Look Micro, Think Macro: The Legacy of 40+ Years of Electron Microscopy at MLML

By Ivano Aiello (28 July 2016)

Popular science magazines and documentaries depict marine scientists as sea going adventurers equipped with a pair of binoculars or a fish net, or explorers who dive in the abyss using SCUBA or with submersibles to observe the ‘big’ things that populate the oceans.

The development of modern marine science in the last century has demonstrated that it is only by fully understanding the small-scale processes and features that we improve our knowledge of the vastness and complexity of the ocean’s habitats. In a sense, the small (the ‘micro’) is the new frontier to understand the big (the ‘macro’).

The numbers speak for themselves. According to recent estimates, about ½ of the global biomass (the weight of all living things) could be made of single celled microbes most of which live in or underneath the oceans. Big living things are at the top of very complex food webs while foundations are made of often very small organisms: for instance a whale can consume as much as 40 million krill per day. Big geologic features like mid-ocean ridges (the largest mountain chains on earth) are made of minerals invisible to the naked eye. And much of the sediments that fill up the ocean basins are made of the hard remains of tiny planktonic organisms that populated the oceans thousands to millions of years ago.

To study the small world of the oceans, classic tools of marine science are not enough to observe and collect valid scientific data. The observation of the microscopic features of marine organisms such as corals, foraminifera, diatoms or sponges or the interior structures of organic cells (nucleus, mitochondria...etc.) requires very high magnifications, 10,000 and larger, more powerful than the optical microscopes, limited by the physics of light can yield.

The invention of the first electron microscope by Max Knoll and Ernst Ruska and the production of the earliest scanning-transmission electron microscope (SEM) by Manfred Von Ardenne in Berlin in the 1930s allowed scientists to finally observe the microscopic world to magnifications before unthinkable. The introduction of the first commercial scanning electron microscopes (SEMs) in 1965 opened up a new world of analysis for materials scientists.

Electron microscopes are scientific instruments that use a beam of energy electrons that allow us to ‘see’ objects on a very fine scale. The electrons are accelerated by a high voltage electron gun in a cathode ray tube (yes like the one used in the old school televisions) and condensed in a beam that scans and interacts with the specimen: the interactions produces new (secondary) electrons or backscattered (primary) electrons that are captured by a detector and turned into an electrical signal. A computer analyzes the signal and based on the location of the beam and intensity of the signal converts it into an image.



Moss Landing Marine Laboratories has been at the forefront of scanning electron microscopy to study of the ultrasmall world in marine science since the very beginning of this technology. In the early 1970s, the lab acquired a Topcon SEM. It was the work of MLML’s first faculty member Dr. James Nybakken used the SEM to explore the world of marine invertebrates (James Nybakken: the first faculty member of MLML; https://mlml.sjsu.edu/2016/06/16/james-nybakken-the-first-faculty-member-of-mlml/). Signe Amanda Lundstrum a lab technician for Dr. Nybakken in the early 1970s served as the first SEM technician until 1989 the year when the Loma Prieta 1989 earthquake destroyed the old building.

After the earthquake the SEM was setup in the Salinas trailers with the help of Signe. Guillermo Moreno then replaced her for a few years and finally Sara Tanner has been the main SEM technician until 2015. While MLML was in Salinas, Sara operated an ISI SX30 SEM from 1994 until the lab moved to its present location at Moss Landing, when we purchased a Hitachi S520 in 2000.

Sara Tanner’s specialty has been to distinguish and define fine structures necessary for phytoplankton identification, and she has numerous collaborations including important studies on iron fertilization with Kenneth Coale.

In 2009, through an institutional grant supported by the NSF Major Research Instrumentation Program, MLML acquired a Hitachi S-3400N-II, a modern low-vacuum SEM, equipped with an X-ray spectrometer EDX. These state of the art instruments and the large sample holder (10cm) of the new SEM have significantly increased the ability of faculty, research and scientists from nearby institutions to conduct microanalysis of biological material, sediments, rocks, hard skeletal parts, and other materials.


The low-vacuum capability of the new SEM together with the X-ray spectrometer combine the power of back-scattered electron imaging with the ability to display the distribution and quantification of elements therefore the stoichiometry of the targeted material. This technique, based on the characteristic X-ray radiation produced by a substance bombarded by an accelerated beam of electrons, is fundamental to determine the composition of unknown minerals and other biological and non-biological materials at the nanno-scale.

Since 2009, there have been many examples of multidisciplinary studies done by faculty and students in many labs within and outside MLML.

Undoubtedly this relatively new instrument with its incredible imagining and compositional capabilities will give further opportunities to investigate the micro-world of marine sciences and will inspire future generation of MLML’s students.

Special thanks to Sara Tanner and Lynn McMasters for helping with pictures and stories for this blog!

The K-T Boundary of Moss Landing Marine Labs

By Gary Greene ( 21 July 2016)

The Cretaceous-Tertiary (K-T) boundary in geologic stratigraphy marks a seminal time in geologic history, a time when dinosaurs and other organisms were extinguished from the surface of the earth and the rise of new genera and species occurred. A similar type of evolution can be said to have occurred at the Moss Landing Marine Labs, a time line marked by the earthquake of 1989.

Earthquakes are not unusual along active plate boundaries such as the one that MLML sits on, but they are always a surprise when they occur. This of course is what makes MLML such an attractive place to study marine geology and has attracted faculty and students to the place in the past 50 years. Situated on the Pacific-North American plate boundary at the continents’ edge and overlying a block of Cretaceous granite known as the Salinian Block, the Labs’ geographic location has been transported from where Santa Barbara is located today to its present position since the mid-Tertiary time, in the past 27 million years.

The dynamic edge of the continent is expressed in many faults mapped both onshore and offshore. In the Monterey Bay region the San Andreas is the master plate boundary fault, rupture along which produced the 1989 earthquake, but just offshore of MLML in Monterey Bay are several other active faults, faults of the San Gregorio and Monterey Bay fault zones that control the geomorphology of Monterey Canyon and part of the San Andreas fault system.

Monterey submarine canyon, eroded deeply into the granitic rocks of the Salinian Block, sits just offshore of Moss Landing and is the largest such feature along the contiguous U.S. It is the size of the Grand Canyon of the Colorado River and its active heads are a stone throw from the beach. Here the canyon heads intercept sand transported along the coastal nearshore areas and sends the sediment down to the abyss. Cold nutrient waters upwell in its heads inviting in marine fauna including whales that feed and frolic in its waters. Fran Shepard, the father of Marine Geology, recognized the geological significance of this canyon in the 1930s and it has been intensively studied ever since, being the most studied canyon in the world. Scientific contributions from students, faculty, and researches at MLML often in cooperation with colleagues at the Monterey Bay Aquarium Research Institute have furthered the understanding of submarine canyon processes.

From 1966, when I first came to the Labs to study marine geology, to 1989, MLML resided in a converted cannery and the former Beaudette Foundation’s marine laboratory on the Moss Landing Spit, with the ocean waves lapping at its backside. The library, hosting wood paneling, a fire place, and windows to the sea was a warm, ideal, and inviting snug place in which to learn, and was lovingly overseen by one of the most gracious and welcoming librarians I have ever known, Sheila Baldridge. After the Labs were expanded in the 1980s, the library was moved to an upstairs location in the old cannery building, again overseen by Sheila, where Director John Martin provided the first USGS Pacific Marine Geology field office, which I was able to occupy until the earthquake hit and pulled the Labs apart.

The earthquake, of course, destroyed this quiet, bucolic setting, but it had fostered a hidden strength in its students, faculty and staff, and the community that rose to tackle the rebuilding of the Labs. From the dust, or should I say from the sand boils and liquefaction, was born the: “Friends of Moss Landing Marine Labs,” “Back-to-the Bay” movement, “Save the Water Tower,” and the fight to build a new laboratory, despite “Sally,” Noel Mapstead, and Native American objections to rebuilding the Labs on “The Hill.”

After the earthquake, faculty, staff and students moved to a temporary trailer campus in Salinas, far from the sea and where chocolate permeated the air rather than salt spray. It is a wonder that anyone teaching, studying or working at the Salinas facilities can eat chocolate today. Nevertheless, all persevered with each and everyone connected to, or in support of, the Labs (far too many people to list here), in good faith and selflessly, sometimes on conflicting courses, undertook personal and team efforts to return the Labs to Monterey Bay and to build a lasting institution for the coming generations of students.


It was my privilege to come to the Salinas Labs in 1994 as Director to assist in guiding through the hurdles in the path to the sea. Cloaked in the likes of a larvacean house, a fitting costume for any of the Labs’ Halloween parties at Elkhorn Yacht Club, I appeared on the scene with the intent to filter out the bull s___ (B.S.) that falls from above and pave a smooth path forward. I was pleased to receive considerable support and with this support we were able to turn back opposition. In spite of finding Native American midden remains, and a multitude of legless lizards on the hill, the Labs received the funding necessary for reconstruction (thanks at least partially to the David and Lucile Packard Foundation). The new MLML facility was completed after nearly a decade of struggle.

The time line (MLML’s K-T boundary) was transcended once the new facilities were in place. The faculty had designed a magnificent building, well laid out for teaching and research. It now stands as the window into the ocean and from its expansive backside overlooks the Pacific and the head parts to Monterey Canyon, where geological processes and active marine mammal and bird activity can be observed first hand. Survival of the fittest occurred and new generations of faculty, students and staff are carrying the Labs across its K-T boundary and into a future with great promise. Being on the MLML scene 50 years ago seems like yesterday, but I am a geologist and 50 years is the blink of the eyelid in geologic time.






The Pacific Shark Research Center (PSRC)

By Joseph J. Bizzarro (14 July 2016)

Sharks are sexy, sure – but skates and chimaeras are sexy too. You want proof? Well, good (or too bad, because here it comes). This week’s blog is about MLML’s Pacific Shark Research Center, an extremely productive program that was initiated in 2002 and has graduated 25 students and produced > 250 conference presentations, 180 peer-reviewed publications, and 22 books.

Back at the turn of the century, three prominent shark research programs at Mote Marine Laboratory, the Virginia Institute of Marine Science, and the University of Florida were working to secure federal funds to conduct biological research on elasmobranchs (sharks, skates, and rays) with direct applications for fishery management. East coast populations of several shark species were in trouble, mirroring a global trend of severe declines in many species – especially those that are extremely k-selected and/or subject to intense exploitation – and shifts in the composition of skate assemblages. The greatest federal advocates of the program, however, were congressional representatives from California. This was fortuitous for Greg Cailliet, who had a long professional and personal history with the major players from each of the east coast institutions and had carved out his own prominent elasmobranch research program at MLML. Phone calls were made, many long emails were surely exchanged (this is Greg we’re talking about), and behold. In 2001, Congress approved $1.5 million in funding to the National Shark Research Consortium through the National Marine Fisheries Service’s (NMFS) Highly Migratory Species program. With this award the only west coast representative, the Pacific Shark Research Center (PSRC), was born.

At establishment, the PSRC consisted of three staff members in addition to Greg, who served as the Program Director: David Ebert, who acted as Program Manager, and Project Managers Joe Bizzarro and Wade Smith. For the first few years, Joe and Wade were still toiling on their MS degrees while also working for the PSRC. The influx of funding also helped to support MS research for Greg’s ichthyology students who were interested in elasmobranchs, and the targeting of new students whose interests aligned with the goals of the program. These goals were to conduct basic and applied biological research on chondrichthyan fishes (elasmobranchs plus chimaeras, a poorly known sister group to the sharks, skates, and rays), establish the PSRC as a resource center for scientific information on chondrichthyans to public policy makers, provide scientific expertise to NMFS and state management agencies to help better monitor and manage chondrichthyan fisheries off the U.S. Pacific Coast and in Alaskan waters, and participate in collaborative research on national and international issues involving shark, ray, and chimaera biology. Research was focused on addressing major gaps in our understanding of the life history (age, growth, reproduction, and demography), stock structure, ecology, and fishery biology of commercially and recreationally important chondrichthyan species.


“Shark” is a great buzz word – appealing to funding agencies – but in practice, the PSRC could have been dubbed the Pacific Skate Research Center, as the majority of the research has focused on this group of batoids (skates and rays). Skates are exploited in commercial groundfish fisheries throughout the world’s temperate and boreal regions, primarily as bycatch in other fisheries. Despite this incidental take, fishery mortality has altered species composition of skates and caused substantial declines in the populations of many large, nearshore species. Skates were afforded little scientific or management attention in the past because they have not supported lucrative or sustained fisheries. However, this situation is changing because skates are predators and competitors of other commercially important groundfishes, and because dramatic changes in the population sizes of exploited species have occurred. In the water off the U.S. Pacific Coast and in Alaska, management regulations either have curtailed or severely reduced commercial shark landings, but skate bycatch remains a major problem throughout the region, and skate management is therefore a primary concern.

Skates are represented by nearly 300 species of benthic, egg-laying cartilaginous fishes that constitute one-quarter of all extant chondrichthyans. Although they are extremely speciose, skates have conservative morphology, consisting of a dorso-ventrally flattened body and a limited color pallet that includes shades of brown, grey, and black. Skate identification therefore is difficult, and skate species have been historically misidentified or grouped into generalized categories by fishery scientists and managers for convenience. Describing new skate species and addressing current identification problems  therefore has been a research priority of the PSRC.



Since 2009, the PSRC has mainly functioned under the direction of Dave Ebert on shoestring budgets, as no steady or substantial source of direct funding has been available. The main objectives of the program remain the same, but Dave began to focus more effort on discovering “Lost Sharks,” poorly known or unidentified/misidentified species and especially those that are exploited in commercial fisheries. This focus builds on some of the major misconceptions of chondrichthyan fishes. The public’s perception of sharks often conjures up images of a large, fearsome, toothy predator, with its large dorsal fin cutting its way through the waters’ surface. However, the reality is that sharks come in a variety of sizes and shapes, from the whale shark (Rhincodon typus), the world’s largest fish, to the dwarf pygmy sharks (Squaliolus spp.). In addition, the batoids and chimaeras have historically received considerably less scientific attention than sharks, but are similarly exploited directly as fishery targets, or indirectly as bycatch.

Our awareness of the diversity of sharks and their relatives has increased substantially in contemporary times, with more than 240 new species described over the past 15 years. This represents nearly 20% of all shark species that have been described throughout human history. Most of these new discoveries have come from the Indo-Australian region, followed by the Western Indian Ocean and western North Pacific regions. However, despite such a rich and diverse fauna, the majority of sharks and their relatives have largely been “lost” in a hyper-driven media age whereby a few large charismatic shark mega-stars overshadow the majority of shark species. While these mega-star’s, such the great white shark (Carcharodon carcharias), receive much media adulation and are the focus of numerous conservation and “scientific” efforts the “Lost Sharks” remains largely unknown not only to the public, but also to the scientific and conservation communities.



Currently, Dave advises 11 graduate students that comprise the PSRC. Joe is back from UW, working with Mary Yoklavich at the NMFS facility in Santa Cruz, and Greg is enjoying his retirement and no longer directly involved in the day-to-day operations of the PSRC. Greg and Joe do, however, collaborate regularly with Dave and his students and have several research projects in progress on chrondrichthyans. The hope is that Dave’s Lost Sharks program will garner the attention of an interested funding agency, restoring a much needed financial infusion to the program. Regardless though, in true MLML fashion, Dave continues to work (gratis) for the PSRC in order to educate MLML students and continue to build our knowledge base about chondrichthyans. The accomplishments and productivity of the PSRC are considerable (see below) and speak to the dedication of the staff and students involved, and their love of these ancient cartilaginous fishes.







PSRC Facts:

  • 25 MLML/PSRC graduate students completed their degrees; 13 of these students have gone on and enrolled into Ph.D. programs with 5 having completed their Ph.D.
  • Since inception the PSRC has conducted >100 research projects, mostly in the California Current, Gulf of Alaska, and Eastern Bering Sea large marine ecosystems, but also in collaboration with colleagues in Canada and Mexico.
  • During this project period we have produced approximately 700 publications (average 56/year) including those that have been published, are in press, or are currently in review; this includes 22 books.
  • PSRC Students were lead or co-authors on approximately 350 of these publications.
  • PSRC students averaged 10 publications each of all kinds including book chapters, IUCN Red List Assessments, popular articles and electronic on-line publications.
  • PSRC staff and students published 180 papers (average 14.4/year) in peer-reviewed professional journals.
  • Individual PSRC graduate students averaged 3 peer-reviewed publications each.
  • The PSRC has contributed to about 130 IUCN Red List Assessments.
  • The National Shark Research Consortium received $11,088,174 in Federal funding from 2002-09.
  • $1,400,000 in extramural funding was additionally secured by PSRC personnel, which helped support graduate students at MLML and provided additional support for field work and travel.
  • 25 MLML Graduate students were partially or fully supported.
  • PSRC staff and students attended over 80 professional conferences and gave 250 presentations.
  • PSRC personnel delivered the keynote address at 10 International Conferences.
  • Six PSRC students won individual conference presentation awards for best student presentation.
  • The PSRC has named 30 new species of chondrichthyans, making us the 2nd leading institution globally for discovering and naming new species.
  • The PSRC has discovered 5 chondrichthyan species from off the California coast that had not previously been known.

Friends lecture Wednesday July 20th at 7pm

Come spend the evening at Moss Landing Marine Labs to hear Jason Adelaars speak about a few of the projects happening at Moss Landing Marine Labs. Learn how we are using cutting-edge technology to remove nutrients from agricultural run-off, identify areas vulnerable to the impacts of sea level rise around Monterey Bay, and create real-time oceanographic monitoring to achieve results. The lecture starts at 7:00pm and will be in the main seminar room. Recommended donations for non-friends of MLML is $8. If you are unsure if you are a friend of MLML you can check by calling 831-771-4100 or emailing friends at friends@mlml.calstate.edu. Hope to see you there!

MLML Student Life in the 1990s

By Erica J. Burton ( 8 July 2016)

Being a MLML student during the post-earthquake 90s meant learning, working, studying, and maybe living (caretakers) in the Salinas trailers (Fig. 1). Sitting in the middle of agriculture fields may have made a student question their recent arrival and admission to the lab. However, the Salinas office staff (including Gail Johnston and Sandy Yarbrough) made students feel welcome and connected to their home campuses. The Librarians, Sheila Baldridge and Sandy O’Neill, took great interest in the students and their projects; and could always retrieve the most obscure, needed references. And the faculty had an energetic quality that inspired, united, and promoted the student body.

As a first-year student, you may have attended a core class (or two) in the triple-wide trailer on the island in Moss Landing (neighbors to the bait & tackle shop, and the original Phil’s Fish Market (Fig. 2); land now occupied by the MLML aquaculture facility).   Also on the island was (is) the MLML Small Boat and Diving Operations building (Fig. 3); a student’s gateway to small boat usage in Elkhorn Slough or SCUBA diving field work (Fig. 4).

Although the temporary MLML campuses were separated by ~16 miles, the MLML community was tight-knit, and chock-full of camaraderie and can-do attitudes. There was nothing we couldn’t do (or at least try). Close-quarters in the trailer labs may have aided our tight-knit community, as shown in the Ichthyology Lab (Fig. 5).

Class projects and thesis work brought students together. Students were always willing to lend a hand; near or far. It could have been an ecology class project collecting rocky intertidal fishes, manipulative experiments in Stillwater Cove, class cruises aboard the R/V Point Sur and R/V Ricketts (Figs. 6, 7), or convincing excuses to conduct field work in Baja California, Mexico (Fig. 8).

Graduate school kept us busy days, nights, weekdays, and weekends. But those who worked hard also found time to let off steam at house parties, local watering holes, extracurricular sports, poker games, bus rides to a SF baseball/football game, ski trips, etc. The Blue House (Fig. 9) was a good place to start or end an evening; and typically involved a crooked stroll to, and from, Ray’s (aka The Moss Landing Inn). House parties may have had a live band, and there was almost always dancing involved. Monterey hot spots included Doc Ricketts, Players, Planet Gemini, Blue Fin Billiards, karaoke at the Marriott, Mucky Duck, and $2-Tuesdays at the Dream Theater (Fig. 10). The annual Bowling Tournament among faculty, staff, and students was always a big hit (Figs. 11, 12). And occasionally, faculty would host a their own lab party (Fig. 13).

During the 90s, there was a constant effort to rebuild the lab; especially for the faculty and staff. But the students were involved, too. It was part of our psyche. There were awareness campaigns; Open House events to let the public know we were still part of the community and that we’d return to Moss Landing; visits to the Salinas courthouse for hearings; and finally celebratory events on the hill (Fig. 14).  The new lab opened in January 2000. Many of the students during the trailer years would never occupy the new lab. But, I think many would agree, the 90s weren’t about the lack of a permanent lab structure; they were about the MLML spirit, quality of education, and long-lasting friendships that were made during our Salinas years.