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Archive for the ‘Clear Lake’ Category.

A morphological study of living and fossil Quercus (oak) pollen from California using scanning electron microscopy

California has more than 26 oak (Quercus) species, many of which have widespread distributions and different habitats. For example, the California black oaks (Q. kelloggii) are distributed in foothills and low mountains (altitude ~4750 feet), while the Coast live oak (Q. agrifolia; altitude ~830 feet) lives near the coast. Palynologists study the distribution of plant pollen and spores in space and time, and changes in their assemblages reflect changes in regional and local vegetation.

Oak pollen

Oak pollen grain

In the study of past climates, palynologists have used oak pollen as an indicator of relatively warm environments. But in the examples given above, we see that the range of different oak species varies, so the temperatures in their respective habitats must vary as well. If palynologists treat all the oak species the same — as indicators of a "warm environment" — could this lead to wrong interpretations of the environmental conditions? If the answer is yes, why do palynologists still treat all the oak species the same?

This question could be answered if we resolve a basic problem in pollen taxonomy: how to distinguish between the pollen of different oak taxa. All oak pollen have similar characteristics: three colpi (furrows) and a verrucate surface (small surface features under two microns). Even the ratio of length and width of each species overlaps. These nearly uniform morphological features make identifying oak pollen very difficult at the species level, at least using Light Microscopy (LM).

I am studying pollen samples from Clear Lake to understand climate and vegetation change in California during the last interglacial period (~120-80 kyr ago). See earlier blogs: Dispatches from Clear Lake, part 1 and part 2; California pollen taphonomy and pollen trap study in Clear Lake, California. After studying the lower part of a 150-meter-long lake core that includes sediments from the interglacial period I'm interested in, I found two distinct oak pollen numerical peaks. Before categorizing all oak pollen in the samples as "indicators of warm environments," I would like to know which species of oak they represent. Since it's so difficult to detect morphological differences using Light Microscopy, I wondered if I could identify more diagnostic features on pollen grains using Scanning Electron Microscopy (SEM). Serendipitously, a paper was published on how to use SEM and quantitative analysis to identify grass pollen at the species level. Like oak pollen, grass pollen is also difficult to differentiate using LM identification. Thinking that the methods described in the article could be applied to oak pollen identification, I decided to take SEM images of California oak pollen to see if a systematic identification method could be developed. Then, I'd use quantitative analysis methods to identify the oak species in my Clear Lake interglacial samples and see if there were particular taxa appearing and/or disappearing in the area during times of climate change.

Last summer (July, 2014) I visited Dr. Luke Mander, author of the grass pollen paper, at the University of Exeter, UK, to investigate the possibility of identifying oak pollen using SEM and computer statistics. In an SEM lab, I took 70 images of pollen from 23 extant California oak taxa and 150 images of fossil California oak pollen.

Winnie with SEM

Winnie using the Scanning Electron Microscope.

A preliminary analysis has already revealed that at least three pollen wall morphotypes, two of which represent habitat-specific oak types, can be recognized in extant California oak species. Most specimens in Type-1 represent shrub oaks, adapted to dry environments. Type-3 pollen neatly matches specific phylogenetic lineages. We were able to assign the fossil oak pollen from Clear Lake to the three categories of extant California oak pollen. Interestingly, the change in oak pollen groups in Clear Lake sediments suggests species replacement during the start of the interglacial period. I have found that more precise and objective identification of oak pollen types is possible using automated digital image analysis algorithms and a larger training set of SEM photographs of pollen from known species, so I will be working on that in the Fall. I hope to amass more detailed vegetation analyses for past periods of climate change.

Pollen wall morphotypes

The three pollen wall morphotypes.

All photos courtesy of Winnie Hsiung.

Dispatches from Clear Lake, part 2

 

UCMP's Cindy Looy is leading a project to collect 130,000 years worth of sediment data from Clear Lake in order to better understand how life has adapted to climate change. Along the way, members of her team reported back to us with all the progress and drama from the field.  Read part 1 here.

From UCB undergrad research assistant Robert Stevenson:

Robert documenting a core section.

Fri 4/27-Sat 4/28 Night Shift
First night shift was tough. Even with the nap I took to prep for the difference in sleeping schedule, staying awake was still pretty hard. We took the first core around ~2300 and new cores came up slower and slower as the night progressed and the deeper we went. Other than the desire to sleep, the worst experience of the night was the bitterly cold winds. Thankfully, I brought my phone out so I could listen to podcasts and audiobooks or browse the internet when I got really bored. When shift change finally happened at 0700, I fell asleep on the boat ride back. After unloading the cores from the boat and getting out of my coveralls and boots, I ate what I could and crashed within minutes of lying down in bed.

Sat 4/28-Sun 4/29 Night Shift
The second night out went much smoother. Temperatures were up and winds and waves were down. The weather change and bright lights on the barge sparked a torrent of midges to engulf the barge. Other than trying not to swallow the occasional bug, most of my time is spent listening to podcasts and audiobooks as I did the night before. Cores came up as slowly as the night before (1-1.5 hrs) but the waiting and sleep deprivation haven't been as bad. Shift change and everything else happened the same as the day before. However, after waking up from my sleep, Katherine and I decided to go fishing for bass with the kayak. The only thing we caught were the many plants in the shallow areas we ventured...

Mon 4/30
Media day. Katherine and I got up at 0500 to prep the breakfast for the scientists, drillers, and journalists.  No sooner had most of the day crew finished their breakfast, the first journalists arrived sooner than Cindy hoped. She had been practicing her answers at the table while still in her pajamas. About an hour after the day shift left, the other journalists began to trickle in. While being on the news seemed like fun, my body told me sleep was far more interesting and I fell back asleep until about 1400.

Thu 5/3-Fri 5/4 Night Shift
Cores were coming up relatively quickly for most of the night; every ~30min in comparison to the 1+hr waits from my first first two night shifts. I worked on removing material from the core catcher, a small nozzle shaped piece at the front of the tool with teeth that love to grab fingers. Things went relatively smoothly until what seemed like a relatively calm night after a day of rain changed for the worse around 0100. A light drizzle of rain and increased wind speeds meant the barge began to roll and yaw quite profusely. By ~0330, drilling had to be stopped due to the amount of wind and the possibility of damaging the drilling equipment. For the rest of the night, we all huddled up in the 10' x 6' science shack to wait out the poor weather until the day shift relieved us at 0700.

Fri 5/4-Sat 5/5 Night Shift
Wind conditions were as bad as the night before. For the first several hours, everyone stayed in the science shack and watched movies until the winds and waves finally subsided around 2000. Drilling started up again around 2030 and we got back to the dirty work of handling the cores. We got about another 15m before we hit the gravel layer again. Around 0300 and one failed attempt to drill through the gravel layer, it was decided that the drilling was done and the drill string should be brought up before the forecasted bad weather struck us again. While the drillers worked, Katherine and I tried to get what little sleep we could in the science shack. At 0700, the day shift drillers arrived and we headed out from our last day on the barge. About ⅔rd the way back from the barge, the engine on the fire boat gave out on us and we drifted aimlessly. Jokes and curses were abounded and we pulled out the two paddles on the boat as well as made a couple more paddles from core liners and duct tape. By the time we had almost agreed on who to eat first, a boat finally reached us and towed us back to the rental house. A 2 hour ordeal but not the longest time I have waited for a tow by AAA.

From grad student Tripti Bhattacharya:

Friday, May 4th
Today was a reminder that, despite the best laid plans, successful fieldwork often hinges on forces beyond any PI’s control. In short, it requires the weather to cooperate. The day started out windy, with choppy waves, which made it too risky to operate the coring system. We spent the day hoping for conditions to improve, which left a lot of time for staring off into the distance, sleeping, and being frustrated. Despite the lack of core recovery, the day did offer a chance to observe the aquatic birds of Clear Lake, which seemed drawn by the film of dead midges perpetually on the water’s surface around the barge. Among others, we saw a pair of mallard ducks (Anas platyrhynchos), as well as several western grebes (Aechmophorus occidentalis) and eared grebes (Podiceps nigricollis). The day ended with a relatively wild boat ride home, and the hope that conditions would improve during the night shift.

From project lead Cindy Looy:

On Tuesday May 1 we started drilling the second core. It went extremely well the first shifts at the new hole, but unfortunately the weather started to change on Thursday. We had to stop coring 2:30 pm that night because of the wave action. The weather predictions for the weekend were even more wind, with a short window during the night of Friday-Saturday. During that interval the night shift managed to get to the gravel layer 140 meters deep. Because we knew our towboat could not operate under the high wind speeds that were predicted, and we had to get off the lake by the end of Sunday, we decided to play it safe and quit operations the end of that night. The barge was towed back to Lakeport Saturday morning.

This may not sound like a happy ending, but we had a great time at Clear Lake and ended up with two perfect 140 meters of clays plus 12 meter of gravel-rich layers (that might be volcanic). The cores have been boxed up and on their way to their megafridge at LacCore in Minnesota...

Dispatches from Clear Lake, part 1

UCMP's Cindy Looy is leading a project to collect 130,000 years worth of sediment data from Clear Lake in order to better understand how life has adapted to climate change. Along the way, members of her team will report back to us with all the progress and drama from the field. Here's our first set of dispatches.

 

Assembling the barge

From Ivo Duijnstee:

Thu, April 26

First mud
It has begun. Except for some minor delays, the Clear Lake drilling expedition had a relatively smooth start. When our seven-headed UC Berkeley team arrived on site in Lakeport California, six members of the not-for-profit drilling company DOSECC had already assembled the large drilling barge to the point that it was almost good to go. Not much later, three sediment core curators of the National Lacustrine Core Facility (LacCore) arrived; completing the drill team in charge of the first days of this enterprise.

Fri, April 27

Today, a boat pushed the barge to its first drilling position in the southeastern part of the northern branch of the lake. This is in a part of the lake with a thick continuous sediment package. The deeper layers date back at least to the warm part of the previous interglacial (~130,000 years ago), a period we are very much interested in, as it may provide an analog for the current climate change in California.

Sat, April 28

From our Rocky Point base camp on the other side of the water, we can barely make out the barge’s position, as the sizeable drilling barge is reduced to a mere speck on the horizon. The inconspicuousness changes dramatically when night falls and the needle in the haystack turns into a beacon of light, as soon as the flood lights on the barge are switched on.

Tonight, the night crew (on the barge everyone works in two 12-hour shifts) made their way to the barge in the former county fire boat. This boat was made available for the crews’ semidiurnal commute by our collaborators of the Lake County Water Resources Department. Around 11PM, word reached base camp that the DOSECC drillers hoisted the first sediment core up on deck.

The barge has been moved out to the drill site.

Sun, April 29

This morning the night crew brought the uppermost 28 meter (93 ft) of sediment cores ashore, so the Holocene is taken care of. Let’s dig deeper into the Pleistocene!

Cindy Looy with the first core sample.

We have some cores!

So far, things are going smoothly on the drill platform. The day crew is off to their 12 hour shift, and the night crew is heading to bed. At the house in Rocky Point — our base camp — we are starting our pile of sediment-filled transparent tubes in the garage.

Mon, April 30

It’s media day!

Almost all day, camera crews, radio journalists, newspaper photographers and reporters were buzzing around, interviewing UCB/UCMP’s Cindy Looy and Liam Reidy, DOSECC Director of Operations Chris Delahunty and LacCore scientist Ryan O’Grady as they made visits to our floating drill site. We’ve had so much attention already, and the UCB press release is yet to come!

Chris Delahunty being interviewed for KQED radio.

The timing of the media is perfect: just like the weather, everyone in the team is in a sunny mood since the team has reached a greater depth than the USGS did at the same location during its 1973 Clear Lake drilling program. That means that the teams first target (115 m, or 377 ft) has been reached, and there is more to come.

Gravel.

At about 140 m (460 ft) into the sediment, it’s over with the monotonously greenish grey playdough that has filled the plastic core linings so far. In the dark, the night crew has struck gravel, making it impossible to get anything out of the lake bed. Fortunately, the drillers have some tricks up their coverall sleeves. For now they are mixing a special kind of mud that the day shift will use to get through the gravel layer. They will pump the muddy mixture into the borehole so that the gaps between the chunks of gravel will be filled with sticky goo; enabling the drillers to get the loose gravel out.

Tue, May 1

Alas, despite the fact the DOSECC team successfully crossed the gravel layer, things are not going well. Beyond the gravel layer there is sand and more gravel. Now things are going this slow, we decide that it is better to stop drilling at this site, and get started on a second hole nearby. As the two drillers prepare the drilling equipment for the move to the next hole, the scientific part of the night shift gets to spend an unexpected night in the house, where it is warm and couches are comfy... perhaps a bit to comfy when you are trying to stick to the nocturnal routine of the graveyard shift...

 

Renske with an armload of cores.

From Renske Kirchholtes:

Wed, May 2

*S*  hifts are 12 hours long and days start incredibly early

*C*  ores are covered in mud and so are we

*I*  ncessant noise of the generators, shrouding the barge in heavy diesel fumes

*E*  very day starts at 5.45am

*N*  o matter what happens, the entire crew is always in great spirits

*C*  lear Lake is a neat location and the weather is close to perfect

*E*  asily one of the coolest projects I have ever been part of!


See more text, audio, and video coverage of the Clear Lake drilling project here.