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Archive for May 2014

Mighty microbes implicated in Permian mass extinction

Ninety-six percent of marine and 70% of terrestrial species died in the Permian mass extinction, which began about 252 million years ago and lasted for over 20,000 years. Geochemistry tells us that this extinction coincided with a severe and rapid change in the Earth’s carbon cycle, but this alone could not have been the cause of the extinction. Initially it was thought that carbon dioxide released by Siberian volcanism explained this change in the carbon cycle but the volcanic outgassing was not large enough to have been responsible for this big a disruption. So if not volcanoes, what could have produced so much carbon in the atmosphere?

A new study shows that the speed and exponential growth of carbon had to be of biological origin. The study proposes that the emergence of a new group of microbes, Methanosarcina, was responsible for producing the methane in the atmosphere that led to the extinctions. At around 250 million years ago, these microbes acquired fancy new machinery, or a new metabolic pathway through lateral gene transfer that made them capable of taking advantage of the large amounts of marine carbon produced at the time and converting it to methane. This also required large amounts of nickel that was released by the volcanoes. The new source of nickel, a limiting resource in the ocean, combined with increases in marine carbon created a feeding frenzy of bacteria. Following the production of methane by Methanosarcina, other microbes, anaerobic methanotrophs, turned the methane into carbon dioxide further lowering oxygen levels in the ocean.

Today we see similar short-lived low oxygen events in the ocean, but these are driven by algal blooms. Marine algae (i.e., marine plants) are responsible for most of the photosynthesis that occurs on the planet and the resulting oxygen and marine organic carbon. Just like the plants that grow in your garden, these algae rely on nutrients to grow and reproduce. When there’s a new source of otherwise limiting nutrients, they often grow rapidly and we call this a “bloom.” As the algae use up the nutrient source, they begin to die and microbial decomposition begins. These microbes consume oxygen in the water as they feed on the algae and release hydrogen sulfide gas as they have their own population explosion. Just as scientists have observed in the fossil record for the Permian extinction, we see low oxygen levels in areas of the ocean following algal blooms and increases in microbial digestion. The hydrogen sulfide gases released during decomposition of modern algal blooms often produce mass die-offs of marine animals.

Ulva releasing life history stages

Ulva releasing microscopic life history stages. Photo by Rosemary Romero.

I study microscopic life history stages of modern bloom-forming algae, green seaweeds in particular. These life stages are similar to invertebrate larvae in that they are released into the ocean by adults and can be carried long distances by waves and currents. Last spring I set out to learn how to detect these life stages in coastal waters using their genetic code, or DNA. I was hoping that I could use this method to predict when these seaweed blooms were more likely to happen. My first challenge was to find out if I could extract DNA from these life stages. I went to the rocky intertidal at the Romberg Tiburon Center (RTC) and collected some specimens of adult Ulva, the alga responsible for most of the worlds green seaweed blooms. I brought the algal specimens back to the lab and kept them dry, dark, and cold for a week. When I submerged the algae in artificial seawater they began to release what looked like green ooze. Upon closer investigation under a microscope this ooze proved to be microscopic swimmers, Ulva's tiny planktonic life history stage! I filtered this solution of swimmers to concentrate them and stored them in the freezer for DNA extraction at a later time. Just to make sure my procedure for DNA extraction would work for green algae, I extracted DNA from as many morphologically different specimens of adult Ulva I could find at RTC. These included specimens taken in small volume from the solution of swimmers and I filtered them on the the same day. After the extraction procedure I used a method called gel electrophoresis to test if I had successfully extracted DNA from my samples. This method works by adding a fluorescent dye that will bind to any DNA present and produce a glowing band under UV light. Unfortunately, the first four times I tried this, no glowing bands resulted. After taking a few more classes and working with other scientists that have experience extracting DNA from algae, I finally had a breakthrough. I successfully extracted DNA from the adult Ulva specimens I collected in December 2013. I’m still tying to figure out what went wrong with the filters, but I went back to RTC in April 2014 to do another survey of Ulva species. By the end of this spring I will be able to test for changes in Ulva species composition across different seasons.

Tracking down ammonites in the Denver, Colorado, area

In July 2013, I visited the Denver, Colorado, area to collect data from two collections housed at United States Geological Survey (USGS) facilities and the University of Colorado (CU) Museum of Natural History. The USGS collections are housed in the Core Research Center on the Denver Federal Center campus. The building is also a repository for a large collection of soil samples and approximately 1.7 million feet of drilled rock, sediment, and ice cores. The Museum of Natural History is located at the University of Colorado campus in scenic Boulder, Colorado.

Though these collections cover a wide range of organisms from all over the world, my purpose there was to visit the fossil collections from the Western Interior Seaway. The Western Interior Seaway was a widespread shallow sea that flooded the North American continent from the Gulf of Mexico to the Arctic Ocean during the Late Cretaceous Period (about 100 to 65 million years ago). My work focuses on the faunal dynamics associated with invasion into these shallow sea environments. By more closely examining natural experiments in the past when biota encountered widespread novel physical conditions, we can better inform our predictions of how organisms will respond to the rapid global change happening today.

To that extent, I was interested in photographing and documenting a portion of the vast numbers of ammonites the two institutions have amassed over the years. Ammonites are a completely extinct group of hard-shelled cephalopods, related to the modern-day squid, octopus, and nautilus. Their fossils are often sold in rock shops because their beautiful undulating suture lines make them aesthetically pleasing items. They were incredibly diverse and abundant during the time the Western Interior Seaway existed, and so are an ideal study group to explore the dynamics of this system.

Acanthoceras sp.

An Acanthoceras sp. specimen (UCM11843) collected from the Lower Cretaceous rocks in Colorado, now housed at the CU Museum of Natural History.

The large collection of Cretaceous bivalves, gastropods, and ammonites kept in the USGS collection is primarily the result of work done by USGS geologists, such as William Cobban, who collected and published on the Western Interior throughout the late 20th century and is still at the USGS facilities in Denver today. The collection contains drawer upon drawer of specimens. With the generous help of curator Kevin “Casey” McKinney, I photographed hundreds of ammonites, including many unpublished specimens. These photographs will be used to identify morphological features that may have influenced the degree to which ammonites were able to invade or adapt to the seaway. It was an adventure exploring the dusty cabinets, where every drawer held a surprise.

Drawer of ammonites

A drawer filled with nothing but ammonites at the USGS facilities.

After four days in the suburbs of Denver, I took a bus up to beautiful Boulder, Colorado, just 45 minutes outside of Denver proper. After winding my way through the University of Colorado-Boulder campus, I arrived at the Bruce Curtis Building where the museum collections were housed. Collection manager Talia Karim greeted me and helped me get set up before showing me around the collections housed in the basement. Here, there were not as many specimens as at the USGS, but they were no less impressive. During the next three days, I photographed about a hundred more beautifully prepared specimens before I had to say goodbye to the Denver area.

The richness of the collections were such that, no matter how often I visit, there will always be much more to discover. I have plans to return in the near future to continue my explorations of these amazing and underused resources.

Examining morphologic variation in varanid skulls through time and space

As a graduate student affiliated with the UCMP, there are many resources readily available to me. Not only does the museum have the largest university research collection, but the curators, museum scientists, and staff are some of the most knowledgeable and helpful anywhere. UCMP is recognized for taking care of its graduate students, and one of the ways they do it is by providing multiple funding opportunities. I applied to UCMP for funding last year in order to conduct museum travel for my research and I was fortunate to get an award from the Welles Fund.

One major aspect of my research focuses on looking at shape differences in the skulls of monitor lizards. Monitor lizards, or varanids, are generally thought of as being fairly large lizards (e.g., Komodo dragon), but some may be no longer than a pencil. Although there are many extinct species and genera within this group, there are approximately 70 living species in the single genus Varanus. They live in Africa, Southern Asia, and Australia, and are ecologically versatile, with some being strictly terrestrial, arboreal, or even semi-aquatic. Fossil varanids from Asia may be as much as 90 million years old; varanid fossils are also found in North America and Europe.

Two varanids

Left: A Komodo dragon (Varanus komodoensis) from the Cincinnati Zoo. Photo by Mark Dumont (CC BY 2.0). Right: The smallest monitor lizard, a neonate Varanus brevicauda. Photo courtesy of Eric R. Pianka.

Thanks to my Welles Fund award, last year I was able to visit the American Museum of Natural History in New York, The Yale Peabody Museum in New Haven, CT, and the Australian Museum in Sydney, Australia. At these museums I photographed the skulls of over 300 modern varanid skulls, getting top, side, and bottom views of each. I use these photos for a technique called Geometric Morphometrics. Morphometrics (greek “morphe” or shape, and “metria” or measurement) is a general term used for describing the quantification of shape. Many fields within biology use this technique to study numerous questions, like changes from juvenile to adult morphologies, how ecology influences shape, and in my case, comparing species from different regions to each other and to those in the fossil record. Geometric Morphometrics is a technique that uses landmarks (coordinates) placed on photos of specimens that can be regarded as a a similar point in each specimen in the study. There are various ways of analyzing the data, but essentially the locations of the landmarks on different specimens are compared and quantified. One main analysis conducted with this data is called Principal Component Analysis which tells you where the maximum amount of variation in your specimens happens to be. This allows the researcher to determine how much shape difference exists in their specimens of interest. In my case, museum visits are essential since they allow for adequate sample sizes to compare the species found in different locations of this group.

Varanid skull

Example of a Varanus skull with landmarks. Photo of AMNH specimen by Elizabeth Ferrer.

I was able to analyze the data to answer various questions, and one of the most interesting discoveries was that the varanids in Africa, where there are only about six species, are almost as morphologically variable as those in, for example, Australia where there are approximately 30 species (depending on where you designate certain groups). I am continuing to analyze and collect data, but I am thankful to the UCMP for providing the finanical assistance necessary for me to complete a large portion of my dissertation project. As a side benefit, traveling to distant museums allowed me to visit interesting and beautiful locations!

Freemantle Beach and Sydney Opera House

Fremantle Beach, Western Australia (left), and Sydney Opera House, Sydney, Australia (right). Photos by Elizabeth Ferrer.

California pollen taphonomy and pollen trap study in Clear Lake, California

Pollen analysis (or palynology) has been used to study Quaternary changes in vegetation and climate in North America since the nineteenth century. Palynologists generally compare plant assemblages in spatial-time frames instead of focusing on particular plant species. These changes in plant assemblages across landscapes through time are a good indication of vegetation shifts caused by environmental changes. Besides using pollen assemblages to reconstruct parent plant communities in a particular area, certain species, which are sensitive to changes in temperature or precipitation, are of special interest. By comparing assemblages of plant communities and these indicative species through time and space, we can infer how regional flora responded to environmental changes such as changes in climate.

Before comparing these past assemblages of plant communities and inferring environmental changes, palynologists carefully consider the processes leading to pollen accumulation. Do their pollen and spore assemblages accurately reflect local or more regional vegetation? Are certain pollen types over- or underrepresented? Does the assemblage include the majority of taxa present in the local plant communities? Pollen assemblages are incorporated in sediments at the end of a long taphonomic pathway, and are affected by temporal and quantitative aspects of pollen and spore production, differential dispersal characteristics, secondary transport, and other taphonomic processes.

How could we get hints of that process throughout geologic time? Wind-pollinated assemblages are most often transported and they are usually produced in large amounts and have wider dispersal ranges. To study the taphonomic process of pollen and spores, palynologists often use surface samples to research the discrepancy between vegetation composition and pollen assemblages. Such analysis also might help to understand the taphonomic conditions in the sample area and provide a reference point for a regional paleopalynological study.

First version of pollen trap

First version of a modified Olefield pollen trap (Jantz et al. 2013).

For my dissertation research, I am compiling a California pollen reference collection. Focused on the last interglacial period, I plan to reconstruct the vegetation from a relatively warm period during that time interval. My methods involve extracting pollen from core samples from Clear Lake. Clear Lake is the largest lake in California with a sedimentary record going back at least to the last interglacial period (~130 ka) (see Scientists core into Clear Lake to explore past climate change). The microscopic pollen grains are expected to yield important clues on the history of vegetation communities and the taphonomic process surrounding Clear Lake; data from pollen traps set in different vegetation areas in the vicinity of the lake — forests up to 2 km from the lake, or small, more distant upstream communities — will enable further analysis of modern vegetation types.

The most common pollen in Clear Lake samples is wind-pollinated, mostly pine and oak pollen. An important question is: does this pollen mainly originate from the northwestern forests, the southwestern forests, or other adjacent places? To solve this question, I started to look for appropriate types of pollen traps to collect surface samples and, with the help of my undergrads, Mary Grace Rodriguez and Rebecca Shirsat, we built some traps to position in the field.

After visiting the Clear Lake area a couple of times, I positioned the first 10 pollen traps close to the lake — many thanks to Carolyn Ruttan from Lake County Water Resources who helped me obtain landowners' permits for this.

The first time doing field research is often filled with anticipation. On January 20, I left Berkeley in the early morning. I was so excited — not only because I could finally install my pollen traps, but because it would be only my second time driving through winding mountain roads!

After meeting Carolyn Ruttan I set off to Clear Lake State Park, our first pollen trap site. I selected a rocky corner of the lake that had a gorgeous view. Securing this first pollen trap to the ground was a challenge, but we stabllized the base with pebbles and used a small iron wire to prevent the trap from blowing over in the wind.

The next trap was easier to position, being on soft soil in Anderson Marsh. We only had to avoid picking a spot where weeds might cover the area later in the year.

The Lake County Land Trust’s Rodman Preserve is another one of my research sites. The trust was formed as a non-profit organization in 1994 and it works to protect important land resources, wetlands, forests, etc., in Lake County, CA.

Preparing to install a trap and one in the Rodman Preserve

Left: Preparing to install pollen traps in Clear Lake State Park. Right: Pollen trap in the Lake County Land Trust's Rodman Preserve.

The Elem Indian Colony, near Clearlake Oaks on the eastern shore of Clear Lake, is my fourth research site. It is a Native American colony of Pomo, associated with the Sulphur Bank Rancheria. The residents were friendly and curious about our purpose. I am sure they will help prevent tourists from removing the trap that we placed near a power station.

We then attached pollen traps to railings and floating platforms at three sites. Installation of the first 10 pollen traps was completed on this first trip; we went back two weeks later to complete the west side of the lake.

Pollen traps on platforms

Two pollen traps attached to floating platforms.

The most serious threat to my traps is the strong winds around Clear Lake, especially on the northwest side. Strong, seasonal winds can take down deeply-rooted trees and it could damage the pollen traps. Squirrels and birds might also be a problem but hopefully, the iron wires we used will keep them safe from animals. I plan to return to Clear Lake later in the year to replace trap materials and to see what my pollen traps have collected (if the squirrels and birds have not absconded with my trap materials)!

The hunt for a Ph.D. thesis: Collecting Late Cretaceous plant fossils in New Mexico

"It ain't Mexico and it ain't new" [quoted from a postcard in a gift shop]

Armed with hammers, chisels, pry-bars, boxes of newspaper, and sunscreen, two trusty assistants (recent graduate Meriel Melendrez and current undergrad Nicolas Locatelli) and I drove from Berkeley in our 4WD extra-long SUV heading for southern New Mexico. There, we met up with paleobotanist Dr. Gary Upchurch and crew from Texas State University and geologist Dr. Greg Mack from New Mexico State University for two weeks of field work in Late Cretaceous plant localities of the Jose Creek Member. It was a bona fide tri-state expedition working on multiple projects. My interests were to set the foundation for my dissertation work on the ecological diversity of Late Cretaceous forests in warm-wet climates. For this I needed a primary study site to generate new collections and data. The trip wasn’t entirely exploratory — I was familiar with some of the localities from my undergraduate days with Dr. Upchurch, and had collected here previously. Based on this earlier work, we knew that there was an abundance of plant fossils, and preliminary studies have indicated that the fossil assemblages of the Jose Creek Member represent a subtropical-paratropical forest. That’s right, in the present day desert of New Mexico, rich in angiosperms but mixed with conifers and ferns.

Late Cretaceous plant communities often contain interesting combinations of plants that are no longer found living together under the same climatic conditions (for example palms and redwoods). That is because the Late Cretaceous represents an important transitional time, as flowering plants (angiosperms) rapidly diversified and rose to dominance in warmer climates. During this time, the typical early to mid-Mesozoic forests that were dominated by ferns and gymnosperms (conifers and other non-flowering seed plants) transitioned to the modern, angiosperm-dominated forests. This begs several questions: what were the different ecological roles of angiosperms and conifers in these forests, and did conifers and other gymnosperms serve functions that have now been replaced by angiosperms? How has the structure of plant communities in warm-wet climates changed from the Cretaceous to present, and how does this inform our understanding of the evolution of modern tropical forests? These are the questions that fueled my quest into the southwest last summer. The New Mexico sites seemed like an ideal place to start my investigations, and we ambitiously set out to do some major collecting.

In the Jose Creek Member, the best-preserved plant fossils come from beds of recrystallized volcanic ash. My initial goal was to collect quadrats from multiple volcanic ash beds, which would give an indication of the vegetation through time (because beds are not necessarily deposited at the exact same time). But things don’t always work out like you plan, and luckily this was one of those times ….

Field site

Field site on the distant hills (can you see the exposure?), but with modern vegetation of course! Photo by Meriel Melendrez.

Dori with palm frond

Fossil palm frond (with Dori for scale). Photo by Meriel Melendrez.

Preparing a collecting site

Meriel and Nick preparing a collecting site. Photo by Dori Contreras.

The first locality we went to had an ash bed that was known for its abundance of plant fossils and beautiful preservation. After setting up the first collecting quadrat with Meriel and Nicolas, Dr. Mack and I headed off to investigate how far we could track the exposed bed, as its lateral extent was hitherto unknown. To our amazement, we were able to track the deposit for ~1.2 km! This was an incredible revelation; here were the remains of a forest preserved in ash for quite an impressive spatial extent, which would enable the reconstruction of a plant community at a single instant in time. This was considerably more attractive for my questions than reconstructing vegetation from multiple beds comprising an unknown amount of geologic time. I adjusted plans and concentrated our efforts on this deposit alone (rather than a compilation of sites) and spent the next nine days collecting small quadrats along the length of the bed. The deposit is so rich that virtually every rock we cracked open had multiple fossil plant specimens! Consequently, almost everything we touched was wrapped in newspaper, hiked out of the field site, and brought back to the UCMP. This was no light task — thank goodness for the incredible Meriel and Nicolas! In total we collected samples from 14 sites along the exposure. These initial collections reveal a rich and laterally diverse flora, and yet are only the tip of the iceberg!

We headed back west with the SUV packed to the brim and riding low from the weight of the fossils; it was the maximum that could possibly be brought back. I should also mention — Cindy Looy and Ivo Duijnstee, along with some of the other Looy Lab members (Jeff, Renske, Robert) — were in New Mexico for a conference and we arranged to meet them. This was particularly fortuitous, not only for good company, but also because they took two large tubs of fossils back with them! Another two tubs went back to Texas, and made it to Berkeley later that summer. All in all, it was enough fossils to fill two double-door cases in the museum!

Of course, the field work is only the beginning and, since then, a lot of work has gone into getting these first collections organized and examined. Currently, two students (James Buckel and Negin Sarrami) and I are describing and photographing leaf morphotypes from the collections to assess the diversity of plants in the flora. A large portion probably represent unknown/undescribed species, so we differentiate ‘species’ as morphotypes based on detailed descriptions of leaf characteristics. The flora includes a diversity of herbaceous and woody ‘dicots’, monocots (e.g., palms and ginger), cycads, ferns, an abundant extinct sequoia-like conifer and several extinct conifers probably related to the Araucariaceae. Overall, it is clear that it will take several more field excursions and countless hours of lab work to understand the taxonomic and structural diversity of this amazing flora. And, of course, I am eagerly looking forward to the return trips and uncovering the treasure trove of fossils still entombed in the rock out in the desert!

Fossil fern

Fossil fern. Photo by Dori Contreras.

Angiosperm leaf

Angiosperm leaf with insect feeding damage (holes). Photo by Dori Contreras.