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Project Lab 

August 28, 2013

Faux food

Last week Carissa wrote about the Plastisphere and how it has become a floating habitat for microbes.  But what happens when a larger animal comes into contact with these plastics?  The Laysan Albatross is one species negatively affected by plastics in the oceans.

Laysan Albatross breed on the Hawaiian Islands, with over half breeding on Midway Atoll.  During breeding season it may be hard to walk between all of the nesting seabirds – hundreds of thousands of Laysan Albatross come to Midway Atoll.


Adults arrive in November to court, mate and lay an egg, and the chick will fledge and leave Midway in July.  This long process means that most birds will only lay one egg per breeding season.  After a few weeks together, the nestling is left alone on the island for the next few months while both parents forage at sea.  Unfortunately an increasing amount of the “food” periodically brought back to these chicks is actually bits of plastic.  The Great Pacific Garbage Patch can be found in the same area that Laysan Albatross forage for food and these plastics are making their way back to land in the stomachs of birds.

Why would a bird intentionally ingest plastic?  Albatross primarily eat invertebrates such as squid and jellyfish and shredded plastic bottles floating on the water can resemble either of these foods.  Plastic of various colors and sizes are mistaken for other marine invertebrates as well, and scooping up the pieces the Albatross fly back to Midway and feed it to their young.  Many nestling Albatross are unable to survive due to malnutrition or punctured stomachs from the plastic they are fed.


Although not currently considered a threatened species, over time this could

become problematic for the Laysan Albatross population as a whole.  If each pair is only laying one egg a year and that chick dies before leaving the nest the number of chicks replacing older adults could dwindle.

Plastic ingestion is a scary thought, but even when it is not being incidentally eaten, plastic can still affect birds through entanglement.  Plastic entanglement is a problem not only on Midway Atoll, but even closer to home here in San Francisco.



This Common Murre (Uria aalge) was found on Ocean Beach caught up in netting.  The netting has actually wrapped itself around the wings and feet in such a way that the bird would not have been able to fly or walk.  I prepared the bird as a study skin to have a record of the way plastics can negatively impact our avian community.  Many animals can have limbs or even necks caught in plastic bottles, plastic rings that hold soda cans or even plastic bags.

While San Francisco has already banned plastic bags, there are many other items that we throw away or recycle that can accidentally end up in the ocean.  Unless you already have your next arts and crafts project mapped out, it’s always good to pause and think about whether you need that extra packaging or plastic bottle.  Sometimes plastic can be “reused” in ways we had not anticipated!


Codie Otte

Curatorial Assistant and Specimen Preparator

Ornithology & Mammalogy Department

Filed under: Uncategorized — project_lab @ 10:25 am

August 21, 2013

The Plastisphere- an artificial marine ecosystem

This week I attended the event Women in Ocean Science at the Aquarium of the Bay. Here I learned about the plastisphere, an ecosystem of marine microbes living on plastic floating in the ocean. How trash is dealt with has always intrigued me. When I see mounds of garbage on the streets and beaches of San Francisco I become disgusted. Some of this garbage makes its way to the Great Pacific Garbage patch, estimated to be about twice the size of Texas! About 4.7 million tons of garbage enters the world’s ocean in a year, which contribute to the five trash gyres found in the oceans.  If we do not clean up our act, the ocean will one day be a giant plastic soup!

Image 2

The plastisphere is extremely biodiverse. Plastic collected in the North Atlantic contained 50 species of single- celled plants, animals, and bacteria comprised of photo-synthesizers, herbivores, predators, and decomposers. Another study discovered 1,000 different kinds of microbes on a piece of plastic only about 5 mm across.

Plastics are energy rich substances consumed by some species of terrestrial bacteria and fungi. The marine microbes living on floating plastic may also be capable of breaking down plastics. Electron microscope images of bacteria living on plastic surfaces have shown spherical pits surrounding the bacteria. More research needs to be done to substantiate this claim. Despite this, plastics in our oceans will not be able to be degraded at the rate at which plastics are entering the ocean.

Photo 1

Overall, the plastisphere is bad news for natural marine ecosystems. The microbes in the plastisphere may use up phosphorus and strip it away from other marine organisms. In addition, the plastisphere could serve as a source for human disease transmission since fish and shellfish ingest tiny pieces of plastic harboring Vibrio and cholera-like bacteria, which cause food-born illnesses. Finally, plastics may also transport microbes long distances leading to more occurrences of invasive species.

On a more positive note, the plastisphere may possess non-harmful bacteria containing compounds useful for drug discovery. It is an extremely interesting artificial biosphere since it harbors a vast diversity of microbes and illustrates the amazing adaptability of nature! It is an entirely new ecosystem awaiting scientific discovery.


Stay tuned for next week’s post on plastics and albatross.


Carissa Shipman

Graduate Assistant in Public Programs

Invertebrate Zoology and Geology

Filed under: Uncategorized — project_lab @ 12:23 pm

August 15, 2013

Numbering skeletons

Recently, I’ve been working in the Project Lab on a different kind of task than usual: numbering bird and mammal skeletons. While I’m usually busy preparing research specimens for our collections, there are other steps that bridge the time a specimen is prepared to the time that it can be integrated into our collection. With study skins, this involves allowing the skin to dry, freezing it (to kill off any pests that may have hitched a ride during the preparation process), cataloging it (giving it a number that identifies it in our collection), and then integrating it into the collection. Skeletons, however, require the additional step of having each bone numbered after the specimen is cataloged.

I commonly get the question of whether I put a different number on each bone to identify what bone that is, helping to make putting the skeleton back together easier. The answer is: no! The number that goes on the bones is the same for each bone and is the specimen’s catalog number – its unique identification number within our system. We also keep our skeletons disarticulated, or not put together. This makes it easier for researchers to look at specific bones. For instance, if a researcher brought in a vertebra (part of the back bone) from a mystery animal and wanted to identify it by comparing it to skeletons in our collection, it would be much easier for them to compare all of the details of the bone if the skeletons were completely disarticulated.

What’s the point of all the numbering? Shouldn’t we be fine as long as we put the number on just one bone in the box? The answer again is: no! Imagine a tray of 50 boxes of skeletons. If that tray fell and each skeleton scattered, how would we know which bone goes with which specimen? This is why we put the catalog number on each bone, with the exception of tiny skeletons where the bones are too thin to write on. In those cases, we write on as many bones as possible.

numbering skeletons_photo1 copy

Similarly, if a skeleton is mostly articulated (the bones are still attached), we still number every single bone. If the skeleton was to fall and the bones separated, we would still need each bone to have its own number.


numbering skeletons_photo2 copy


Numbering is a slow process, but someone has to do it!


Laura Wilkinson

Curatorial Assistant and Specimen Preparator

Ornithology & Mammalogy

Filed under: Uncategorized — project_lab @ 3:55 pm

August 9, 2013

Summer Systematics Institute

Systematics: The study of the evolutionary history and diversity of living things and the relationships among these through time.

This week I decided to write about a great program that we have available to undergraduates within our Institute for Biodiversity Science and Sustainability, called the Summer Systematics Institute (SSI).   This program is partially funded by the National Science Foundation’s Research Experience for Undergraduates (REU)  program and the Academy’s Robert T. Wallace endowment.   It is an 8-week paid internship working with an advisor, usually an Academy curator or post-doc.  This summer, the program is in its 18th year and there are 12 participants from all over the country, including a biological illustrator.   During the 8 weeks, the interns learn new techniques and conduct original research, all while attending a series of lectures on themes related to the field such as phylogenetics, collections management, bioinformatics, morphometrics, nomenclature, and biogeography.

SSI taxa compilation

For the past three summers, I have had the wonderful opportunity of helping students in the molecular lab as the Teaching Assistant in the Center for Comparative Genomics.  In this role, I train students how to extract DNA from their specimens and how to use molecular techniques in order to sequence the DNA from those specimens.   The students then use these data to help answer research questions about the evolutionary histories of species or populations.  Not all interns use DNA data as a part of their projects, but since molecular data is commonly used in our field of biology, this is a great opportunity to either learn new techniques or refine techniques that students may have had some exposure to previously.  This year I was able to train some of the interns in the Project Lab, so if you visited in the last few weeks, you may have seen some of them working on their projects!

Yesterday, after a busy 8 weeks, the program culminated in a day where the students gave scientific presentations on their projects.    This year’s projects were quite impressive, and the students worked very hard.  Below are photos of some of the presentations.






To me, the most exciting thing about this program is that the interns get authentic research experience.  I know this to be true because in 2006, I was an SSI intern!  This program really fostered my understanding of and passion for the field of systematics.  If I had not done this program back when I was an undergraduate, I probably wouldn’t be earning a master’s in this field today.  For more information on the SSI program, click here.


Til next time!

Vanessa Knutson

Graduate Student, IZG Dept

Project Lab Coordinator

Filed under: Uncategorized — project_lab @ 12:07 pm

August 1, 2013

Of Sea Monkeys and Fairies

Many folks that I have spoken to in the last week remember the enticing advertisements that used to commonly appear in comic books and kid’s publications, promising amazing experiences with the new pet craze, the Sea Monkey aquarium.  Containing a small plastic aquarium, a packet of dried eggs, some food and minerals, and a magnifying glass, “just add water” and soon you would have a flotilla of tiny, shrimp-like creatures rapidly swimming around on their backs, darting hither and yon around your new instant aquarium.  It sounded great to me as a 10 year old, but I never knew anyone who actually had them.




These tiny creatures bear no resemblance to monkeys, but are in fact small crustaceans commonly referred to as brine shrimp when they are found in salt water or hyper-saline pools, or fairy shrimp when they are found in fresh water.

These are not shrimp at all, but belong to the crustacean class Branchiopoda, in the order Anostraca.  Usually between 6 to 25 mm long, they have paired eyes and from 14 to 16 pairs of legs used both for locomotion and to stir up water currents around their gills to aid breathing.


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Here in California, fairy shrimp are found in vernal pools, also known as ephemeral ponds. These habitats form for only a few months from about December to May, as low lying areas of wetlands fill with water, which then evaporates leaving the pools dry by summer’s end.  Throughout the U.S., wetlands are an endangered habitat closely regulated by the federal government.  Here in California, many vernal pools are found in the Central Valley, often in agricultural areas and places ripe for development.  The delineation of wetlands on private property often causes controversy and clashes between owners, conservationists and the government.




There are several species found throughout California, but this blog focuses on the California Vernal Pool Fairy Shrimp, Branchinecta lynchi, which is federally listed as a threatened species.  These suspension and filter feeders eat unicellular algae, bacteria, and ciliate protists, and also scrape diatoms, algae and protists off of rocks and twigs.  They are an important food source for migrating birds and other organisms using and visiting the pools.  They exhibit sexual dimorphism (physical differences between the male and female), the smaller female recognizable by the attached egg sac, while the male is bigger and more robust, with a pair of large claspers, which are greatly enlarged second antennae, used in mating.  Females of this species lay two different types of eggs.  Summer eggs are soft, and will hatch within the season. Winter eggs have a tough skin, which allows them to form a cyst as they dry. These encysted eggs can survive in soils and sediments for an amazingly long time, up to 10 years!  Winter eggs can be blown long distances, or carried by birds.  This transport from pool to pool increases genetic diversity, aiding species survival.  Pools with lower genetic diversity are more susceptible.  The prevalence of pesticide usage, filling and paving over of wetland areas, and other human activities are the major threats to populations in California, and elsewhere.


The photographs were taken by me with the Big Kahuna digital imaging system, and are voucher specimens from a government survey in the collection of our Invertebrate Zoology department.


Until next time,


Vic Smith

Digital imaging specialist/Invertebrate biologist

Filed under: Uncategorized — project_lab @ 10:28 am

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