The Microbiome of the Ocean & Beaches

The Microbiome of the Ocean & Beaches

And the livin’ is easy.”
-George Gershwin


Summer feels different. Even if it’s the same temperature outside, the longer summer days provide more vitamin D and bring joy. When summer rolls around, our activities shift. We plant gardens and enjoy the sweet fragrance of flowers. Most of us trade our jeans and sneakers for shorts and flip flops. And in summer, when record heat chases us out of our homes, we go to the beach. Whether the beach you seek out is on a lake, river, or ocean, getting in the water and walking on the beach affects your microbiome. Microbes are everywhere – including in the water.

The Rich Microbial Ecosystems of Freshwater Lakes & Rivers

Freshwater lakes have microbes in the soil, the air, and the plants in and around the water. The lakes are ecosystems and microbes contribute to all the pathways that regulate carbon, nitrogen, and sulfur composition. The microbiome of freshwater lakes around the world have been investigated in countries like India, China, Japan, Switzerland, and the US.1 Researchers have reported an enormous number of novel bacteria belonging to different classes and families. When we swim in these lakes, we pick up some of the microbes, diversifying our microbes.

Lakes and rivers are a relatively small amount of the water on earth – less than 0.02%. However, their relatively small footprint doesn’t mean they aren’t important. Freshwater lakes and rivers are the most easily accessed waters for humans and animals.2 And the microbiome of the lake may reflect this. Not only does the microbiome come from the plants and soil in and around the lake, it comes from the wildlife that uses the water: the fish and birds.

The Highly Organized Microbial “Factories” in our Oceans

The ocean has bacterial communities that are different than those in lakes. Even though we might think of the ocean as a big pool that isn’t well organized, that isn’t true. Bacteria, viruses, fungi, marine archaea, and protists change and are predictable over seasons, ocean depth, and organic matter features.3 Furthermore, researchers can show that each microbe has its own domain and a microbe will stay 200 body lengths from another microbe.3 Think of that as people laying on a beach – 200 body lengths between people? That’s a lot of space.

Sunny days impact the ocean microbiome in distinct ways. The sun reaches certain ocean depths, and it follows that the microbes that require sunlight will be found in these depths. These sun-seeking microbes undergo photosynthesis and produce oxygen.3 In places that the sun doesn’t reach, microbes undergo chemosynthesis. Seasons determine the amount of sunlight available and impact the flow of currents. Thus, microbes shift seasonally. Additionally, if there are beaches or rocks or cliffs, different microbes will be associated with each of these features.

As the primary producers of photosynthesis and chemosynthesis, the ocean produces half of the oxygen we consume. That’s a lot of oxygen. If the ocean temperature changes with climate change, it affects which microbes can be present and what they can do. For example, researchers think that the changing temperatures of the ocean favor smaller phytoplankton over larger plankton - and that’s going to change the microbiome of the ocean and reduce the amount of CO2 that can be absorbed.4

Ocean Microbes and Us

The ocean is refreshing on a hot summer day. Swimming in the ocean has an interesting effect on a person’s microbiome. To study the effects of swimming in the ocean on the microbiome, researchers examined nine people, six women and three men.5 In order to make sure it was only the ocean having an effect, the researchers made sure these happy beach goers weren’t wearing sunscreen, hadn’t bathed in 12 hours (because soap and scrubbing can wash away normal skin microbes), and hadn’t taken antibiotics in 6 months. When they sampled the microbiome (from the back of the calf) of the beach-lovers before they went in the ocean, each of the people had their own unique skin microbiome. After swimming in the ocean, the skin microbiomes of the nine people looked similar to each other. Their skin was covered in microbes from the ocean. Specifically, 17.2% of the microbes on the skin were from the ocean.5

The swimming-acquired microbes hung out on the skin for several hours, and didn't start to decline until six hours post swim.5 By 24 hours, almost all of the swimming microbes were gone and the normal microbiome was back. There was one microbe that tended to stick around a little longer – Vibrio, a potentially pathogenic bacterium. Vibrio is not one of the major bacteria in the ocean, yet five of the nine swimmers had Vibrio on their skin after swimming.5 One theory is that when swimming washes off normal skin microbes, it makes skin susceptible to picking up pathogenic bacteria like Vibrio. None of the swimmers became sick with Vibrio as this microbe is usually only dangerous when it’s ingested.

There is a special class of swimmers who swallow a lot of water – surfers. It’s estimated that surfers swallow up to 10 times as much ocean water as other swimmers.6 A study done in the UK on surfers and bodyboarders showed that they are three times more likely to have antibiotic resistant E. coli in their gut than non-surfers due to sewage in the water.6 Antibiotic resistance in the ocean has become a major concern. In fact, in 2018, the UN Environment Assembly recognized the spread of antibiotic resistance as one of the world’s greatest emerging environmental concerns.7 In the meantime, researchers are studying surfer microbiomes on five continents.8

“Bacteria, viruses, fungi, marine archaea, and protists change and are predictable over seasons, ocean depth, and organic matter features..”

Microbes in the Sand

What if getting wet isn’t your preference? What if you prefer to just lay on the beach? The beach has its own microbiome, and just like water, freshwater beaches and ocean beaches have different microbes.9 Microbes keep beaches clean by digesting and decomposing organic matter. While there may be different types of microbes on different beaches, their roles are similar. They clean the sand of organic matter and use the sunlight to make energy. As long as you don’t have cuts in your skin, your skin protects you from most pathogenic bacteria that might be in the sand. Surfers who have cuts in their skin often report getting staph infections from the beach.9 Staying off the beach for 72 hours if you have breaks in your skin should prevent infections.

Whether your way to cool off involves freshwater or seawater, whether you’re on a ‘surfin’ safari’ or ‘nightswimming’, rest assured that the microbes that are joining you intend to make the world a better place. They produce oxygen, reduce carbon dioxide, and clean up the messes we leave behind. When they join our normal microbiome, it’s temporary (24 hours or less) and they provide a little extra diversity. Some researchers are even looking for new medicines from the water-dwelling microbes.10

Learn More


  1. Microbiomes of freshwater lake ecosystems. J Microbiol Exp. 2018;Volume 6(Issue 6). doi:10.15406/jmen.2018.06.00223
  2. Schlesinger WH, Bernhardt ES. Chapter 8 - Inland Waters. In: Schlesinger WH, Bernhardt ES, eds. Biogeochemistry (Fourth Edition). Academic Press; 2020:293-360. doi:10.1016/B978-0-12-814608-8.00008-6
  3. Moran MA. The global ocean microbiome. Science. 2015;350(6266):aac8455. doi:10.1126/science.aac8455
  4. Phytoplankton Dynamics Under Climate Change | Frontiers Research Topic. Accessed July 22, 2022.
  5. Nielsen MC, Jiang SC. Alterations in the human skin microbiome after ocean water exposure. Mar Pollut Bull. 2019;145:595-603. doi:10.1016/j.marpolbul.2019.06.047
  6. Leonard AFC, Zhang L, Balfour AJ, et al. Exposure to and colonisation by antibiotic-resistant E. coli in UK coastal water users: Environmental surveillance, exposure assessment, and epidemiological study (Beach Bum Survey). Environ Int. 2018;114:326-333. doi:10.1016/j.envint.2017.11.003
  7. Environment UN. Antimicrobial resistance: a global threat. UNEP - UN Environment Programme. Published September 17, 2020. Accessed July 23, 2022.
  8. Surfing the World for Microbes. Accessed July 23, 2022.
  9. Sandy Beach Microbes: the Good, the Bad, and the Flesh-eating. Accessed July 23, 2022.
  10. Paoli L, Ruscheweyh HJ, Forneris CC, et al. Biosynthetic potential of the global ocean microbiome. Nature. 2022;607(7917):111-118. doi:10.1038/s41586-022-04862-3