Archive for the ‘Research: Live from the Labs’ Category

MLML goes to Baja – the trip continues

March 17, 2014

Jackie Lindsey By Jackie Lindsey, Vertebrate Ecology Lab

For the next two weeks Moss Landing Marine Labs will be a little quieter, and not just because of spring break.  A large class of graduate students has just departed for Baja California Sur for two weeks of field research, and I am lucky to be among them!   Many of us have never been to this part the world, and we are full of hopes and dreams that we can pull off the projects we designed back in the classroom.

El Pardito

El Pardito

We are spending the majority of our trip on a tiny island called El Pardito, located within the Sea of Cortez.  This island is home to a small community of fishermen who have lived on the island for generations.  Many of us are depending heavily on their expertise to set up our projects and navigate the local waters.

Our projects range from mapping benthic habitat, to monitoring Marine Protected Areas, to studies of sea turtles and damselfish. We are spending full days in and on the water around El Pardito, and the weather should be just about perfect (fingers crossed)!

Turtle captures on El Pardito

When we get back there will be plenty of pictures to post, commemorating our journey and all our hard work, but for now let me leave you with this image of NOT EVEN ALL OF THE GEAR!  Food, cooking tools, boats, compressors, dive gear, camping gear, sampling gear…the list goes on and on (and on and on).

Sampling gear

Sampling gear

Dive gear explosion

Dive gear explosion

I hope we didn’t forget anything because it’s too late now!  See you in two weeks!

Sometimes You Have to Celebrate!

March 5, 2014

Back in December 2013 I went on my last sampling bout for my thesis to Santa Catalina Island. My team included three amazing colleagues from Moss Landing Marine Laboratories. We conducted surveys in sand and rhodolith beds which will be used to compare the communities. Rhodoliths are free-living calcareous algae that look like little pink tumbleweeds and propagate above sand.


They appear to provide diverse structure increasing abundance and diversity of flora and fauna, similar to how trees provide habitat for epiphytic plants, climbing vines, and animals like birds and mammals.

Mantis shrimp in a rhodolith bed

A mantis shrimp in the rhodolith bed. They are holding a scallop shell probably found within the bed.  Filamentous red algae is covering the pink rhodoliths.

We conducted surveys to estimate the abundance of macroalgae growing on each substrate, macroinvertebrates, fishes, and took cores for later sorting under a microscope to estimate microinvertebres within each substrate. We celebrated by wearing santa hats which made the long sampling dives more fun. It was a great way to finish up my thesis.

Gabara December 2013 Thesis Team

The Catalina Island December 2013 sampling crew. (from left to right) Sarah Jeffries, Scott Gabara, Will Fennie and Kristin Meagher (taking the photo).

Sarah Jeffries

Sarah Jeffries holding a quadrat and bags filled with core samples, whilst wearing our symbolic santa hat.

Appropriate boat name

An appropriate boat name at Avalon Harbor during my thesis sampling.

Ballast water and epifluorescence microscopy

January 13, 2014

by Liz Lam, Biological Oceanography Lab

The Golden Bear Facility, home to MLML's ballast treatment testing team

The Golden Bear Facility, home to MLML’s ballast treatment testing team

Ballast water treatment and testing is a big focus here in the Biological Oceanography lab, and this is no exception even when it comes to class projects.  Last semester, I started a project aiming to improve one of our counting techniques.  I’d previously written about IMO’s restriction to 10 organisms per 1,000 liters of discharged ballast water and counting zooplankton under a microscope in order to check for these results.  But when it comes to even smaller organisms, such as algae and other even tinier phytoplankton, different methods are called for.

We already have a pretty clever way of quantifying such microscopic organisms by using a few chemical and optical tricks.  The first key ingredient is fluorescein diacetate, or FDA.  One of the special features of this molecule is that it can only be cleaved by certain proteins in live cells.  Once FDA is split, what remains is fluorescein, a compound that glows bright green when excited under blue light. We can then use an epifluorescence microscope to both shine the right wavelength of light and magnify a sample in order to count any green organisms.  If it glows green, then it means it’s alive!  This allows us to quantify the number of live organisms that are extremely small and difficult to see.


Ballast Water Creature Counting

October 7, 2013
The Golden Bear Facility at the Cal Maritime Academy is the site of all our ballast treatment testing

The Golden Bear Facility at the Cal Maritime Academy is the site of all our ballast treatment testing. Photo: CMA

Although I’m only a first-year graduate student here at Moss Landing, I’ve had the pleasure of working on the ballast water testing team with the Biological Oceanography lab for over a year now.  Aquatic invasive species have become an increasingly large problem across the globe and one of the ways organisms make their way to non-native waters is through the ballast tanks of ships.  The IMO (International Maritime Organization) is now requiring all ships to reduce the number of live zooplankters in their ballast tanks to only 10 in every 1000 liters.  Since most zooplankton are microscopic, you can imagine that this is an incredibly challenging thing to accomplish!

Samples are carefully collected so we can compare the treated water with the control

Samples are carefully collected so we can compare the treated water with the control. Photo: GBF Staff

But another huge challenge that our team directly faces is determining whether certain treatment methods have worked.  How do we do this?  With some good old fashioned counting!  First, samples are filtered through a net that catches only organisms that are greater than 50 um in size (which is the size class we count by eye).  Then, 5 mL of that sample are pipetted into a serpentine tray, which allows us to count what is in the sample row by row.  We can then look under a microscope and manually count every single living zooplankton found in that 5 mL sample.  This is sometimes known as the “poke and prod” method, since we may not even be sure if a zooplankter is alive or dead until after we’ve poked them with a small poker stick.  Afterwards, we can use our 5 mL sample counts to extrapolate how many total organisms were found in 1000 liters of the treated water and determine whether the treatment method passed.

Counters use microscopes and serpentine trays to count every zooplankter in a 5mL sample

Counters use microscopes and serpentine trays to count every zooplankter in a 5mL sample. Photo: Kevin Reynolds

In order to make sure our zooplankton counts are as reliable as possible, we have to count samples multiple times.  Although the work is time consuming and sometimes back-straining, it’s fun and fascinating to discover all of the tiny, microscopic organisms found in just a few drops of water.  Everytime I count a new sample, I wonder what kind of alien-like creatures I’ll find swimming around!

“Tails” from The Field

August 7, 2013

Angieby Angela Szesciorka, Vertebrate Ecology Lab

Since May, the mammal lab has been as quiet as a post-apocalyptic library (yep, that quiet).

For the marine mammologist (and birder), summer time is all about fieldwork — followed by lots and lots of data crunching and thesis writing. So with fall drawing ever closer (noooooo!), I wanted to check in with my labmates to see what they have been up to.

Below is a quick summary from each of us. We’ll see you soon!

Ryan Carle: Ryan continued working on Año Nuevo Island, finishing data collection for his thesis on Rhinoceros Auklet diet and reproduction. He spends most of his waking hours on the Island identifying prey, restoring habitat, counting burrows, collecting boluses — you name it. When he’s not on Año, he’s trekking about California and making apple cider!

Casey Clark: Casey has been fervently writing up his thesis as he prepares to defend in the fall. Draft one? Check! Falling asleep on your keyboard? Check! He has also been helping out with seabird research in Astoria, Oregon. He did save time for fun too — camping, hiking, and kayaking. Jealous!

Marilyn Cruickshank: Marilyn spent the summer analyzing BeachCOMBERS data. She’s looking to see if the residence times of stranded birds on Monterey beaches can help with damage assessments and as a predictor of where most birds will wash ashore in future oil spills. Marilyn continued working for the stranding network and learned how to program in Matlab. She even found time to carve a new banjo. Nice wood-working skills, Marilyn!


Adventures in Madagascar or On The Importance of Doing a Pilot Study!

September 4, 2012

by Angela Szesciorka, Vertebrate Ecology Lab

This summer I hopped on a plane, flying 29 hours one way (via Paris — ooh la la) over a period of three days to spend nearly a month on the island of Madagascar working on my pilot study.

Madagascar, a former French colony until 1960, is the fourth largest island in the world. Don’t let it fool you. It looks so tiny next to Africa, but it has 44 percent more area than California, and boasts more than 4,800 km of coastline.

Rocky coastline in Madagascar. Photo by Angela Szesciorka.

Most of the country’s export revenue comes from textiles, fish/shellfish, vanilla, and cloves. Newer sources of income include tourism, agriculture, and extracted materials (titanium ore, chromite, coal, iron, cobalt, copper and nickel). Madagascar provides half of the world’s supply of sapphires! But with a GDP of around $20 billion, The Economist rated Madagascar as the worst economy in 2011. Most of Madagascar’s inhabitants are subsistence livers, meaning they live off of what they can grow or catch.

Local fisherman spear hunting for crabs. Photo by Angela Szesciorka.


That’s Not a Seashell!

June 28, 2012

By Michelle Marraffini

Invertebrate Zoology and Molecular Ecology

Massive dock from Japan that washed ashore in Oregon. Photo by Oregon State Parks and Recreation Department.

At 66 feet long, 19 feet wide, and 7 feet tall, the massive dock that washed ashore on Oregon’s Agate Beach is larger then anything I have ever found on the beach.   This dock is one of the first large pieces of debris to make it across the Pacific ocean from Japan after the earthquake and tsunami in March of 2011.   According to news reports, the debris came from the northern Japanese city of Misawa, arrived almost nine months earlier than officials originally thought.

Hitchhikers from Japan made it alive and well despite the almost 5000 mile journey.
Photo by Oregon State Parks and Recreation Department

But this dock did not arrive alone.   Many organisms hitched a ride on this dock for the almost 5,000 mile journey across the ocean.   Floating docks and other harbor structures provide habitat for many invertebrates and algae.   The movement of these organisms to the Pacific Northwest, many of which are not native to this coast, may pose a threat to the diversity of native species that live there.   To prevent these possible problems, scientists and managers took samples of organisms that arrived on the dock then scrapped the remaining organisms, buried them deep in the sand up the beach, and then used blow torches to dock to remove all remnants and reproductive material of the organisms.


Battle Under the Docks

June 25, 2012

By Michelle Marraffini

Invertebrate Zoology and Molecular Ecology Lab

With continued global expansion of humankind and climate change, how will native communities be affected by introduced species?  Recent state surveys identified at least 312 non-native species in California coastal waters, many of which are known to have strong negative impacts on shipping, recreational and commercial fishing, and native habitats and local species (CDFG, 2008).  Factors regulating the success of non-indigenous species are of interest to scientists and managers.

A view of boats that use Monterey Harbor and may unknowingly transport invertebrates from other marinas and harbors.

Artificial habitats like floating docks and pontoons act as ground zero for newly arrived non-indigenous species.  These species arrive though many mechanisms, such as ballast water and fouling on the bottom of boats; we heard all about ballast water from fellow MLML student Catherine Drake, The Ballast Water Balancing Act.  Species that settle in marinas and harbors can than travel along the open coast and into estuaries, where they may outcompete native species for resources and become dominant on human structures such as water pipes, sewer grates, and aquaculture cages.

Dockside view of my thesis installation with helpers Hannah and Heather. Photo by Scott Gabara

Under the floating docks of Monterey Harbor animals are battling for space. For my thesis at MLML, I am studying the role of native invertebrate species on invasion success.   I will look at the sessile invertebrates like tunicates (Phylum Chordata), mussels (Phylum Mullusca), bryozoans (Phylum Byrozoa), hydrozoans (Phylum Cnidaria), feather-duster worms (Phlyum Annelida) and anemones (Phylum Cnidaria).   By making experimental treatments that vary the number of species, the amount of native verse non-native species, and the amount of open space in artificial communities hopefully I can untangle part of the story about how non-native species become established.

Take a look under the dock as the battle is under way and stay tuned for the winner!

Diver, Heather Hawk helps steady treatment plots of native and non-native sessile invertebrates Photo by Scott Gabara

It’s Whale Soup Out Here!

June 5, 2012

Looking for whales in Monterey Bay

Ok, so it’s not literally whale soup out here, but Monterey Bay has been full of humpback whales for the past few weeks.  Casey Clark, a graduate student at Moss Landing Marine Labs, has been taking advantage of this opportunity to investigate migrations and feeding behavior humpback whales in this region.  Each whale’s tail (known as a fluke) has a unique pattern of black and white markings and scars, which can be used to identify individual whales, much like fingerprints are used to identify humans.  As part of his research, Casey has been photographing the flukes of whales encountered in the bay and referencing them to a catalog to determine when and where they have been seen in the past.  Spring and summer are great times to see humpback and blue whales in Monterey bay, so keep your eyes out for a glimpse of these huge marine mammals!

Last look at a humpback whale.

The Ballast Water Balancing Act

March 13, 2012

By Catherine Drake, Invertebrate Zoology Lab

Docked in the Carquinez Strait, an offshoot of the San Pablo Bay in the city of Vallejo, is the TS Golden Bear.  It is a training ship for the California Maritime Academy, which—like MLML—is a campus of the California State University.  The Biological Oceanography lab at MLML utilizes the ship for ballast water research.  As ships traverse the globe, they pick up ballast water from one area and release it back into the ocean once they reach their destination.  Ships uptake seawater into their ballast tanks to optimize balance and streamlining when traveling a great distance.  During this process, potentially invasive planktonic organisms are brought into the tanks and transported by being held in the ballast tank during travels.  As these organisms are released back into the ocean, they are now introduced into a new environment.

The TS Golden Bear, which houses the laboratory and is the source of ballast water used in the research conducted by the MLML Biological Oceanography lab.

Ships take in seawater and store it in ballast tanks in order to remain balanced as they glide through the oceans. Then, they discharge the ballast water as they enter a port or harbor.

This can pose a problem, as some plankton can become invasive, meaning that they can outcompete native organisms in a habitat.  According to Ruiz, et al., shipping is considered the largest transfer mechanism for coastal invasions.   As a result, regulations developed by IMO (International Maritime Organization) are implemented to reduce invasive plankton.  One of their requirements forces ships to reduce the number of live zooplankton to 10 live zooplankters per 1000 liters after the water has been treated with a kill-factor (toxic reagents, oxygen reduction, UV light, heat, etc).  “Though the challenge of coming up with an effective but environmentally safe kill factor is still up and coming, so are the methods to determining the quality of the treatment system,” says Julie Kuo, a student in the Biological Oceanography Lab.  Consequently, this has enhanced the collaboration between engineers, and scientists to construct standard operating procedures to determine the quality of a treatment system based on IMO regulations.

Copepods, tintinnids, rotifers, and cladocera are all zooplankton that can be found in ballast water.

Enter Dr. Welshmeyer and the Biological Oceanography lab: the purpose of their project is to count the number of live zooplankton alive before and after the treatment.  This process is used to determine whether or not the treatment tested on the Golden Bear is successful at meeting the IMO regulations.  As we boarded the ship, we carried microscopes and coffee down through the ship to a room that was designated as our lab.  In the 8 by 15 foot room, we setup our microscopes and began counting zooplankton.  That particular day, we were counting pre-treated water, which was full of zooplankton swimming around; this included tintinnids, copepods, rotifers, and nauplii.  After our counts of the live and dead zooplankton, we extrapolated that there were anywhere from 100,000 to 200,000 live organisms per cubic meter; up to 60% were alive in an untreated sample that was concentrated from one cubic meter of water from the Carquinez Strait.  So, treatment systems have to be incredibly affective in order to kill all but ten zooplankton in ballast water!

Julie Kuo, a graduate student in the Biological Oceanography lab at MLML, counts the number of zooplankton in a sample of pre-treated ballast water.


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