The origins of life: microbial evolution

Question 1

Studying early life

Answer 1

There is evidence for ancient life on earth from about 3.8 BYA

Studying the evolution of life over this timescale is extremely challenging.

Evidence has come from the fields of geology, chemistry, and biology

These different fields complement each other and together allow us to make many inferences and the sequence of events in early life.

Question 2

The evolution of the biosphere: The Hadean Sea before life

Answer 2

Once the earth cooled enough for liquid oceans to form life began to develop

Question 3

Geochemical evidence for life

Answer 3

Some of the earth’s oldest rocks are present in the Greenstone Belt east of Hudson Bay, Canada.

They have been dated to about 3.8 BY based on radioactive decay of uranium to lead in zircon particles within the rocks.

There may be microfossils already present within these rocks.

The earliest undisputed physical evidence for early life was found in the Greenstone Belt near Barberton, S Africa, dated around 3.24 BY.

Cell-sized microfossils were found in this ancient sedimentary rock.

Their carbon isotope ratio (δ13 C) was biased relative to the atmosphere indicative of cellular metabolism.

Structures in these rocks appear to be early cellular life, isotope analysis revealed carbon bias so likely formed by ancient microbes

Question 4

Universal genetic markers (found in all life)

Answer 4

The discovery that some RNA molecules were involved in catalytic activity (ribosomes) led to the RNA world hypothesis that the first life was RNA-based (Joyce 2002). Proteins and DNA were recruited soon after.

These ribosomal RNA molecules consist of highly conserved domains interspersed with more variable regions and allow identification of taxa at different taxonomic resolutions

16S rRNA is the most popular universal marker as it is reasonably long and informative with highly conserved sequences at the 3’ and 5’ ends to design universal primers.

Question 5

Building universal phylogenetic trees

Answer 5

A statistical approach needed to take into account the amount of genetic mutations that have occurred

Building a universal phylogenetic trees is especially challenging due to comparing organisms that have diverged deep in evolutionary time.

Difficulties in aligning highly divergent sequences

Sequence differences stop increasingly linearly with evolutionary time

Phylogenetic reconstruction needs models that can account for multiple base substitutions at a single site and changes in mutation rate over long periods of time (e.g. Jukes and Cantor model)

Question 6

Lateral gene transfer complicates the sequence of events

Answer 6

Trees assume vertical gene transfer but horizontal gene transfer does occur in archaea,bacteria and eucaria turning the tree into ‘spaghetti’

Lateral gene transfer via plasmids is a feature of prokaryote evolution

Evolution with LGT is more of a network than a tree

The evolutionary origin of metabolomic novelty becomes difficult to trace

Question 7

The three domains

Answer 7

Ribosomal RNA studies split the previous Prokarya:Eukarya dichotomy in the tree of life and showed that all cellular life belongs to three domains: Bacteria, Archaea, and Eukarya.

Question 8

LUCA – last universal common ancestor

Answer 8

Who was LUCA?

The characteristics of the last universal common ancestor can be inferred as the minimal shared set of attributes at the tree of life’s first branch.

The tree of life’s first branch currently splits Bacteria and Archaea.

LUCA probably had 500 to 1000 genes close to the theoretical minimum necessary to maintain a functional cell

The tree of life’s first branch currently splits Bacteria and Archaea so LUCA probably had more in common with these groups than the later group Eucaryotes

We assume LUCA is unicellular as are the first two groups

Cannot confirm if LUCA was auto or heterotrophic from this data

Question 9

Chemical processes in the first microbes

Answer 9

Before molecular phylogenetic methods, microbial evolution was studied in terms of chemical processes and their sequential evolution.

Atmospheric oxygen is a byproduct of life, therefore the earliest life must have been anaerobic.

Autotrophs such as photosynthetic cyanobacteria already show complex physiology so earlier life was probably chemotrophic.

We assume first life was anaerobic – before life there was very little free oxygen in the atmosphere

Question 10

Autotrophic vs. Heterotrophic origins

Answer 10

The heterotrophic hypothesis posits that the first life sustained itself by fermenting a prebiotic organic soup (e.g. Miller-Urey 1953 experiment)

(achieved by heating/cooling natural chemicals)

The autotrophic hypothesis posits that the first life was driven by pyrite synthesis, a kind of reverse tricarboxylic acid cycle driven towards reduced carbon compounds starting with the synthesis of pyrite (FeS2) from FeS (Wachtershauser 1988)

(energy generation used to fix CO2)

The geochemical events at hydrothermal vents can produce the conditions (H2, pH gradients) for simple autrophy

(Sousa and Martin 2014) (plausible as hydrothermal vents produce conditions for bio processes)

Question 11

Possible Thermophilic Origins of life

Answer 11

Thermal vents are:
- oases of life in the deep ocean
- life with high temp. tolerance
- anaerobic autotrophic bacteria

Potential thermophillic origins
- high pressures at depth prevents water boiling off
- at this temp fewer enzymes are required for metabolism
- fossil evidence suggests hydrothermal vents in the distant past

Hydrothermal vents today support rich communities of microbial thermophiles (Brazelton et al. 2006), the upper limits for life being about 121 C (Kashefi and Lovley 2003)

Biologically relevant spontaneous chemical reactions proceed faster above 100 C, potentially allowing the gradual evolution of enzymes that accelerate the rates of these reactions at lower temperatures (Wolfenden 2011)

Geochemical evidence suggests there were thriving microbial communities present at hydrothermal vents as far back as 3.3 BYA

Brazelton et al. 2006 Appl Environ Microbiol 72: 6257
Kashefi and Lovley 2003. Science 301: 934
Wolfenden 2011. Annu Rev Biochem 80: 645
Westall et al. Geology doi: 10.1130/G36646.1

Question 12

Early microbial pathways

Answer 12

(see diagram in notes)

Archaea and bacteria each evolve anaerobic chemotrophic electron transport pathways producing methane and acetate, respectively.

What is the most basic shared metabolic pathway?
Archaea main output methane
Prokaryotes main output acetate

Question 13

The evolution of the biosphere:
The Archaean Methanogenic Era

Answer 13

Gave rise to new metabolic pathways
- Novel anaerobic metabolomic pathways evolve to utilise these outputs accompanied by lateral gene transfer (LGT) between groups
- Photosynthesis evolves that outputs oxygen
- Aerobic metabolomics pathways evolve with oxygen as the terminal electron acceptor

^ Martin and Sousa 2016 Cold Spring Harb Perspect Biol 8:a018127

Question 14

Evolution of microbial metabolism

Answer 14

Enzymes evolved that were capable of using sunlight for Photosynth producing O2

Resulting in oxygen availability for aerobic respiration

Question 15

Fossil evidence of photosynthesis

Answer 15

Filamentous fossil reefs
stromatolites – bacterial mass of cyanobacteria

Question 16

The evolution of the biosphere:
The great oxidation effect
(life takes advantage of oxygen as a new resource)

Answer 16

Geochemical analyses of ancient rocks indicate that the atmosphere became oxygenated between 2.3 to 2.5 BYA e.g. rust formed on iron in sedimentary rock

Aerobic respiration also provides up to 6 times more ATP per glucose than anaerobic respiration.

Aerobic respiration is more energy rich producing 6x more energy

Also O2 is toxic to early anaerobic life so beneficial to adapt to use it

Question 17

Origins of eukarya

Answer 17

The oxidation event is the beginning of the rise of eukaryotes (multicellular organisms)

What triggered this complexity?
- better energy source (aerobic resp)
- endosymbiosis gave rise to mitochondria in eukaryotes

Life began to increase in complexity around this time, particularly with the rise and diversification of Eukarya.

However, increasing atmospheric oxygen alone cannot explain why other aerobic prokaryotes did not become similarly complex.

The resolution of the ribosomal tree of life has improved sufficiently to conclude that Eukarya branch is within the Archaea (e.g. Williams and Embley 2014). The tree of life is better described as a two domain structure.

This means the ancestor of Eukarya was an Archeaon that acquired a free-living Prokaryote mitochondrion ancestor through endosymbiosis.

Williams and Embley 2014. Genome Biol Evol 6: 474

Question 18

Complex life

Answer 18

Investing extra spare energy from aerobic resp to increase complexity - proteins and enzymes

Protein synthesis consumes 75% of a cell’s energy budget versus 3% for DNA synthesis.

Mitochondria provide the host cell with 4-5 orders of magnitude more energy per gene allowing the evolution of expensive proteins underlying new eukaryotic traits.

Question 19

Life gets more complex

Answer 19

Multiple endosymbiosis events have occurred to give rise to Eukaryotes

The origins of Eukarya are complex and difficult to decipher because of multiple rounds of ancient endosymbiosis leading to multiple different classes of Eukarya (Maier et al. 2013)

• no endosymbiosis = 1 set of hydrogenosomes or ribosomes
• 1 x endosymbiosis = 2 sets of ribosomes (mitochondria)
• 2 x endosymbiosis = 3 sets of ribosomes (mitochondria + chloroplasts)
• 3 x endsymbiosis = 4 sets of ribosomes (some groups of algae)

Question 20

Social microbes

Answer 20

Some microbes face selective pressures for cooperation and division of labor that lead to sociality.

Selective pressures that can be addressed by sociality include: shelter, foraging, reproduction, and dispersal

Sociality means that individual cells don’t need to do everything at once

Question 21

Microbial communication

Answer 21

Cooperating cells communicate via secreted chemicals and physical contact.

At its simplest, quorum sensing involves converting the concentration of a secreted chemical into a local cell density signal.

For example, Vibrio fischeri, a bioluminescent bacterium inhabiting the light organs of some fish and squid use secreted N-acyl-L homoserine as a signal of optimize cell density.
Bob-tail octopus symbiosis with fluorescent vibrio for vision and signalling. Bacteria must regulate reproduction to stay at ideal density and not negatively affect the octopus

Ruby 1996.Annu. Rev. Microbiol. 50: 591

Question 22

Social microbes examples

Answer 22

Biofilms:
Biofilms develop into complex three dimensional structures bound together by a secreted extracellular polymer matrix. Differential gene expression occurs in different regions indicating the emergence of specialism.
Secreting structural components ‘biofilms’ into the environment providing shelter and bioengineering surrounding environment, altruistic behaviour of individual cells observed sacrificing themselves on their behalf.

Cytoplasmic male sterility in mitochondria:
mitochondria in male tissues sacrifice themselves by suppressing male function to promote female function and vertical transmission of their kin.

Clumping of bacteria forming 3d structures differentiating into reproductive structures – not all individuals get to reproduce
- Myxobacteria and Dictyostelium form multicellular fruiting bodies that generate tough spores under stressful conditions. Only some cells develop into spores. The rest form stalk structures or even purposefully lyse to provide nutrients to their neighbours.

Question 23

Evolution of the biosphere: Eukarya and multicellularity

Answer 23

Early multicellularity

Ancient multicellular fossils have similar modern counterparts (on a physical level)
e.g. fossils of Bangiophyta pubescens (~1.2 BYA)
are similar to present day Polysiphonia brodiaei
(Butterfield 2000. Paleobiology 26: 386)

Multicellularity can evolve quickly under artificial selection
e.g. unicellular C hlamydomonas reinhardtii evolves a
clumping phenotype after about 315 generations of
selection
(Ratcliff et al 2013 Nature communications 4: 2742)

Question 24

Lecture summary

Answer 24

Studying the ancient past is difficult but combined evidence from multiple scientific fields helps us build plausible scenarios.

The geochemical properties of ancient rocks can provide clues about when and where life was present.

Biology itself contains traces of its past evolutionary history that can be uncovered by studying the highly conserved sequences of essential genes such as the ribosomal subunits.

These studies provide clues about LUCA such as its closest extant relatives and the minimum number of genes for life as we know it.

Current thinking is that earliest life was autotrophic and thermophilic

Biological complexity evolved over time

Oxidative era shows the evolution of Eukarya

The first life was probably autotrophic and thermophilic – archaeal methanogens and bacterial sulphur reducers.

Metabolic complexity increased with the help of lateral gene transfer and photosynthetic autotrophs arose.

Atmospheric oxygen levels subsequently increased until respiration via oxidation reduction arose (the great oxidative event).

The great oxidative event created the opportunity for more efficient energy redox chains to evolve.

These adaptations spread through endosymbiosis events leading to the origin of eukarya, with efficient mitochondria for oxidative reduction.

Some microbes developed more and more elaborate social interactions to better find shelter, forage, reproduce, and disperse, eventually becoming permanent multicellular associations.