Fish in the Bay – January 2022: Mud Shrimp Alert – Upogebia Explosion on New Year’s Day!

Happy New Year!  The new word for 2022 is “Upogebia,” aka Mud Shrimp.

We caught our first Upogebia in Pond A21 on New Year’s Day.  Then we caught 163 more of them in Coyote Creek later the same day and five more upstream on January 2nd.  We had never caught deep burrowing Upogebia mud shrimp before.  This represents a profound ecological disturbance that I reported on Facebook a few days later.


Part 1: The original Facebook post.

Mud Shrimp Mystery of 2022!  On January 1st and 2nd, we caught a total of 170 Mud Shrimp (at the time these were thought to be native Upogebia pugettensis) in the main stem of Coyote Creek (62 at Coy2, 101 at Coy3, five at UCoy2 and one in Pond A21).  We have only ever caught one (1) Mud Shrimp in June 2021, and another one a few years earlier.  These shrimp burrow deep in mudflats, so our trawls do not normally catch them.  What is going on here???


Laine’s Bait Shop ad on December 31st.

Our first suspicion was that these critters might be escaped bait.  Mud Shrimp are similar to Ghost Shrimp (Neotrypaea californiensis) used by people fishing for Sturgeon.  Coincidentally, Laine’s Bait Shop in Alviso announced on Facebook that it had Ghost Shrimp for sale on December 31st


The “Mud Shrimp” we caught definitely didn’t look like the bait Laine’s was selling.  But just to be sure, I called Laine’s bait (  Laine’s sold a limited quantity of translucent Ghost Shrimp for $12/dozen. Those shrimp were shipped from Oregon or Washington state.  And, Laine’s was sold out by the time I called.


Why would anyone throw away $170 worth of bait anyway!  Plus, our trawls only sample small sections of the creek bottom.  If we caught 170 Mud Shrimp, there must be thousands of homeless Mud Shrimp creeping along several miles of Lower Coyote Creek. If not escaped bait, where did these midget-sized lobsters come from?


Recent weather has been a bit unusual.  Most of 2021 was affected by La Nina: extremely dry with practically no rain.  Then a bomb cyclone of rain hit us on 24-26 October as the season changed. Another atmospheric river storm arrived on 13 December then more rain at the end of December.  Overall, the Bay Area received more rainfall since October than in the entire previous 12 months.


Did a burst of freshwater and flushing dislodge thousands of entrenched Mud Shrimp?  Where else could they have come from?


BTW: All Mud Shrimp were released after a brief examination.


All Upogebia shown here and above were caught at stations Coy2 and Coy3 on 1 Jan 2022.


Part 2: Expert opinion arrived a few days later.

After posting the above story and photos on Facebook, we were contacted by Dr. Kerstin Wasson, the research coordinator for Elkhorn Slough, and later by Dr. John Chapman at Oregon State University.  Dr. Chapman identified at least some of our photographed Mud Shrimp as non-native “Upogebia major” that arrived from Asia sometime in the last two decades.  Earlier in 2021, he and his associates published an analysis and history describing what we really caught.

Chapman’s paper tells the tale of a Bopyrid Isopod parasite that first invaded San Francisco Bay sometime in the 1980s.  This particular parasite wiped out our native Upogebia pugettensis by inhibiting their reproduction.  As near as anyone knows, U. pugettensis went extinct in SF Bay around a decade after the parasite arrived.

The loss of our native Mud Shrimp was, and is, very bad news.  According to Chapman et al. (2021), Upogebia pugettensis are ecosystem engineers that form dense burrow galleries in intertidal estuary mudflats.  Like other Upogebia “Mud Shrimp” species around the world, they “expand effective estuary sediment surface areas and circulate oxygenated water deep into suboxic subsurface sediments. Upogebia burrowing accelerates sediment remineralization and can dominate estuary biogeochemistry.”

SF Bay got a one-two invasive punch:  The Bopyrid Isopod parasite arrived first.  It appears to have killed off the native Upogebia by the mid-1990s.  Then, around a decade later the non-native Mud Shrimp, Upogebia major, arrived.  U. major evolved with the Isopod parasite and is highly resistant to infestation.  Both the isopod and new mud shrimp are now common in coastal estuaries from Southern California to Washington State.

Chapman suggests that this newer Asian Upogebia performs similar beneficial ecosystem engineering functions of the extinct native variety.  But, for better or worse, U. major doesn’t perform those functions the same way or to the same extent.  These new engineers are bound to have a different impact. 


Two of five Upogebia, with American Shad and Anchovies, caught at station UCoy2 on January 2nd.

Summary of key similarities and differences between U. pugettensis and U. major from the most recent Chapman paper:

  • “Upogebia major are similar in general morphology and color to U. pugettensis but mature U. major are readily distinguished in the field by the smooth, unadorned the cheliped thumb inner face.”
  • In both species, “Upogebia can burrow to more than two meters below the sediment surface … where they are beyond the reach of conventional sampling devices.”
  • Free swimming larvae of both species tend to settle and develop in existing Upogebia burrows. Adult U. pugettensis are unable to excavate new burrows.  An adult removed from its burrow is defenseless and will quickly become fish or bird food.  It is unknown whether adult U. major also suffer this handicap. (This video shows how to catch Upogebia on a mudflat in South Africa and how to return them to their burrows after examination:
  • Native Upogebia pugettensis have separate male and female sexes as indicated by a 1:1 sex ratio in collected specimens. They tend to be aggressive and live in solitary burrows.  
  • Non-native Upogebia major are hermaphrodites as indicated by their 2:1 (f:m) sex ratio, and burrows can be shared by multiple adults.
  • The parasitic bopyrid isopod, O. griffenis, attacks both Mud Shrimp species, but the infestation rate is 10 times greater in native U. pugettensis. (This video shows how to remove isopod parasites from Mud Shrimp in Oregon:
  • Interesting fact: Mud Shrimp burrows are also used by a native clam, Cryptomya californica. ( Researchers may be able to track historical presence or absence of Mud Shrimp from distribution and age of C. californica shells in a mudflat.  The absence of C. californica shells at some SF Bay stations after 1996 suggests that final disappearance of native Upogebia pugettensis occurred close to that year. 


Upogebia at UCoy2.


Part 3:  Why here?  Why Now?

Another Upogebia from UCoy2.

All of the above leaves unexplained why wandering Upogebia suddenly blanketed the bottom of Lower Coyote Creek on New Year’s Day.  As far as we know, adult Upogebia of either species never leave the safety of their burrows.  Why they did so all at once remains a mystery for now.

This event also indicates that a dense and thriving subterranean Upogebia community exists along the muddy banks of Coyote Creek somewhere between stations Coy2 and the freshwaters upstream of UCoy2.  

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