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Marine microbes and ocean deoxygenation

J. Cameron Thrash, Ph.D.

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What are marine microbes?

Sieburth et al., Limnol & Oceanog, 1978

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Size in perspective

via James Tyrwhitt-Drake, University of Victoria Advanced Microscopy Facility 

https://youtu.be/h0xTKxbIElU

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Despite their smallness, some marine microbes can be seen from space

https://eoimages.gsfc.nasa.gov/images/imagerecords/44000/44073/natlantic_tmo_2010142_lrg.jpg

http://blacksea-education.ru/SEM.htm

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Which is appropriate given their numbers

  • Each mL of seawater can contain 104-107 bacteria + archaea1,2
  • By comparison, there are now ~7x109 humans on earth
  • Estimated stars in the visible universe3: 1024
  • Estimated bacteria + archaea in the world’s oceans4,5: 1029

107 = 10,000,000

7 x 109 = 7,000,000,000

1024 = 1,000,000,000,000,000,000,000,000

One hundred thousand times more than the number of stars

1024 = 100,000,000,000,000,000,000,000,000,000

  • And there are 10x more viruses!

Sources: 1- Aristegui et al., L&O, 2009; 2- National Research Council 1999; 3- SPACE.com; 4- Whitman et al., PNAS, 1998; 5- Bar-On et al., PNAS, 2018

Copley, Nature, 2002

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Marine microbes also dominate ocean biomass

Modified from Hatton et al. Science Advances, 2021

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But they are not one type of thing- microbes are incredibly diverse

Hug et al., Nat Microbiol, 2016

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Why else do microbes matter? Oxygen

O2

Photosynthesis

O2 &

Organic

Carbon

Respiration

CO2

CO2

The vast majority of photosynthesis and respiration is carried out by microorganisms

Photosynthesis creates oxygen, respiration consumes oxygen

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Oxygen deficient zones: open ocean and coastal hypoxia

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The global oxygen cycle

Petsch, Treat on Geochem, 2014

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How does oxygen get into seawater?

  • Equilibration with the atmosphere (dissolution)
  • In situ production
  • Transport and mixing with other water (advection)

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How much oxygen can you put in seawater?

Dissolved oxygen (ml/L, or ppm) solubility (maximum expected concentration) in waters of different salinity (parts per thousand). Seawater typically has a salinity of 35 parts per thousand, whereas fresh water is near 0 parts per thousand. Source: Michael Arthur, Penn State

https://serc.carleton.edu/integrate/teaching_materials/water_science_society/student_materials/649

�

Canfield et al., Advances In Marine Biology Vol 48, Chp 6, 2005

Original eq. from Garcia & Gordon, Limnol & Oceanog, 1992

From Wright et al., Nat Rev Microbiol, 2012

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Oxygen dynamics: sea surface ventilation

Petsch, Treat on Geochem, 2014

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Oxygen dynamics: in situ production

Luimstra et al., Photosynth Res, 2018

O2 production by Synechocystis sp. PCC 6803

(a Cyanobacteria)

Experimental setup

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The deep ocean is oxygenated

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The deep ocean is oxygenated

Petsch, Treat on Geochem, 2014

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The deep ocean usually contains “normal” oxygen minima

Petsch, Treat on Geochem, 2014

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How does oxygen get removed from seawater?

  • Respiration (almost entirely microbial)
    • Dependent upon nutrient and energy sources
    • Also requires lack of ventilation

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Oxygen dynamics: removal via respiration

https://www.genome.jp/kegg-bin/show_pathway?map00190

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Oxygen depletion in marine systems

O2 removal > O2 replenishment

Breitburg et al., Science, 2018

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Coastal hypoxia

Freshwater input

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Coastal hypoxia

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Coastal hypoxia

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Extent of nGOM “Dead zone” hypoxia

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Extent of nGOM “Dead zone” hypoxia

~ Size of New Jersey

2025 Hypoxia Forecast, Turner & Rabalais

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Open ocean oxygen minimum zones are expanding

Stramma et al. Science 2008

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And coastal hypoxia is emerging in the Southern California Bight

Booth et al. Limnol & Oceanog 2014

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We’re trying to understand which microbes remove oxygen in coastal hypoxia, and how, to improve our predictive capabilities

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How do we do the science?

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Our lab’s approach to marine microbiology

100,000 – 10,000,000 cells/ml

Activities

Axenic culture

Genomes, transcriptomes,

metabolomes, etc.

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Getting there: research vessels

R/V Pelican

R/V Atlantic Explorer

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Getting samples from the ocean: CTDs

Conductivity, temperature, depth

(fluorescence, dissolved oxygen, pH, etc.)

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Getting samples from the ocean: CTDs

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Ship-based laboratories

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Tools of the trade

Flow cytometer – cell counts

Laminar flow hood – sterile area for setting up incubations

Sea surface incubators – keeping experiments at ocean temperature

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Tools of the trade

Initiating incubations

Prepping samples and filtering

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Science workflow for our hypoxia project

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Flow cytometry

By Kierano - Own work, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=22102570

Highly accurate

Necessary for:

  • Small cells
  • Low cell density

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Flow cytometry

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Example data from the cruises

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Respiration measurements - optodes

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Example data

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Questions?