The Marine Microbiome: The Biological Pump That Cools the Planet
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🫁
50-80%
of oxygen from ocean microbes
🌊
30%
50-80%
of oxygen from ocean microbes
30%
of human CO2 absorbed by ocean
10B
viruses per liter of seawater
The ocean has absorbed 30% of all human CO2 emissions since industrialization. A continuous shower of Marine Snow transports billions of tonnes of carbon to the deep sea. The biological pump is the planet's primary climate regulator — and microplastics are disrupting it.
This article synthesizes what the peer-reviewed evidence actually shows — what is proven, what is still uncertain, and what you can do.
24 sources23 peer-reviewed papers + 1 scientific background source. Uncertainty stated clearly.
The biological carbon pump is the ocean's mechanism for transferring carbon from the atmosphere to the deep sea. It begins with photosynthesis: phytoplankton at the surface fix CO2 into organic matter. When they die, they aggregate into Marine Snow, a continuous shower of particles sinking from the sunlit zone to the abyss.
This is not a gentle drift. Marine Snow carries billions of tonnes of carbon below 1,000 meters annually, where it is locked away for centuries to millennia. Without this pump, atmospheric CO2 would be twice current levels.
Azam and colleagues discovered that bacteria process 50%% of all marine primary production through the Microbial Loop. Dissolved organic matter released by living and dying phytoplankton is consumed by bacteria, which are eaten by protists, which recycle nutrients back into the food web.
This loop is invisible but fundamental. It determines whether carbon stays at the surface (where it can re-enter the atmosphere) or gets packaged into particles dense enough to sink. The microbial loop is the decision point of the entire carbon pump.
Every liter of seawater contains 10 billion viruses. They kill 20-40%% of marine bacteria every single day, bursting cells and releasing their contents back into the dissolved organic matter pool. This viral shunt redirects carbon from higher trophic levels back into the microbial loop.
Far from being destructive, the viral shunt maintains microbial diversity (no species can dominate), recycles nutrients to the surface, and drives the evolution of microbial resistance. Marine viruses are ecosystem engineers, not pathogens.
Diatoms are large (2-200 micrometers), glass-shelled, and dominant in nutrient-rich coastal waters. They sink fast and drive efficient carbon export. Prochlorococcus is tiny (0.5-1 micrometer), the most abundant photosynthesizer on Earth, and dominant in the nutrient-poor open ocean. It sinks slowly.
Together they produce approximately 40%% of Earth's oxygen. But they contribute to the carbon pump through fundamentally different mechanisms. The balance between diatom-driven export and cyanobacteria-driven recycling determines the ocean's carbon sequestration efficiency.
The ocean twilight zone (200-1000 meters) is where the biological pump's fate is decided. BGC-Argo autonomous floats (Nature Geoscience, 2021) revealed that this zone processes far more carbon than previously estimated. Zooplankton migration, microbial respiration, and particle fragmentation all occur here.
Most Marine Snow is consumed or dissolved before reaching the deep ocean floor. Only 1-2%% of surface production survives to 1,000 meters. But that fraction is enormous at planetary scale, and it is this fraction that determines long-term climate.
Microplastics interfere with Marine Snow formation by altering particle aggregation and sinking rates. Research suggests this could reduce the biological pump's efficiency by 10-25%%. Additionally, microplastics provide surfaces for bacterial colonization that redirect carbon processing away from sinking and toward surface recycling.
The plastics we dump on land end up disrupting the deepest carbon cycle on the planet.
Since industrialization, the ocean has absorbed approximately 525 billion tonnes of anthropogenic CO2, roughly 30%% of all human emissions. This massive buffering effect has slowed climate change. But the cost is ocean acidification: as CO2 dissolves, it forms carbonic acid, lowering pH and threatening the calcifying organisms (corals, coccolithophores, pteropods) that are integral to the biological pump.
The Tara Oceans expedition collected 35,000 samples across all ocean basins, discovering millions of unknown microbial genes and revealing that plankton community networks, not just abundance, predict carbon export efficiency (Guidi et al., Nature 2016).
BGC-Argo floats are now providing continuous, autonomous measurements of ocean biogeochemistry at depth. Together, these programs are rewriting our understanding of how the ocean breathes.
Not all Marine Snow sinks at the same speed. Armstrong et al. (2002) proved that mineral ballast — calcium carbonate from coccolithophore shells and silica from diatom frustules — increases sinking speed 10-100x. Particulate organic carbon flux correlates with mineral flux with R-squared of 0.8.
Without these heavy mineral shells, most organic carbon would be consumed by bacteria before reaching the deep ocean. Diatoms and coccolithophores are not just oxygen producers — they are the gravitational engines of the biological pump.
Jiao et al. (2010) in Nature Reviews Microbiology defined the Microbial Carbon Pump (MCP) — a process distinct from the biological pump. Microbes transform labile dissolved organic matter into Refractory DOC (RDOC) that persists for 4,000-6,000 years.
The RDOC reservoir holds 662 petagramsof carbon — the largest pool of reduced carbon on Earth. This 'invisible' carbon is chemically 'unreadable' to most organisms. The MCP may exceed the biological pump's sequestration in the vast oligotrophic ocean gyres.
Mitra et al. (2014) established that 50%% of marine protists are mixotrophic — combining photosynthesis and phagotrophy. They photosynthesize when light is available and eat bacteria when it is not. This dual metabolism dominates oligotrophic gyres.
Mixotrophy fundamentally changes carbon cycling models. Traditional models assume separate 'producers' and 'consumers.' In reality, the same organism does both, creating a metabolic flexibility that stabilizes the surface ocean food web and buffers it against nutrient limitation.
Without the biological pump, atmospheric CO2 would be approximately twice current levels — returning the climate to a state not seen in 50 million years. The pump fails when surface warming increases stratification, trapping nutrients below the thermocline and starving phytoplankton.
Behrenfeld et al. (2006) in Nature showed this is already happening: ocean primary productivity has declined since 1999. The plankton that produce every second breath are being starved by the very warming they help buffer against. This feedback loop is the most consequential planetary risk that most people have never heard of.
Rivers carry nutrients from the soil that fuel coastal blooms. Those blooms produce DMS that seeds clouds in the atmosphere. Ocean oxygen feeds the holobiont with every breath. The ethology of marine cooperation — cleaner fish markets, whale nutrient pumps — is the biological market theory of the deep.
The mesopelagic twilight zone is the most critical filter in the global carbon cycle. Every night, trillions of zooplankton migrate to the surface to feed and return to depth at dawn — the diel vertical migration, the largest movement of biomass on Earth. By feeding at the surface and excreting at depth, zooplankton inject carbon directly into the deep ocean, bypassing slow gravitational sinking.
Salps create the ocean's high-speed rail. Their membrane-bound fecal pellets sink at over 1,000 meters per day — so fast that bacteria cannot consume them in transit. This fast export is a critical climate buffer that ensures carbon reaches the seafloor for millennial storage.
The Martin Curve describes how organic carbon flux decreases with depth: F(z) = F(euphotic) x (z/z_euphotic) to the power of -b, where b is approximately 0.86 globally. This means 90%% of surface carbon is consumed by bacteria before reaching 1,000 meters. Only about 1%% reaches the seafloor.
Even a small shift in the b-value has massive climate consequences. If warming increases b (more efficient bacterial recycling), less carbon reaches the deep and more CO2 stays in the atmosphere. The plankton that start the cascade determine whether the pump works or fails.
Not all Marine Snow sinks at the same speed. Armstrong et al. (2002) proved that mineral ballast from coccolithophore calcium carbonate shells and diatom silica frustules increases sinking speed 10-100x. Heavy minerals drag organic carbon down faster than bacteria can consume it.
Dust from the air microbiome — Saharan and Gobi desert particles — provides additional lithogenic ballast. In years with high dust deposition, the Martin Curve b-value drops significantly because carbon races past the hungry twilight zone bacteria. The biological pump is not just biology. It is biogeochemistry — minerals and microbes working together.
Robison et al. (2005) in Science discovered that giant larvaceans build mucus houses up to 1 meter across that filter 10-40%% of upper ocean carbon per day. When clogged, the larvacean discards the house. The abandoned structure sinks at 800-1,000 meters per day — 10-100 times faster than individual particle settling. Henschke et al. (2019) quantified 100 million tons of carbon transported annually by these organisms.
Coccolithophores build calcium carbonate shells. The chemical reaction releases CO2: Ca2+ + 2HCO3- produces CaCO3 + CO2 + H2O. For every mole of carbon buried as carbonate, one mole is released as CO2. Yet their shells are the most efficient ballast mineral, increasing sinking speed to 100-200 meters per day.
The CO2 released during calcification is a short-term cost. The increased transport efficiency is a long-term gain. Ocean acidification weakens coccolithophore calcification — thinner, more fragile shells that reduce ballast efficiency at the same time warming increases stratification. Models disagree on whether the net feedback increases or decreases sequestration.
Johnson et al. (2006) revealed that Prochlorococcus is a family of distinct ecotypes. High-Light adapted (HL) ecotypes dominate the surface. Low-Light adapted (LL) ecotypes occupy 100-200 meters. Genomes range 1.6-2.4 megabases — the smallest of any photosynthetic organism. HL ecotypes cannot survive below 50 meters. LL ecotypes are outcompeted at the surface. This vertical partitioning maximizes total water column productivity.
Whether climate change will shift ecotype distributions is uncertain. Warming may expand HL habitat while increased stratification reduces nutrient supply to LL depths. The plankton-oxygen link depends on these dynamics.
Sullivan et al. (2017) defined the dual role of ocean viruses. The viral shunt bursts bacterial cells, releasing their carbon as dissolved organic matter that stays at the surface — feeding the microbial loop instead of sinking. The viral shuttle does the opposite: infected cell aggregates become heavy and sink, exporting carbon to depth.
Which pathway dominates determines whether carbon stays in the atmosphere or reaches the deep ocean. Viruses kill 20-40%% of marine bacteria daily, but this is not destruction. It prevents any single species from monopolizing nutrients. Viral lysis maintains the microbial diversity that keeps the biological pump functioning across all ocean provinces.
Ocean photosynthesizers — [phytoplankton, cyanobacteria, and diatoms](/articles/plankton-microbiome-oxygen-ocean-health) — generate 50-80% of Earth's oxygen. The tiny cyanobacterium Prochlorococcus alone produces more oxygen than all terrestrial forests combined.
Source: Science, 1998 →Since industrialization, the ocean has captured approximately 525 billion tonnes of anthropogenic CO2. This massive buffering effect has slowed climate change — but at the cost of ocean acidification that threatens the very microbes doing the absorbing.
Source: Science, 2004 →A continuous shower of dead plankton, fecal pellets, and organic particles falls from the sunlit surface to the deep ocean floor. This 'Marine Snow' transports billions of tonnes of carbon below 1000m, where it is locked away for centuries to millennia.
The biological carbon pump operates differently in coastal and open ocean environments. Coastal waters are nutrient-rich upwelling zones dominated by diatoms that sink fast. The open ocean is a nutrient desert dominated by Prochlorococcus — tiny but globally significant. Both contribute equally to planetary oxygen.
| Metric | Coastal / Shelf | Open Ocean | Significance |
|---|---|---|---|
| Primary Production | High (200–500 gC/m²/yr) | Low (~50 gC/m²/yr) | Coastal upwelling zones are ocean hotspots. |
| Carbon Export | Rapid burial in sediments | Deep export via Marine Snow | Different mechanisms, same result: long-term sequestration. |
| Microbial Loop | Intense nutrient recycling | Nutrient scavenging (oligotrophic) | Bacteria recycle 50% of all marine primary production. |
Net ocean photosynthesis — roughly equal to all terrestrial primary production combined.
Source: Field et al. Science (1998), IUCN Ocean Deoxygenation Report (2019), Sabine et al. Science (2004).
NASA EXPORTS MISSION / BGC-ARGO GLOBAL ARRAY
Giant larvaceans build massive mucus “houses” that filter particles and sink to the seafloor in hours rather than weeks. Marine Snow — the continuous rain of dead plankton, fecal pellets, and organic detritus — is the primary vehicle for deep-ocean carbon storage. Microplastics interfere with this aggregation, potentially reducing pump efficiency by 10-25%.
80% of ocean plastic starts on land. Cutting single-use plastics at source prevents microplastic interference with the biological carbon pump.
Organizations like the Tara Ocean Foundation are mapping the marine microbiome to understand how it responds to climate change. Fund the science.
Support Tara Ocean Foundation →Watch the MBARI deep-sea footage of Marine Snow — understanding the invisible carbon conveyor changes how you think about the ocean.
MPAs protect not just fish and coral but the microbial ecosystems that regulate global carbon and oxygen. Support policies that expand ocean protection.
Explore marine protected areas →Scientific exploration of the ocean to understand and protect marine ecosystems through the world's largest marine microbiome research program
The Tara Oceans expedition collected 35,000+ samples across all ocean basins, generating the most comprehensive marine microbiome dataset in history
Developing innovative technology and methods for studying the deep ocean
Pioneered deep-sea ROV technology that first filmed Marine Snow in detail — transforming our understanding of the biological carbon pump
Advocating for science-based solutions to ocean challenges including pollution, climate, and biodiversity loss
Organized the International Coastal Cleanup for 35+ years — removing 350+ million pounds of trash from waterways
MBARI deep-sea footage, TEDx talks, and the science of Marine Snow — how the ocean sequesters carbon and why it matters for every breath you take.
Ask a question and we'll find the exact moment in these videos where it's answered.
23 peer-reviewed papers + 1 scientific background source
Science (Tara Oceans), 2020
The Tara Oceans expedition mapped microbial diversity across all ocean basins — the largest coordinated study of marine microbes ever conducted, revealing millions of unknown genes
This article cites 23 peer-reviewed sources from 24 total references. Every factual claim links to its source.
Last reviewed: March 2026. If you find an error or outdated source, contact us at corrections@express.love.
Express Love Science Team (2026). The Marine Microbiome: The Biological Pump That Cools the Planet. Express Love Planetary Health. Retrieved from https://express.love/articles/marine-microbiome-biological-pump-carbon
Indexed via ScholarlyArticle Schema.org metadata. 247 peer-reviewed sources across 10 flagships.
Next in the Circle of Life
The Pathway
How what we put on land ends up poisoning the ocean's oxygen factory
Marine viruses kill 20-40% of ocean bacteria every single day. This 'viral shunt' recycles nutrients back to the surface, prevents any one species from dominating, and drives the evolution of microbial resistance — a hidden engine of ocean biodiversity.
Source: Nature Reviews Microbiology, 2007 →The 'Microbial Loop' — discovered in 2007 — revealed that bacteria consume half of everything phytoplankton produce. This dissolved organic matter recycling is invisible but fundamentally controls ocean nutrient availability.
Source: Nature Reviews Microbiology, 2007 →The ocean has lost 77 billion tonnes of oxygen in 60 years due to warming and stratification. As oxygen drops, microbial communities shift from aerobic to anaerobic metabolism — changing what the ocean produces and what it absorbs.
Source: IUCN, 2019 →These microscopic glass-shelled algae generate more oxygen than all the world's rainforests combined. Diatoms thrive in nutrient-rich coastal and polar waters and are the foundation of most marine food webs.
Source: Nature Geoscience, 2019 →Plastic particles interfere with the formation and sinking of Marine Snow, potentially short-circuiting the ocean's primary mechanism for long-term carbon storage. What we dump on land ends up disrupting the deep ocean's climate regulation.
Source: Science of the Total Environment, 2022 →The largest marine microbiome study ever conducted found that most ocean microbial life was previously unknown to science. The functional potential of these organisms — from novel antibiotics to carbon-processing enzymes — is barely explored.
Source: Science (Tara Oceans), 2020 →Microbial community shifts in the ocean threaten the stability of global biogeochemical cycles. [River pollution](/articles/water-pollution-from-rivers-to-oceans) and [coral reef collapse](/articles/coral-reef-symbiosis-rainforest-of-the-sea) compound the damage — unlike forest loss, microbial biodiversity loss is invisible and potentially more consequential.
Source: Annual Review of Marine Science, 2021 →| Dominant Photosynthesizer |
| Diatoms (large, fast-sinking) |
| Prochlorococcus (tiny, slow-sinking) |
| Diatom-driven export is faster; cyanobacteria dominate volume. |
| Oxygen Contribution | Diatom-heavy (~20% of global O2) | Prochlorococcus-dominant (~20%) | Together: every second breath you take. |
Source: Azam & Malfatti (2007), Boyd et al. (2019). Wikidata: Q885233 (Biological pump), Q213271 (Marine snow).
Source: Boyd et al. Nature (2019), BGC-Argo (Nature Geoscience 2021), Guidi et al. Nature (2016). POC = Particulate Organic Carbon.
Advancing ocean research through innovative technology and open data sharing
Operates the research vessel Falkor (too) providing free ship time to scientists — discovered 50+ new deep-sea species
Ocean & Science
The most detailed educational breakdown of Marine Snow and the Carbonate Compensation Depth — how the biological pump sequesters carbon and what happens when it reaches the deep ocean floor.
Watch on YouTube →
The world's leading deep-sea research institute shares 4K footage of the organisms that drive the biological carbon pump — filmed by remotely operated vehicles at depths humans cannot reach.
Watch on YouTube →
Pulitzer-nominated journalist Tony Bartelme connects plankton science to human survival — why the invisible organisms producing every second breath are under threat.
Comprehensive 18-minute deep dive into the marine carbon cycle — biological pump, solubility pump, and why the ocean is the planet's primary climate regulator.
NASA's PACE satellite mission tracking carbon from terrestrial fires to ocean phytoplankton blooms — showing how the carbon cycle connects land and sea in real time.
Stunning 4K footage from Schmidt Ocean's research vessel Falkor — ROV exploration of deep-sea microbial communities and the environments where the biological pump delivers carbon.
The Tara Ocean Foundation — who collected 35,000 samples across all ocean basins — explains why marine microorganisms are the invisible foundation of planetary services.
How BGC-Argo autonomous floats are revealing that the ocean twilight zone processes far more carbon than previously estimated — filling the biggest gap in global carbon models.
Nature Reviews Microbiology, 2007
The seminal 'Microbial Loop' paper establishing that bacteria process 50% of marine primary production — rewriting our understanding of ocean energy flow
Nature Microbiology, 2017
How warming, acidification, and deoxygenation are reshaping marine microbial communities — with cascading effects on the biological pump
Science, 1998
The foundational study establishing that marine photosynthesis produces 50-80% of Earth's oxygen — ocean microbes, not trees, are the planet's primary lung
Nature, 2019
Documented the complexity of biological carbon pump responses and the critical role of marine snow in long-term carbon storage beneath 1000m depth
Science, 2015
Comprehensive overview establishing that ocean microbes drive Earth's biogeochemical cycles — nitrogen fixation, carbon cycling, and sulfur processing all depend on marine bacteria
Science, 2015
Challenged the simplified view of ocean carbon cycling — showing that viral lysis, microbial mixotrophy, and particle-associated communities are as important as photosynthesis
Nature Reviews Microbiology, 2007
Every liter of seawater contains 10 billion viruses that kill 20-40% of marine bacteria daily — this 'viral shunt' recycles nutrients and shapes microbial evolution
IUCN, 2019
Ocean oxygen content has declined 2% since 1960 — a loss of 77 billion tonnes of oxygen that is restructuring marine ecosystems from the inside out
Science of the Total Environment, 2022
Microplastics interfere with marine snow formation and microbial carbon export — potentially reducing the efficiency of the ocean's primary carbon sink by 10-25%
Science, 2004
The ocean has absorbed approximately 30% of all human-produced CO2 since industrialization — 525 billion tonnes — buffering climate change at the cost of acidification
Trends in Microbiology, 2014
How microbial communities in the deep ocean process sinking organic matter — the final stage of the biological pump where carbon is locked away for centuries
Nature Geoscience, 2019
Diatoms alone produce ~20% of Earth's oxygen — more than all the world's rainforests combined. These glass-shelled microbes are the unsung heroes of planetary respiration
Annual Review of Marine Science, 2021
Marine biodiversity is declining faster than terrestrial biodiversity, with microbial community shifts threatening the stability of global biogeochemical cycles
Nature, 2016
Guidi et al. used Tara Oceans data to show that specific plankton community networks — not just abundance — predict carbon export efficiency. The species interactions determine how much carbon reaches the deep ocean.
Annual Review of Marine Science, 2023
Updated framework for how dissolved organic matter flows through the marine microbial food web — showing that microbial processing determines whether carbon stays at the surface or sinks to depth
Nature Geoscience, 2021
BGC-Argo autonomous floats revealed that the ocean twilight zone (200-1000m) processes far more carbon than previously estimated — a missing piece of the global carbon budget
NOAA, 2024
NOAA's authoritative framework for understanding ocean systems — the standard reference for educators and policymakers on marine science fundamentals
Nature Reviews Microbiology, 2017
Sullivan et al. defined the dual role of marine viruses: the 'viral shunt' (lysing cells, releasing DOC that stays at the surface) vs the 'viral shuttle' (infected cell aggregates that sink, exporting carbon to depth). Viruses control which path carbon takes
PNAS, 2020
Buesseler et al. quantified Carbon Export Efficiency (e-ratio) in the twilight zone — explaining why some blooms sequester carbon efficiently while others are recycled at the surface. The missing piece of the global carbon budget
Deep-Sea Research, 2002
Armstrong et al. proved that mineral ballast (CaCO3 and SiO2 from diatom/coccolithophore shells) increases sinking speed 10-100x — POC flux correlates with mineral flux (R²=0.8). Heavy shells are the carbon elevator
Nature Reviews Microbiology, 2010
Jiao et al. defined the Microbial Carbon Pump (MCP) — distinct from the Biological Pump. Microbes convert labile DOC into Refractory DOC that persists 4,000-6,000 years. The RDOC reservoir holds 662 Pg C — the largest reduced carbon pool on Earth
Science, 2005
Robison et al. discovered that giant larvacean mucus houses filter 10-40% of upper ocean carbon per day and sink at 800-1000 m/day — a high-speed carbon elevator that bypasses the slow Marine Snow pathway entirely
Biogeosciences, 2014
Mitra et al. established that 50% of marine protists are mixotrophic — combining photosynthesis and phagotrophy. This dual metabolism dominates oligotrophic gyres and fundamentally changes carbon cycling models