Marine Bacteria and Archaea

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Metabolic diversity

• Organisms have two fundamental nutritional needs: • 1. Obtaining carbon in a form that can be used to

synthesize fatty acids, proteins, DNA, and RNA

• Autotrophs get their carbon from CO2

• Heterotrophs get carbon from organic sources vs

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Metabolic diversity

• Organisms have two fundamental nutritional needs: • 2. Acquiring chemical energy in the form of ATP

• Phototrophs: energy from light

• Lithotrophs (or Chemotrophs): energy from inorganic chemicals

such as H2S, ammonia NH3, methane CH4

• Organotrophs: energy from organic sources, such as sugars

Metabolic diversity

Category Energy source Carbon source Hydrogen or electron source

Examples

Photolithoautotrophy Light CO2 Inorganic Cyanobacteria, purple sulfur bacteria

Photoorganoautotrophy

Light Organic compounds Organic compounds or H2

Purple non-sulfur bacteria, aerobic, anoxygenic bacteria, archaea (?)

Chemolithoautotrphy Inorganic CO2

Inorganic Sulfur-oxidizing bacteria, nitrifying bacteria, archaea

Chemoorganoautotrophy

Organic compounds

Organic compounds

Organic compounds Wide range of bacteria and archaea

Mixotrophy (combination of lithoautotrophy and organoheterotrophy)

Organic compounds

Organic compounds

Inorganic Sulfur-oxidizing bacteria

Evolution of life

Prebiotic chemistry

Precellular life

Early cellular life

LUCA Evolutionary diversification

Biological building blocks Amino acids Nucleosides Sugars

4.3-3.8 bya 3.8-3.7 bya

RNA world

Protein synthesis

DNA Lipid bilayers

Divergence of Bacteria and Archaea

Catalytic RNA Self-replicating RNA

RNA – templated translation

Replication Transcription

Cellular compartments Early cells likely had high rates of HGT

Components of DNA replication, transcription, and translation all in place

Submarine mounds and their possible link to the origin of life. Model of the interior of a hydrothermal mound with hypothesized transitions from prebiotic chemistry to cellular life depicted

Differences between Archaea, Bacteria and Eukaryotes

Characteristic Bacteria Archaea Eukaryotes

Cell type Prokaryotic Prokaryotic Eukaryotic

Histones No histones Have proteins similar to histones

Have histones

Introns No introns Some introns Most contain introns

Ribosome size 70S ribosomes 70S ribosomes 80S ribosomes

Cell wall composition

Peptidoglycan Made of protein (lack peptidoglycan) plasma membrane

Not always present Plants: cellulose Fungi: Chitin

Cell membrane composition

Ester linked lipids with D-Glycerol (straight chain)

Ester linked lipids with L-Glycerol (branch chain)

Ester linked lipids with proteinf (straight chain)

Themes: Growth & reproduction by fission

A. Bacterium before DNA replication. Bacterial chromosome is attached to the plasma membrane.

B. DNA replication starts. It proceeds in two directions

C. The new copy of DNA is attached at a membrane site near the parent DNA molecule.

D. New membrane grows between the two attachment sites.

E. Deposits of new membrane and new wall material extend down into the cytoplasm.

F. The ongoing deposition of membrane and wall material divides the cell in two.

Themes: conjugation

A. A conjugation tube forms between a donor and a recipient cell. An enzyme has nicked the donor’s plasmid.

B. DNA replication starts on the nicked plasmid. The displaced DNA strand moves through the tube and enters the recipient cell.

C. In the recipient cell, replication starts on the transferred DNA.

D. The cells separate from each other; the plasmids circularize.

nicked plasmid conjugation tube

Themes: Morphological diversity

• Many have flagella for swimming and pili for clinging to surfaces

• Typical Shapes:

Pili

Cocci Bacilli Spirochetes

Marine bacteria

Planktonic Bacteria and Archaea

• Relatively few major clades Bold = ubiquitous in seawater, others are specialized

Roseobacter • 25% marine bacteria • Plankton • Sediments • Microbial mats • Sea ice • Association with animals • Important in carbon and sulfur cycles

Marine bacterial phenotypes

• Anoxygenic • Eg Purple phototrophs • Do not evolve Oxygen during photosynthesis • Bacteriochlorophyll as photosynthetic pigment • Many in shallow marine sediments

Rhodospirillum

CO2 + H2S + H2O = (CH2O) + S + H2O

Marine bacterial phenotypes

• Oxygenic Photosynthesis • Cyanobacteria

• Ancestors – evolution of oxygen • Chlorophyll a and accessory photosynthetic pigments • “Blue green algae” but many “red orange” • Very diverse habitats, including extreme temperatures and hypersaline environments • Plankton, sea ice, shallow sediments, microbial mats • Many carry out nitrogen fixation • Only recently grouped together (16S sequencing)

Synechococcus Prochlorococcus

Account for between 15-40% of carbon input to ocean food webs

• Nitrifying bacteria • Major role in nitrogen cycling, especially shallow coastal sediments, and

beneath upwelling areas • Nitrosomonas and Nitrosococcus oxidize ammonia to nitrate

• Chemolithoautotrophs

• Nitrosobacter, Nitrobacter, and Nitrococcus oxidize nitrite to nitrate • Usually chemolithoautotrophs also mixotrophs

Marine bacterial phenotypes

• Chemolithotrophs

Beggiatoa Aerobe in top few mm of marine sediments Uses reduced sulfur compounds

Thioploca Multicellular filamentous bacteria Upwelling Anoxic reduction of H2S and reduction nitrogen Auto- or mixo-trphic

Thiomargarita namibiensis Largest known bacteria, filaments with common mucus sheath Upwelling Oxidizes sulfite using nitrate

Marine Archaea

Archaea

• Methanogens • Anaerobic process carried out only by Euryarchaeota (major clade) • Large amount of methane is produced in marine sediments, but

disappears before oxygen zone, where methane would be reduced • Sulfate-reducing bacteria oxidize methane using sulfur

Methanosarcina Desulfococcus

Archaea • Extreme Thermophiles

Thermococcus Anaerobic chemoorganotroph, optimum growth at 800C

Pyrococcus Anaerobic chemoorganotroph Optimal growth at 100oC

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Archaea

• Halophiles • Grow in concentrations

greater than 9% NaCl