Category Archives: Microorganisms

What is this green jelly slime in my garden?

The Question: Three days ago I noticed this green jelly-like substance on the top of a moss covered rock in my garden. The recent weather has been very wet and about a week ago we experienced a couple of frosty nights, but the last three days have been dry. Can you tell me what this green jelly slime is, please?

Submitted by: Virginia, Scotland

The Short Answer: I’m pretty sure this is a colony of cyanobacteria in the genus Nostoc, probably Nostoc commune. At the microscopic level, Nostoc forms long strands of individual cells that multiply by dividing. Colonies can grow large enough to form mats like the one in your photo. Nostoc commune typically forms leathery ear-shaped colonies. I suspect that what you have is a deteriorating mat of Nostoc commune. Dr. Walter Dodds, an expert on aquatic ecology at the University of Kansas, believes this is Nostoc commune, but suggests that if you want to be sure, you could take a sample, dry it, and send it to a phycologist at a nostoc communeuniversity in the U.K.

Despite the fact that it is phycologists, specialists in algae, who study Nostoc, Nostoc is not actually an algae. Cyanobacteria like Nostoc used to be called blue-green algae, but it’s now known that they are not algae at all, though they perform photosynthesis the way algae and plants do. So although Nostoc looks like some kind of green slime algae, it’s actually some kind of green slime bacteria.

More Information: Dr. Dodds suggested you dry the specimen before mailing it because Nostoc species have an interesting ability to survive drying and then revive once re-wetted. In fact, one laboratory specimen that sat dried in a museum collection for more than a hundred years was revived and grew normally. For all we know, Nostoc can survive hundreds of years dried.

Nostoc has other abilities that help it survive in difficult conditions. It can withstand freezing, for example, and is found in both the Arctic and the Antarctic. Its cells can sometimes be cultured from thin air, suggesting that it is dispersed around the globe on the wind. And it is able to grow in areas of low nitrogen because some of its cells differentiate into “heterocysts” that can fix nitrogen from the air. Earth’s surface atmosphere is nearly 80% nitrogen, and the process of pulling nitrogen out of the air for use by living organisms is called “nitrogen fixation.” The vast majority of animals and plants on earth can’t perform this trick and must rely on fixed nitrogen in their environment. That’s why nitrogen is a key component of fertilizer for plants. Animals get their nitrogen from the plants and animals they consume.

Nostoc, however, is one of the organisms that can fix nitrogen directly, and in some environments, Nostoc is a major source of the fixed nitrogen that eventually sustains all the plants and animals.

So don’t look down on this green slime. It plays a key role in the biological productivity of natural habitats. And it’s probably adding nitrogen to your garden!

Star Jelly: When Nostoc dies and dries and then gets rewetted, it is usually white. Because these white jelly objects seem to show up out of the blue, they are one of the things that have traditionally been called “star jelly” because they were thought to have fallen from the sky. Nostoc is not the only organism that can produce a white jelly, however, and the white jellies called “star jelly” include other substances, including amphibian eggs and slime molds.


Dodds, W.K., Gudder, D. A. (1995). The ecology of nostoc. Journal of Phycology. 31, 2-18.

What are these green jelly blobs?

The Question: I saw these bright green jelly like blobs in Easdale Tarn, in Cumbria, England. The blobs ranged in size from about 1.5 cm (1/2 inch) to 4 cm (1 ½ inches) cm.  There were quite a few of them, some floating in the water and a couple attached to rocks. What are they? Are they some sort of egg?

Submitted by: Alison, Cumbria, England

The Short Answer: These blobs are made by a colonial microscopic single-celled protozoan called Ophrydium versatile. They can be found all over the world in fresh water. The individual cells line up side by side in the “blob” and attach themselves to a jelly-like substance they secrete. They are symbiotic with microscopic Chlorella algae which live inside the Ophrydium cells and give the blob its green color. This page shows a number of pictures of the blobs in the water:

This brief youtube video clearly shows the hundreds of green Chlorella cells living inside the Ophrydium cell:

This one shows the cilia that Ophrydium uses to gather particles including bacteria, other organisms and detritus from the water:

ophrydiumMore Information:  Ophrydium cells reproduce by dividing.  As the number of Ophrydium cells increase, they remain on the outside of the growing blob, and the interior, which is now empty of Ophrydium cells, becomes a watery gel. This soupy interior gel can become home to all kinds of microorganisms such as mastigotes, euglenids, chlorophytes, heliozoans, diatoms, bacteria, rotifers, nematode worms, other ciliates, and even tiny crustacean copepods, leading some to compare Ophrydium blobs to a floating zoo of tiny creatures.

Ophrydium is always found with its algal symbionts. The Ophrydium structure probably helps the algae gather light efficiently. The Ophrydium also shares nutrients like nitrogen it gains from the bacteria and other particulate material it sweeps from the water with its cilia. In return, the algae supplies Ophrydium with sugars it makes through photosynthesis. During the summer, the majority of the carbon assimilated into the colony comes from photosynthesis. In the winter, the colonies remain active, but most of the carbon assimilated comes from the organisms Ophrydium gathers from the water column.

Other Common Blobs: One of the most common questions to is “What is this blob I found in the water?” I’ve written about Bryozoan blobs and amphibian egg masses. Other possibilities for fresh water blobs include snail egg masses, fish egg masses and freshwater jellyfish. Keep those blob questions coming!


Thanks to Ophrydium expert and University of Saint Joseph professor Mark Johnson for his help identifying these blobs and for the information in his dissertation Seasonal Changes in Distribution and Tropic Mode of the Mixotrophic Ciliate, Ophrydium versatile, in a Freshwater Pond Ecosystem.

Sand-Jensen, K, Pedersen, O, & Geertz-Hansen, O. (1997). Regulation and role of photosynthesis in the colonial symbiotic ciliate ophrydium versatile. Limnology and oceanography, 42(5), 866-873.

Duval, B, Margulis, L. (1995). The microbial community of ophrydium versatile colonies: endosymbionts, residents and tenants. Symbiosis, 18:181-210.

What is causing this vinegar smell?

The Question: Whenever I walk by this certain house, there’s a noticeable smell, like vinegar, but more chemical. Very hard to pinpoint the source. Now at the same time, they had a giant white oak cut down, and some of the 5-foot diameter rounds from the trunk are still in the yard, freshly cut. Is it possible that the wood is the source of the smell?

Submitted by: Tom, Washington, DC, USA

Cut logsThe Short Answer: I suspect that you are smelling acetic acid being given off by the cut tree. Acetic acid, is, of course, the component of vinegar that gives it both its acidity and its characteristic smell. Healthy trees, when first cut, can release acetic acid, which evaporates and contributes to the fresh cut wood smell. Some reports suggest that oaks (especially red oaks, more on that later) in particular have an acetic acid smell when cut. There is also the possibility that the tree had a condition called bacterial wetwood. Some refer to this condition as slime flux, but the slime is really a symptom of the bacterial infection. The anaerobic bacteria that cause wetwood can create acetic acid as a byproduct of metabolism. It’s unlikely that wetwood would weaken such a large tree enough to cause it to be cut down. On the other hand, it seems that most trees, if they live long enough, are eventually infected, and if this tree were taken down for some other reason, it might still have had bacterial wetwood, which might be contributing to the acetic acid smell.

Slime Flux More Information: Acetic acid is a very common chemical in nature, found in metabolic pathways and produced by both aerobic and anaerobic bacteria (oxygen-loving and oxygen-hating, respectively). It’s been known to humanity for at least as long as we’ve been making beer and wine, because acetobacteria will convert alcohol to acetic acid in the presence of oxygen, souring beer and turning even the finest wines to vinegar. The various species of bacteria that cause wetwood are anaerobic, however, so they can thrive in the interior wood of trees, where there is little oxygen.

Ted Leininger, PhD., of the USDA Forest Service, points out that the slime flux/wetwood bacteria don’t actually destroy the wood. However, the bacteria release enzymes that degrade the walls of the wood cells. This degradation causes the cells to leak and the wood to take on a water-soaked appearance. Hence the name, wetwood. The typical sign that a tree has bacterial wetwood is when all that released water begins oozing out of any wounds the tree may have. This oozing has been given the descriptive name slime flux. It’s possible that a buildup of gaseous pressure caused by the byproducts of the bacteria can actually crack the tree and create the wounds from which the “slime” oozes, but in most cases, the slime exits through existing wounds. Dr. Leininger explains why wetwood can cause a tree to smell: “Wetwood bacterial infections can produce fatty acids such as acetic acid, butyric acid, valeric acid, caproic acid, or propionic acid, which impart the odor and cause bleaching or staining to the bark.  The odor has been described as rancid, fetid, fermented, or like vomit.”

Because AskaNaturalist reader Tom reported the smell as vinegary and not particularly fetid, Dr. Leininger thinks the smell may be simply cut oak smell. “It’s possible that healthy oak wood will have a distinct, perhaps acidic, odor because of tannins.” After looking at the photo of the cut sections of the tree, Dr. Leininger doesn’t believe the tree was suffering from an acute wetwood infection, as he says it would probably be visible in the cross section as darker, water-soaked areas.

At least one source also reports that red oaks are particularly high in natural acetic acid. Tom reported the tree as a white oak, but oak species are notoriously hard to identify, in part because they are highly variable and often hybridize. From the bark shown in the photo, Dr. Leininger is pretty sure this tree was a red oak, not a white oak. White oak, he says, tends to have scaly or shaggy bark. So the best guess seems to me to be that this is a red oak, and the remaining cut rounds are giving off a natural acetic acid odor, and imparting that salad dressing smell to the neighborhood.

There is yet another connection between wood and acetic acid. In an early case of making lemonade when life gives you lemons (though lemons have citric acid, not acetic), people quickly figured out that spoiled wine had its own benefits, both as food (vinegar) and as an acidic chemical agent. So they soon developed ways to deliberately manufacture it. One way is to simply encourage those acetobacteria that ruined the wine in the first place. This is done by inoculating wine with acetobacteria culture and then aerating the wine to make sure the bacteria have plenty of oxygen. Another method is to “cook” wood and distill off the acetic acid, both the acid naturally in the wood, and the acetic acid formed by the action of high temperature on the many biological chemicals present in wood. The resulting amber-colored liquid in its raw form is called pyroligneous acid, but its main acidic component is none other than our familiar acetic acid. Cooking wood remained the primary method of preparing acetic acid until methods of direct synthesis from methanol were invented in the 20th century.

Acetic Acid Trivia: Acetic acid as vinegar and in biological systems is dissolved in water. But if you hang around chemistry labs, you’ve probably heard of “glacial acetic acid.” This is simply pure acetic acid, with absolutely no water. Pure acetic acid freezes at 16.5 °C (62 °F), just a little below room temperature, forming acetic acid “ice,” hence the “glacial.”


Wilson, A. 2008. Incidence of bacterial wetwood in southern bottomland hardwood logs and lumber. Phytopathology 98 (6): S172-S172.

MURDOCH, C., and R. CAMPANA. 1983. BACTERIAL SPECIES ASSOCIATED WITH WETWOOD OF ELM. Phytopathology 73 (9): 1270-1273.

Xu, Z., et al. 2001. Physical, mechanical, and drying properties associated with bacterial wetwood in red oaks. Forest Products Journal 51 (3): 79-84.

Granstrom, K., and B. Mansson. 2008. Volatile organic compounds emitted from hardwood drying as a function of processing parameters. International Journal of Environmental Science and Technology 5 (2): 141-148.