Microbial Diversity

Tree of Life

Key organising principle in biology representing the evolutionary relationships among organisms.

Ernst Haeckel

discovered, described and named thousands of species and designed a tree of animals, plants, and protists.

Robert Whittaker

added unicellular organisms like cyanobacteria to the tree of life and categorised organisms based on their nutritional modes.

Carl Woese

defined archaea as the third domain of life through molecular phylogeny, identifying the universal ancestor using 16S ribosomal RNA.

Why was the study of microbial abundance and diversity not possible until recently?

Traditional taxonomy and systematics relied on morphology and biochemistry. However microbes are very small and often similar in appearance, and some are not possible to cultivate.

Phylogenetics

Science of studying evolutionary relationships by comparing gene sequences among different species.

Qualities of a phylogenetic marker gene

• orthologous

• present in all species being compared

• conserved but with observable differences

• slow and steady to evolve (purifying/negative selection → stabilising selection)

Orthologous

Genes descended from the same ancestral sequence, separated by speciation events, indicating vertical descent.

vertical descent

line of descent which occurs when all microbes arise as the result of parental fission

Why is whole genome sequencing becoming a more frequently used analysis technique?

WGS has become much cheaper and quicker since it was discovered.

Why is the 16S rRNA gene used in phylogenetic studies?

It’s highly conserved across all life forms, allowing universal PCR primers for gene amplification. It can be put through high throughput methods using next gen sequencing - amplicon sequencing/metagenomics.

What is the 16S rRNA gene?

RNA component of the 30S subunit of the ribosome. Recognises the Shine-Dalgano sequences of the promoter.

Metagenomics

Isolation of cells to extract DNA, which is then fragmented and sequenced into ‘raw reads’. These raw reads are aligned and annotated.

Tree of Life two domain model (Hug et al, 2016)

Ribosomal protein genes linked with the 16S rRNA gene across thousands of organisms → eukaryotes and archaea similar enough to be same ‘branch’, and bacteria dominate the tree of life.

LUCA

Last universal common ancestor, possessing universal genes seen in all organisms today, representing the root of the tree of life. May have been a single cell or a community of populations.

True ‘root’ of the tree of life

the chemistry and cells LUCA originated from - LUCA was NOT the first cell.

Life for the first 2 billion years of Earth

All microbes, initially with anoxic metabolisms (eg methanogenesis) due to the atmosphere of mainly nitrogen and carbon dioxide

When did anoxic phototrophs evolve?

3.5 billion years ago

When did oxygenic phototrophic microbes eg cyanobacteria evolve?

2.5 billion years ago

What did evolution of oxygenic phototrophic microbes allow to occur?

Oxygen dependent metabolisms developed, eventually forming multicellular life forms

How old is the earliest evidence of cellular life that’s been discovered so far?

3.8 to 3.9 million years old

What are the two main hypotheses for the emergence of viruses? (neither are widely accepted)

• genome reduction to the point of an obligate intracellular parasite

• genome escape - aggregations of genes that somehow escaped cellular regulation

viral genome structure

Suggested by bacteriophage genome based evidence to be ancient, from before bacteria and archaea split apart. The viral genome is mosaic - modules recombine and exchange.

estimated eukaryotic diversity on Earth

8.7 × 10⁶ species

prokaryotic diversity in 10g soil (bacterial and archaeal)

10¹⁰ cells, estimated 8.3 × 10⁶ species

bacterial growth form

eg cocci, bacilli, appendaged or ‘other’. Typically reflects the bacteria’s biology and lifestyle.

example bacilli

bacillus, coccobacillus and palisades

example cocci

streptococcus and staphylococcus

example ‘other’ bacteria

club rods, vibrio and helical

Genome

Full set of genes for an organism

structure of bacterial and archaeal genomes

typically a single circular DNA molecule but there’s exceptions such as linear or multiple chromosomes, and plasmids. Bacterial genome often haploid and genes often found in operons. Little non-coding DNA between genes.

first free-living organism to have its genome sequenced (1995)

Haemophilus influenzae

E.coli number of base pairs

4.4 million

E.coli number of genes

4300

E.coli coding density

1000 genes/Mbp

How long is the human genome?

6.2 Gbp

How many protein coding and non-protein coding genes do humans have?

20 to 25 thousand coding and about the same number non coding

Human coding density

10 genes/Mbp