Microbio Phylogeny and Diversity

LUCA

Last Universal Common Ancestor; population of early cells from which Bacteria and Archaea diverged

Early Earth atmosphere

Anoxic; primitive metabolism was anaerobic and likely chemolithotrophic (autotrophic)

Carbon and energy source of primitive cells

Carbon from CO2; energy from H2, likely generated by H2S reacting with FeS or by UV light

Phototrophs

Use light energy to oxidize molecules and synthesize complex organic molecules from CO2

Role of Cyanobacteria in early Earth

Earliest oxygen-producing organisms (oxygenic phototrophs); O2 was a waste product, shifting the biosphere from anoxic to oxic

Ozone shield

Conversion of O2 to O3 forms a shield that absorbs UV radiation; allowed organisms to colonize terrestrial habitats instead of only oceans or subsurface

Why UV radiation matters

It damages DNA and can be lethal to cells

Endosymbiosis

Well-supported hypothesis for the origin of eukaryotic cells; mitochondria and chloroplasts arose from symbiotic prokaryotes living within another cell

Consequences of O2 for evolution

Ozone layer formation (UV barrier), evolution of organelle-containing eukaryotes, and new aerobic pathways yielding more energy than anaerobic ones

Mutation

Change in the nucleotide sequence of a genome; caused by replication errors, UV, and other factors; can be neutral, deleterious, or beneficial

Adaptive mutation

A mutation that improves fitness, increasing an organism's survival

Other genetic changes besides mutation

Gene duplication, horizontal gene transfer, and gene loss

Evolution (definition)

A change in allele frequencies in a population over time; results in descent with modification

Allele

Alternative versions of a given gene; arise from mutation and recombination

Recombination

Segments of DNA are broken and rejoined to create new combinations of genetic material

Selection

Defined by fitness (ability to produce offspring); can act on deleterious or beneficial mutations

Genetic drift

Random process that changes gene frequencies over time; produces evolution in the absence of natural selection, simply due to chance

Phylogeny

The evolutionary history of a group of organisms; inferred indirectly from nucleotide sequence data

Molecular clock (chronometer)

Genes or proteins used to measure evolutionary change (the rate at which a locus accumulates mutations)

Assumptions of molecular clocks

Nucleotide changes occur at a constant rate, are generally neutral, and are random; these are not completely valid assumptions

SSU rRNA

Small-subunit ribosomal RNA genes; the most widely used molecular clocks; found in all domains of life

16S rRNA

The SSU rRNA found in prokaryotes and in mitochondrial and chloroplast organelles

18S rRNA

The SSU rRNA found in eukaryotes

Why SSU rRNA is a good molecular clock

Functionally constant, sufficiently conserved (changes slowly), and of sufficient length

Limitation of SSU rRNA

Poor at distinguishing closely related species because it does not change rapidly enough (intragenic)

Carl Woese

Scientist associated with SSU rRNA gene analysis for phylogenetics

Steps of comparative rRNA sequencing

Amplify the gene encoding SSU rRNA, sequence the amplified gene, and analyze the sequence relative to other sequences

First step in sequence analysis

Aligning the sequence of interest with homologous (orthologous) genes from other strains or species

Phylogenetic tree

A graphic illustration of the relationships among sequences; composed of nodes and branches

Branches of a tree

Define the order of descent and ancestry of the nodes

Branch length

Represents the number of changes that have occurred along that branch

Universal phylogenetic tree

Based on SSU rRNA genes; a genealogy of all life on Earth (Bacteria, Archaea, Eukarya) rooted at LUCA

Application of SSU rRNA PCR to communities

Amplify, sort, sequence, and analyze SSU rRNA genes from a community to reveal who is there and the diversity present

16S rRNA as gold standard

Serves as the gold standard for identifying and describing new species

Threshold for a new species

16S rRNA gene sequence differs by more than 3 percent from any named strain

Threshold for a new genus

16S rRNA gene sequence differs by more than 5 percent from any named strain

Why a multi-gene approach is used

The 16S gene lacks divergence, limiting discrimination between bacteria at the species level

Example of multigene analysis

16S rRNA plus gyrB and luxABFE gave clear resolution of 3 Photobacterium species where 16S alone was poor

Whole-genome sequence analysis

Increasingly common; compares genome structure (size, chromosome number, GC ratio), gene content, and gene order

Phylogenetic diversity

Evolutionary relationships between organisms; diversity of phyla, genera, and species; most commonly defined by rRNA phylogeny

Functional diversity

Form and function related to physiology and ecology; organisms with shared traits or genes often share physiological characteristics and ecological roles

Three reasons functional traits appear in different species

Gene loss, convergent evolution, and horizontal gene transfer

Gene loss

A trait present in a common ancestor is lost

Convergent evolution

A trait evolves independently in two or more lineages and is not encoded by homologous genes

Horizontal gene transfer (of traits)

Homologous genes coding for a trait are exchanged between distantly related lineages

Physiological diversity

Functions and activities in terms of metabolism and biochemistry

Ecological diversity

Relationships between organisms and their environment

Morphological diversity

Relationships based on outward appearance; shape and structures often carry ecological significance

First phototrophs

Anoxygenic phototrophs that do not generate O2; arose when Earth was anoxic; originated within Bacteria

Electron donors of anoxygenic phototrophs

H2, Fe2+, or H2S instead of water

Carbon use by phototrophs

Most phototrophs are also autotrophs

Phototroph reaction centers

Type I (FeS) and type II (quinone or Q-type); Cyanobacteria have both, anoxygenic phototrophs have only one

Cyanobacteria key genera

Prochlorococcus, Crocosphaera, Synechococcus, Trichodesmium, Oscillatoria, Anabaena

Cyanobacteria overview

Oxygenic phototrophic Bacteria; first oxygen-evolving phototrophs; morphologically and ecologically diverse; unicellular or filamentous; 0.5 to 100 micrometers

Five morphological groups of Cyanobacteria

Chroococcales, Pleurocapsales, Oscillatoriales, Nostocales, Stigonematales

Chroococcales

Unicellular, divide by binary fission; includes prochlorophytes

Pleurocapsales

Unicellular, divide by multiple fission (colonial)

Oscillatoriales

Filamentous and nonheterocystous

Nostocales

Filamentous, divide on a single axis, can differentiate

Stigonematales

Filamentous, divide in multiple planes, forming branching filaments

Order of Prochlorococcus

Chroococcales

Order of Oscillatoria

Oscillatoriales

Order of Trichodesmium

Oscillatoriales

Order of Anabaena

Nostocales

Cyanobacteria morphology vs phylogeny

Pleurocapsales, Nostocales, and Stigonematales form coherent groups; Chroococcales and Oscillatoriales are dispersed

Cyanobacteria physiology

Oxygenic with both FeS and Q-type photosystems; fix CO2 by the Calvin cycle; many fix N2; most make their own vitamins

Cyanobacteria day and night metabolism

Harvest light and fix CO2 by day; generate energy by fermentation or aerobic respiration of storage products such as glycogen at night

Cyanobacteria metabolic flexibility

Some perform photoheterotrophy in light; some switch to anoxygenic photosynthesis using H2S as electron donor

Thylakoids

Specialized membrane systems that increase light harvesting; site of photosynthesis in cyanobacteria

Cyanobacteria cell wall

Contains peptidoglycan

Cyanobacteria pigments

Chlorophyll a and phycobilins (accessory pigments)

Cyanobacteria motility

Many show gliding motility; most show phototaxis; gas vesicles regulate buoyancy for optimal light position

Sheaths

Mucilaginous envelopes that bind groups of cells or filaments together

Hormogonia

Short motile filaments that break off to facilitate dispersal under stress

Akinetes

Resting structures with thickened outer walls that protect from darkness, desiccation, or cold

Cyanophycin

A nitrogen storage product

Heterocysts

Thick-walled cells along or at the ends of filaments providing an anoxic environment for nitrogen fixation; lack photosystem II and cannot fix CO2; exchange materials with adjacent cells

Why heterocysts are needed

Nitrogenase is oxygen-sensitive, so fixation cannot occur during oxygenic photosynthesis

Cyanobacteria importance in oceans

Synechococcus and Prochlorococcus are the most abundant ocean phototrophs, contributing about 80 percent of marine photosynthesis and 35 percent of all Earth's photosynthesis

Cyanobacterial nitrogen fixation

The dominant input of new nitrogen in oceans

Cyanobacteria ecology

Tolerant of extremes (hot springs, saline lakes, desert soils); can be the phototrophic partner in lichens; produce neurotoxins, toxic blooms, and geosmin (earthy smell)

Proteobacteria

The largest and most diverse phylum of Bacteria; all Gram-negative; most metabolically and morphologically diverse

Six classes of Proteobacteria

Alpha, Beta, Delta, Gamma, Epsilon, and Zeta

Purple phototrophic bacteria

Carry out anoxygenic photosynthesis (no O2); contain bacteriochlorophylls and carotenoids; found in illuminated anoxic zones where H2S is present

Purple sulfur bacteria

Gammaproteobacteria; use H2S as electron donor, oxidizing sulfide to elemental sulfur (S0) and then to sulfate; found in anoxic lake zones and sulfur springs

Purple non-sulfur bacteria

Mostly photoheterotrophic (light as energy, organic compounds as carbon); alpha or beta proteobacteria; most metabolically versatile; can grow aerobically in the dark; make carotenoids; e.g. Rhodospirillum and Rhodobacter

Nitrifying bacteria

Grow chemolithotrophically on reduced inorganic nitrogen; most are obligate aerobes; widespread in soil and water; vital in wastewater treatment

Nitrification

Oxidation of ammonia to nitrate, carried out as two reactions by different groups of bacteria

Ammonia oxidizers

Bacteria such as Nitrosococcus (gammaproteobacteria)

Nitrite oxidizers

Bacteria such as Nitrobacter (alphaproteobacteria)

Sulfur-oxidizing bacteria

Grow chemolithotrophically on reduced sulfur compounds (H2S, S0, S2O3 2-); can generate sulfuric acid; include neutrophiles and acidophiles

Thiobacillus

Best-studied sulfur oxidizer; betaproteobacteria; rod-shaped

Beggiatoa

Gammaproteobacteria; filamentous gliding bacteria found in H2S-rich habitats such as sulfur springs and hydrothermal vents

Hydrogen-oxidizing bacteria

Grow autotrophically with H2 as electron donor and O2 as acceptor (aerobic); use hydrogenase; some facultative; e.g. Ralstonia, Pseudomonas, Paracoccus

Myxobacteria

Microbial predators; key genus Myxococcus; most complex behavior among bacteria; life cycle forms multicellular fruiting bodies

Myxobacteria vegetative cells

Nonflagellated Gram-negative rods that glide and obtain nutrients by lysing other bacteria; excrete slime trails

Myxobacteria life cycle

Swarm self-organizes; when nutrients are exhausted, cells aggregate into mounds (chemotaxis or quorum sensing) and differentiate into fruiting bodies containing myxospores

Myxospores

Specialized resistant cells found in fruiting bodies

Bioluminescent genera

Vibrio, Aliivibrio, and Photobacterium; also a few Shewanella (marine) and Photorhabdus (terrestrial)

Bioluminescence ecology

Mostly marine; some colonize light organs of fish and squid for signaling, avoiding predators, and attracting prey