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Notes from the Field

Tale of a Plankton Trip

August 15th, 2018 by Dave Siegel/Seattle, Washington

A mixed phytoplankton community. Credit: University of Rhode Island/Stephanie Anderson

I am Dave Siegel, a professor of marine science at the University of California, Santa Barbara. I have been working for many years to implement  the Export Processes in the Ocean from Remote Sensing (EXPORTS) oceanographic campaign: a coordinated field effort to understand the interactions between life in the sea and Earth’s carbon cycle.

Last Thursday night, I watched “my baby” of a campaign sail away, as the Research Vessel Sally Ride left Pier 91 in Seattle for the northeastern Pacific Ocean.

While I am the science lead for EXPORTS, it’s not just my baby—it is truly a group effort. Two teams of scientists created the EXPORTS science and implementation plans, with a lot of input from the greater oceanographic community. The result is a campaign comprising more than 50 funded NASA and NSF investigators from nearly 30 institutions and many graduate students, postdocs and technicians, all excellently supported by the masters and crews of two Scripps Institution of Oceanography’s research vessels: the R/V Roger Revelle and the R/V Sally Ride.

The R/V Sally Ride, operated by the Scripps Institution of Oceanography, anchored at Pier 91 in Seattle before departing for the northeastern Pacific Ocean on Thursday, Aug. 9. Credit: NASA/Katy Mersmann

EXPORTS aims to develop a predictive understanding of the interactions of life in the sea and Earth’s carbon cycle, which is critical for quantifying the carbon storage capacity of the global ocean. The oceans are Earth’s largest active reservoir, or storage, of carbon and carbon dioxide concentrations in the atmosphere and thus helps regulate our planet’s climate. This predictive understanding of the interactions of ocean life and the carbon cycle is especially important as we are seeing that our ocean ecosystems are changing in response to changes in Earth’s physical climate. To do this we need data to test and validate these satellite-based assessments and numerical model predictions.

We are trying to tackle a super hard problem—one I believe to be a true grand challenge in Earth System Science. Our approach is simply to follow the money. For ocean ecosystems, that currency is the energy stored in phytoplankton carbon from photosynthesis. The production of phytoplankton carbon is nearly balanced by its consumption by animals called zooplankton, which in turn provide the energy for the higher trophic levels of the sea, such as fisheries and charismatic megafauna (whales, seals, sharks, and the like).

A mixed phytoplankton community. Credit: University of Rhode Island/Stephanie Anderson

The slight imbalance—roughly 10 percent of phytoplankton production globally—drives an export of organic carbon from the well-lit surface ocean into the dimly-lit twilight zone beneath. Within the twilight zone, microbes and animals of all description consume this exported organic carbon, utilizing their energy for metabolism.  This export of organic carbon from the upper ocean and their consumption within the twilight zone, along with ocean circulation, shape the carbon storage capacity of the global ocean and frame the two major research questions for EXPORTS.

Constructing a field campaign to identify and quantify the flows of organic carbon through the ocean is, of course, a major challenge. Phytoplankton physiologists need to assess phytoplankton growth rates and responses to perturbations in their required nutrients (nitrogen, phosphate, silica & iron). Zooplankton grazing and the carbon cycle impacts of their daily vertical migration to the sunlit layer of the ocean from the twilight zone need to be assessed.

In the hydro lab aboard the R/V Roger Revelle, sampling tubes will collect water samples at varying ocean depths for analysis. Credit: NASA/Katy Mersmann

Sediment traps that catch the rain of sinking particles measure the flux of sinking carbon as well as make detailed geochemical measurements that test how well our measurements of the individual pathways reflect the large-scale mass budgets needed to build and test satellite and computational models. Optical oceanographers make ocean color measurements that link the EXPORTS datasets to NASA satellite data products.  And I feel bad that I left out so many other individual research activities going on, but mentioning each of them would take up another two paragraphs!

For EXPORTS, scientists are deploying robotic explorers, like these from the Applied Physics Lab at the University of Washington. They are traveling with the ships, taking measurements at various depths. Credit: NASA/Michael Starobin

The measurements needed to constrain the various food web and export pathways as well as adequately sample the highly variable ocean environment requires technologists that can overcome these challenges.  For example, the EXPORTS team includes robotics experts who build, deploy, and analyze data from an array of autonomous underwater vehicles (AUV) that sample ocean properties on time scales ranging from minute to years.

EXPORTS has also taken advantage of recent technological advances such as novel high-throughput microscopes and in situ imaging devices that take individual images of billions of phytoplankton cells as well as zooplankton and other various organic matter.  These images are then analyzed using advanced machine learning techniques to provide unique views of the structure of plankton communities.

Advancements are also available from the biomolecular sciences where metagenomic and bioinformatics approaches provide complementary ways to characterize plankton communities and their metabolism. Lastly, several projects include numerical modelers who will use computational approaches to help answer EXPORTS science questions.

The first EXPORTS field deployment will be to Station P (50N 145W) in the Northeast Subarctic Pacific Ocean. Station P (or PAPA) has been sampled and resampled over many decades—from as far back as 1949, when it served as an ocean weather station. Presently, Station P is the terminus of the Canadian Line P transect ocean research program and is an area of focus for the National Science Foundation’s Ocean Observatories Initiative project.

Last week, the R/V Roger Revelle and the R/V Sally Ride sailed to Station P. Both are floating laboratories that enable our research, but they will have different missions.  The R/V Roger Revelle will make detailed rate measurements and conduct a wide variety of experiments while the R/V Sally Ridewill make spatial surveys around its partner ship to assess the three-dimensionality of these processes.  These ship-based measurements will be supplemented by the array of AUVs.  Both ships and robots will make ocean optical measurements linking the EXPORTS field data to present and future NASA ocean color satellite missions.

Graphic representation of the Northeastern Pacific Ocean deployment for EXPORTS.

EXPORTS is also planning a second field deployment in the North Atlantic Ocean in the spring of 2020 to provide contrasting data. Furthermore, NASA has supported a group of Pre-EXPORTS projects aimed at mining available, relevant data sources for use in EXPORTS synthesis analyses and to conduct modeling experiments to help plan this and the North Atlantic expeditions.

So I’m the science lead but I’m not sailing. Seems weird, but early in our planning we were worried about the coordination between all of the things going on. My job back home now is to help coordinate activities on the two ships and assist the four co-chief scientists in fouling off whatever curveballs that may come. I’m sure they will provide blog posts soon introducing themselves.

It is been a long time coming and I realized that as the R/V Sally Ride was sailing away. I have been there from the start pushing this along, so I suppose it is “my baby.”  I do want to thank all involved in the planning and implementation, including the program officers at NASA and NSF.

Further information about EXPORTS can be found at the NASA EXPORTS expedition team blog and the EXPORTS website.

Spruce Beetles and Shrubberies

July 22nd, 2018 by Dave Siegel/Seattle, Washington

This week while the GLiHT crew continued collecting data over the Susitna and Tanana valleys, we focused on collecting on-the-ground data on spruce beetle infestation. Our first day out proved rainy and cold, but we pressed on, only sheltering in the car during a particularly hard spell. Aside from the occasionally torrential rain, we also dealt with clambering over downed logs nearly invisible under thick grasses and ferns, as well as waist-high patches of Devil’s club. This nasty understory shrub is covered in painful thorns tough enough to penetrate through clothing. We often found ourselves having to backtrack and find a different route to our desired tree after realizing we were wading into a sea of the spiky shrubs. As a testament to this somewhat failed effort, my legs were covered in scratches and bruises later that evening.

A Devil’s club patch to be avoided.

Our task was to find and GPS spruce trees within the collected GLiHT imagery and record their infestation status and size so that they can later be used to develop infestation detection algorithms for aerial and satellite imagery. Spirits were running fairly low until we found a big patch of both green-stage infested trees (those that are infested with spruce beetles but have yet to show visual signs in their needles) and non-infested spruce trees. This find was especially exciting because these infested and non-infested trees were experiencing similar site and weather conditions, so differences that we detect in the GLiHT imagery will likely be due to the effects of the beetles, giving more confidence to the infestation detection algorithms that we develop.

An image captured by GLiHT as it flew over a beetle infested area. We have been working on identifying the infestation stage of spruce trees present in this imagery

On our second day the sun was shining brightly through only a few clouds, promising warmer and drier conditions for the day. We were joined by scientists from American University who were flying unmanned aerial vehicles (UAVs) over the beetle infested areas. The UAVs have visible, near-infrared, and thermal cameras mounted on them, which will provide a high resolution look at how trees respond to infestation. Together, the ground surveys, UAV flights, and GLiHT imagery provide information about infestation at broader and broader spatial resolutions, and should help to scale even further towards detecting spruce beetle infestation in satellite imagery.

A 3D image created from the UAV flights. We can see gray/brown infested trees in the middle of the patch of trees, surrounded by other healthy and green-stage infested spruce.

Professor Mike Alonzo from American University getting ready to fly a UAV with a visible and near-infrared sensor. The pool noodle X helps to post-process and correct the collected imagery

The American University team introduced us to some “field equipment” I never thought I would be using: foam pool noodles bolted together in an X formation. They are used as targets in the UAV imagery along with high-accuracy GPS points to post-process the collected imagery. A GPS point is collected at the center of the pool-noodle X, and then later the image is warped so that the center of the X (the bright pool noodles make for highly visible targets) matches the GPS’d point. This process makes sure the image is spatially accurate, and also makes for some entertaining field work.

Another objective of this field campaign is to describe the structure and biomass composition of alder and willow stands in south-central Alaska. Because alders and willows are shrub species (i.e. not trees), they are generally not monitored as frequently or intensely. Recently, however, these shrubs have been growing at much higher rates, with some stands reaching over 10 ft in height. This means there may be a lot of biomass going un-accounted for. With a combination of intensive field sampling, and correlation of that data to imagery from GLiHT and the UAVs, we can try to determine the biomass and structure of shrub stands across the region.

Because of the odd structure of alders and willows, the field sampling is particularly tricky. Each stem and large fork branching off from a main stem must be measured for diameter and length, and this process can take quite a long time and involve scrambling in and under a tangle of branches and woody debris.



An alder forest we sampled along the coast. The complicated mess of stems and branches made for a long day.

Back at “base camp” we seemed to have gained a couple new neighbors: a female moose with gangly baby in tow. We snapped photos of the pair, and while the female didn’t really seem to pay us any mind, the baby alternated between wanting to be near his mom (who was ambling up the path alongside our cabin) and being afraid of getting any closer to us.

The mom and baby moose who liked to frequent our cabins.

Fieldwork in Alaska also has the major perk of spectacular views during afternoon and evening breaks. After a particularly long day of sampling in Denali State Park, we opted to stay in the area rather than drive the long three hours back down to Anchorage and were blessed with a beautiful view of “sunset” over the Alaska Range.

We finally had clear enough skies to get a full view of Denali, and that evening got a great glimpse of an Alaskan Range sunset (at midnight).

Spruce Beetles in Alaska

July 16th, 2018 by Dave Siegel/Seattle, Washington

This summer a team of scientists from NASA Goddard, American University, and the Forest Service are conducting joint field work and flights with Goddard’s LiDAR, Hyperspectral, and Thermal Imager (G-LiHT) within south-central Alaska to study the ongoing spruce beetle outbreak and develop methods for early detection of beetle infestation. The spruce beetle is an aggressive bark beetle that feeds and reproduces in the inner bark of various species of spruce trees. Currently, spruce beetles are affecting over 400,000 acres in the Matanuska-Susitna Valley, resulting in widespread mortality of spruce trees. This infestation has been ramping up over the past few years in Alaska, causing concern for both scientists and Alaskans. Data collected by G-LiHT may provide the ability to detect early stages of infestation, before they would be visible in aerial surveys conducted by the Forest Service, which would allow forest managers and scientists to better predict future infestation locations and extent.

Infested spruce trees

As we pass over the Susitna Valley we can see how far this outbreak has spread. The red-brown and gray trees have been infested for several years. Some of the green trees may be the early stages of spruce beetle infestation.

This past week we have been flying with G-LiHT and visiting areas where G-LiHT data was collected to identify and GPS trees infested with spruce beetles. The infested trees can later be located and analyzed within the collected imagery. This summer, the G-LiHT instrument is flying on a King Air A90. The pilots have to maintain an altitude of 1,100 feet for the best imagery, and this makes for quite an exciting ride over the various mountain ranges in Alaska. The swoops and dives the plane makes as it follows the terrain feel more like a roller coaster than a plane ride.

King Air A90

Our pilot Justice Pousson (on the wing) and co-pilot Sam Wilson (behind the propeller) work on the King Air A90 before take-off.

Outside the windows we get a full view of Alaskan landscape. We pass over the jagged peaks of the Talkeetnas into rolling spruce forests. From up here we can really see the extent of the beetle outbreak. Tendrils of red-brown and gray trees climb northward up the Matanuska-Susitna Valley. The red trees have likely been infested for over a year, and these needles will after three years turn gray and eventually fall off the tree. Though there are still some green spruce that we can see from the plane, there’s a good possibility that many of them are in fact already infested, as infested spruce trees generally maintain green needles for at least a year. The aerial Forest Service surveys can detect trees that have red or gray needles, but detecting trees that have only been infested for one year currently requires on-the-ground inspection of tree trunks. We are hoping these flights with G-LiHT will provide the imagery required to develop algorithms for green-stage detection.

G-LiHT instrument

The G-LiHT instrument in the back of the plane. It includes a 3 cm camera and a hyperspectral, thermal, LiDAR, and solar-induced fluorescence sensor.

G-LiHT computer

The computer used to operate G-LiHT during flights. We have to make sure we turn on and off all the sensors at the right times.

The weather sometimes prevents us from completing all of that day’s planned flight lines. On Thursday we had hoped the clouds that had been hanging low over the Chugach Mountains would dissipate as the day wore on, but we ended up having to turn back after only a few flight lines were collected. While this was disappointing, on the way back to the airport we got a spectacular view of Denali rising above the clouds.


As we transited home we got a great view of Denali to the west.

Earlier this week we drove north from our base at Alaska Pacific University in Anchorage towards Denali State Park, armed with a Trimble GPS, DBH tape, and plenty of bear spray. We stopped off where G-LiHT had flown overhead the previous week and found trees to GPS. As we made our way around moose droppings and hoped not to come upon any bears, we picked out the infested from the healthy spruce trees and measured their position and size. We can identify the infested trees by the characteristic globs of pitch-out sap running down the trees’ trunks as well as red-brown dust along the bark crevices and at the base of the tree. The sap is a defense mechanism used by the trees to trap and kill the attacking beetles. Young, healthy trees are usually successful at fending off these attackers, however older or more stressed trees often succumb to the beetles’ offensive. Swarming pheromones given off by the beetles attract others in a “mass attack” which can overwhelm the defenses of even the more vigorous trees. This snowballing effect of more and more beetles attacking more and more trees, which then leads to more beetles reproducing and attacking in subsequent years is the mechanism behind the growing spruce beetle outbreaks.

Back at the cabins where we are staying we relax by a campfire and grill steaks, veggies, and salmon. I’m still trying to get used to the sunrise and sunset times in Alaska. With a sunrise time of 4:50am and a sunset time of 11:20pm, it barely gets dark at all. On the plus side this allows us to stay out later in the field collecting data without having to worry about daylight hours. On the down side it makes it pretty difficult to discern the time of day (or when you should probably head to bed…).

Our campfire (note: it was 9pm when I took this picture).

Next week we have more plans for field work, including flights with some unmanned aerial vehicles to collect data over the infestation areas. Also on my to-do list: more moose and other wildlife sightings!

A moose we spotted during field work

CYGNSS Accomplishments and New Applications

June 8th, 2018 by Dave Siegel/Seattle, Washington

As we head into the 2018 Atlantic hurricane season, now is a good time to reflect on the accomplishments achieved by CYGNSS since its launch in December 2016. Early mission operations focused on engineering commissioning of the satellites and of the constellation as a whole. One achievement in particular is noteworthy. The satellites have no active means of propulsion, yet their relative spacing is important for achieving the required spatial and temporal sampling. The desired spacing is achieved by individually adjusting a spacecraft’s orientation and, as a result, the atmospheric drag it experiences. This technique is referred to as “differential drag”. An increase in drag will lower a satellite’s altitude, thereby changing its orbital velocity. We adjust the distance between spacecraft by adjusting their relative velocities. This is a new way of managing the spacing between a constellation of satellites, and one that can be significantly less risky and lower in cost than using traditional active propulsion. As a result, we were able to afford more satellites for the same price, which ultimately led to better, more frequent, sampling of short lived, extreme weather events like tropical cyclones.

Here is a figure, provided by CYGNSS team member Kyle Nave of ADS, illustrating the change in relative speed between two of the CYGNSS spacecraft that occurred the first time a differential drag maneuver was performed, on February 23, 2017.

The orbital phase rate between the two spacecraft is shown before, during and after the higher of the two had its orientation changed to maximize atmospheric drag. Phase rate measures how quickly the angle between two satellites changes. By increasing the drag on the higher one, it lowers to an altitude and orbital velocity closer to the lower one, thus reducing the phase rate. This was an important first confirmation of our ability to perform the maneuver. Since then, there have been many more drag maneuvers. Five of the eight satellites are now properly positioned relative to one another at a common altitude, and the remaining three are expected to have their drag maneuvers completed later this year.

The primary science objective of the CYGNSS mission is measurement of near surface wind speed over the ocean in and near the inner core of tropical cyclones. In an earlier NASA blog, (15 Dec 2017), I reported on our measurements of Hurricane Maria made in September 2017. Since that time, we have been examining the quality of our measurements both within and away from major storms. Measurements at ocean wind speeds below 20 m/s (44 mph) were found to have an RMS uncertainty of 1.4 m/s (3 mph).  Measurements of storm force winds during the 2017 Atlantic hurricane season were found to have an uncertainty of 17% of the wind speed. The analysis that produced these results is reported in Ruf et al. (2018). DOI: 10.1109/JSTARS.2018.2825948.

CYGNSS operates continuously, over both ocean and land, and the land data have been another focus of recent investigations. The quality of some of those measurements, in particular regarding its spatial resolution, has come as something of a pleasant surprise. Here is one example of CYGNSS land imagery, of the Amazon River basin in South America, provided by Dr. Clara Chew of UCAR.

In the image, inland water bodies are prominently visible. This includes not only the major arms of the Amazon River but also its quite narrow minor tributaries. Careful examination of this and similar CYGNSS images suggests that the spatial resolution is markedly better here than it is over typical open ocean areas. The explanation lies in a transition of the electromagnetic scattering from an incoherent, rough surface regime over ocean to a largely coherent, near specular regime over inland waters. The fact that coherently scattered signals have inherently better spatial resolution is a well known phenomenon. What was unexpected is the widespread, global extent to which land surface conditions support coherent scattering. It requires the height of the surface roughness to be significantly below the wavelength of the radiowave signal, which in our case is 19 cm. This is apparently a ubiquitous property of wetland regions. It is a very fortuitous property for us, as it should enable an entirely new direction in scientific applications of CYGNSS measurements over land. NASA has recently added new investigators to the CYGNSS team specifically to study these new and exciting land applications.

A recent article summarizing these and other CYGNSS achievements, as well as some of the future applications of its measurements, is available at <>. The mission has demonstrated that smaller, more cost-efficient satellites are able to make important contributions to the advancement of science. In the months and years ahead, CYGNSS will hopefully be able to demonstrate that those advances can lead to practical scientific applications, such as extreme weather monitoring and prediction, that will benefit humankind.

NAAMES-IV Expedition: April 10, 2018 (FINAL blog)

May 16th, 2018 by Dave Siegel/Seattle, Washington

So the challenge of writing the last blog for the NASA NAAMES field campaign has fallen into my hands and I have to admit that I don’t know what to write.  There is a ton of exciting science to share and many stories of adventure, but regaling upon these discoveries and outward experiences seems inappropriate for this final entry.  I think it instead better to try and capture the deeper personal aspect of seeing this long journey come to an end.  And it is here that I find myself at a loss for words.  Perhaps a path for describing this experience is to draw upon one of the final scenes from Peter Jackson’s filming of the Lord of the Rings…

After a tumultuous journey, our four heroic hobbits, Frodo, Sam, Merry, and Pippin, finally find themselves back in the Shire at the local tavern, each with an ale in hand.  All around them, Shirefolk are laughing and carrying-on, but the four hobbits quietly sit around a corner table looking at each other and saying nothing.  They are experiencing the loneliness of a profound shared experience that leaves nothing left to be said between its participants and nothing that can be told to an outsider that will adequately convey the events that have taken place.  Each has seen the strengths and weakness of the others and themselves, and this knowing tightens the bonds of friendship.  It is a moment that needs no spoken words, but it is also a moment that cannot last.  Eventually, the time comes to raise the glasses at the unspoken words and re-engage.  This moment comes for the hobbits and each is soon following their new paths in life, but not without the lasting bond of their shared adventure.

Fortunately, NAAMES has not required us to cross middle-Earth, fight impossible battles, and cast a cursed ring into the fires of Mount Doom, but I believe that, beyond the science accomplished, it has created bonds of friendship linked by a common experience.  Perhaps it is here that the greatest value of NAAMES can be found.  Like the hobbits, we will soon arrive at the shire of Woods Hole and meet together for a final celebration.  As at the end of the first three NAAMES campaigns, I expect this final celebration will once again be similar to the above described scene from Lord of the Rings.  We will be a group of friends celebrating a common adventure that those outside our group cannot fully understand.  We will share stories, relive particular moments, appreciate each other’s company, and raise a glass to a wildly successful cruise and mission before we all depart to reintegrate into our separate lives back home.

Beyond this, I believe there is little left to say other than to extend my personal and profound gratitude to all the loved ones back home who have follow our blogs and waited for us to return safe from the sea, to the captains and crew of the Atlantis and the shore support at WHOI who have made the NAAMES campaigns possible, and to all the scientists involved in NAAMES who have enabled this mission to be successful beyond my wildest dreams.  I simply cannot wait to see and read about all the new insights gained from our work as it emerges over the final year and a half of the NAAMES project!

My deepest thanks to you all,

Written by Michael Behrenfeld