environments (alkaliphiles and acidophiles); while others inhabit more ordinary aquatic and terrestrial niches

• Never form spores• None known as parasites or pathogens

Diversity of ArchaebacteriaTwo Main Phyla

Recognized

Many Other Potential Archaean Phyla Under Study

Some Archaebacterian is the probable ancestor to the Eukaryotes

Archea—Methane Producers

• A motile archean that inhabits hot deep sea vents, uses hydrogen gas as a source of energy, and gives off methane

• Once thought to survive only in extreme environments, Archaebacteria are now known widely in nature in diverse habitats

Methanogens Today?

Globally, over 60% of total CH4 emissions come from human activities (industry, agriculture, and waste management activities)

Thomas Cavalier-Smith'sVarious Kingdoms

• Thomas Cavalier-Smith (1942 - ) has been tinkering with the classification for more than a decade and his taxa remain controversial

• By 1981, Cavalier-Smith had divided the domain Eukaryota into nine kingdoms

• By 1993, he reduced the total number of eukaryote kingdoms to six

• He also classified the domains Eubacteria and Archaebacteria as kingdoms, adding up to a total of eight kingdoms of life:– Plantae, Animalia, Protozoa, Fungi, Eubacteria,

Archaebacteria, Chromista, and Archezoa• We can be sure there will be more alternative

classifications in the future for the higher taxa

Five Kingdoms Became Three Domains

Thomas Cavalier-Smith, who has published extensively on the classification of protists, has recently proposed that the Neomura, the clade that groups together the Archaea and Eukarya, would have evolved from Bacteria, more precisely from Actinobacteria. His classification of 2004 treats the archaebacteria as part of a subkingdom of the Kingdom Bacteria, i.e., Cavalier-Smith rejects the three-domain system entirely.

Thomas Cavalier-Smith: Predation and Eukaryote Cell Origins: A Coevolutionary Perspective (2008)

• The last common ancestor of eukaryotes was a sexual phagotrophic protozoan with mitochondria, one or two centrioles and cilia.

• Conversion of bacteria ( = prokaryotes) into a eukaryote involved 60 major innovations. ∼

• Data are best explained by the intracellular coevolutionary theory, with three basic tenets:

• (1) the eukaryotic cytoskeleton and endomembrane system originated through cooperatively enabling the evolution of phagotrophy;

• (2) phagocytosis internalised DNA-membrane attachments, unavoidably disrupting bacterial division; recovery entailed the evolution of the nucleus and mitotic cycle;

• (3) the symbiogenetic origin of mitochondria immediately followed the perfection of phagotrophy and intracellular digestion, contributing greater energy efficiency and group II introns as precursors of spliceosomal introns.

• Eukaryotes plus their archaebacterial sisters form the clade Neomura.

Two Domains & Six KingdomsThomas Cavalier-Smith

Figure 05: Phylogenetic tree

Adapted from Sogin, M.L., Current Opinion Genet. Devel., 1 (1991): 457-463 and Wheelis, M.L., et al., Proc. Natl Acad. Sci USA 89 (1992): 2930-2934.

The Tree of Life in Your Text

Quite a different tree from those of Thomas Cavalier-Smith

Who is the Last Universal Common Ancestor?

Last Universal Common Ancestor (UCA)

• DNA is the hereditary material• DNA replication with helicases and DNA

synthetases• ribosome-based protein synthesis• several common metabolic pathways and ATP• phospholipid bilayer cell membranes• active transport across membranes

Prokaryote Phylogenies

THE KINGDOMS OF EUBACTERIA• PROTEOBACTERIAE• SPIROCHAETAE• OXYPHOTOBACTERIAE• SAPROSPIRAE• CHLOROFLEXAE• CHLOROSULFATAE• PIRELLAE• FIRMICUTAE• THERMOTOGAE• PHYLA OF UNCERTAIN STATUS

See the Science of Biodiversity web site for more details.

This division into 9 Kingdoms is based on structural differences in RNA

Diversity of Archea and Eubacteria

• FYI: Representative types of Archea and Eubacteria are indicated together with their characteristics

Horizontal Gene Transfer (HGT) and the Tree of Life

• Horizontal Gene Transfer (HGT) is effected by a virus or a small, circular DNA particle known as a plasmid that contains a foreign gene that can be transferred

• Between unicellular organisms– e.g., almost 20 percent of the E. coli genome can be

traced to HGT– overall, as much as one third of the genome of some

prokaryotic organisms has been acquired through HGT– HGT may create nearly as much diversity for prokaryotes

as sexual reproduction does for eukaryotes!

Horizontal Gene Transfer (HGT)

• To or between multicellular organisms– HGT appears most

prevalent among bdelloid rotifers, a group of asexually reproducing fresh-water invertebrates

– Less than 10 percent of eukaryotes acquired one or more protein families by HGT

Horizontal Gene Transfer (HGT)

• The main methods of HGT in prokaryotes are:

• Transformation – uptake of naked DNA

• Conjugation – transfer of plasmid DNA

• Transduction – transfer via viral infection

Horizontal Gene Transfer (HGT)

• This figure illustrates that DNA uptake does not guarantee successful HGT and that the organism which develops from HGT may be more or less fit than its predecessor

• The new phenotype may be inferior, neutral, or superior

Transformation

Horizontal Gene Transfer (HGT)

• Here a plasmid transfers genes to produce pili, adherence structures which can increase virulence

Conjugation

Horizontal Gene Transfer (HGT)

•Viral infection of donor cell•Phage replication and degradation of host DNA•Assembly of new phages particles•Release of phage•Infection of recipient•Legitimate recombination

Transduction

Horizontal Gene Transfer (HGT)

• The classic examples of evolutionarily significant HGT are the origins of mitochondria and chloroplasts from endosymbiosis

• Multiple transfers are hypothesized

Horizontal Gene Transfer of PIB-Type ATPases among Bacteria Isolated from Radionuclide- and Metal-Contaminated

Subsurface Soils

Applied and Environmental Microbiology, May 2006, p. 3111-3118, Vol. 72, No. 5

Robert J. Martinez, Yanling Wang, Melanie A. Raimondo, Jonna M. Coombs, Tamar Barkay, and Patricia A. Sobecky

Horizontal Gene Transfer (HGT)• Here a plasmid

transfers genes to a plant host which stimulate gall formation in the host

A Phylogenetic Tree of MutS2 Subfamily from Representative Species Showing Horizontal Gene Transfer Between Bacteria and Plants

Lin Z et al. Nucl. Acids Res. 2007;35:7591-7603© 2007 The Author(s)

MUTS2 is a locus for proteins involved in DNA mismatch repair

Horizontally Transferred Genes in Plant-Parasitic Nematodes: a High-Throughput Genomic Approach

Elizabeth H Scholl, Jeffrey L Thorne, James P McCarter and David Mck Bird• The HGT genes in this study coded for enzymes which bacteria and

parasitic nematodes can use to degrade plant cell wall cellulose

Genome Biology 2003, 4:R39

American Society for Microbiology Tree of Life (2009)

• Darwin once commented that all true classification is genealogical, but he could hardly have foreseen that among bacteria and archaea the tree of life includes horizontal gene transfer at apparently high rates

• Thus, successive generations may acquire genes from organisms residing on distant branches of the tree of life in addition to the genes vertically inherited from direct ancestors

• This is symbolized by the three domains of life (Bacteria, Archaea, and Eukarya) being connected by vertical (the strictly bifurcating tree) and horizontal gene transfer (the crisscrossing red lines)

More on The Tree of Life

• The Tree of Life: Tangled Roots and Sexy ShootsTracing the genetic pathway from the first Eukaryotes to Homo sapiensChris King 6 Jan 2011

• This is an excellent summary article and includes discussion of horizontal gene transfer

Evolution of Eukaryotes

• Archaebacteria acquired organelles by endosymbiosis

• Early Eukaryotes had cell walls• Early Eukaryotes were aerobic

heterotrophs• Early Eukaryotes developed

sexual reproduction• Horizontal Gene Transfer

became less important in Eukaryote lineages, perhaps because of the alternative of sexual recombination

Chapter 8

End

Biogeochemistry: Early Organisms' Contributions

– Eukaryotic (modern differentiated) cells • Likely formed by symbiosis and incorporation

– Chloroplasts – Mitochondria

• More mobile and adaptable• We’ll meet them in Chapter 9

• The Biosphere is a major force in the Earth's C, P, N, Si, O geochemical cycles – Photosynthesis/respiration

• O2 + CH2O ↔ CO2 + H2O

The Five Kingdoms

Three Domains of Life

• The evolutionary relationships between the three domains of life are shown

• The root of the tree (prokaryote common ancestor) is within the bacteria (eubacteria) domain; archea (archaebacteria) and eukaryotes (eukarya) diverged later

Archaebacterial Character Traits• Archaebacteria are distinguished from

the Eubacteria (and from the Eukaryotes) in a variety of ways– Cell wall chemistry– Membrane lipid chemistry– Major nutrient metabolic pathways– Ribosomes and RNA polymerases– DNA associated with histones, like the

Eukaryotes