Bridging the Gap

Screen Shot 2016-07-29 at 12.48.44 PMContributed by Leah Shizuru


As I stood near the puka and gazed at the raw beauty of the steady flow of incoming ocean water spilling into the fishpond I listened to and appreciated the unmistakable sound of rushing water. What a thrilling experience for both the eyes and ears.

It was hard to fathom that the 80 ft gap directly in front of me would soon be closed. I pondered how the volunteers would ever complete this task when the water appeared to ebb and flow with such impressive speed. Though difficult to imagine, I was told that the enthusiastic bunch of men and women that worked daily on closing the puka, or gap, were making great progress with the help of a campaign to fund this labor-intensive project and raise awareness of the need to close the break in the wall in He’eia fishpondPani ka Puka.

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Bridging the gap would be a crucial step toward restoring this fishpond to its original state and enabling traditional aquaculture to ensue again. Ultimately, caretakers of He‘eia Fishpond would once again be able to raise enough herbivorous fish such as mullet (‘ama‘ama) and milkfish (‘awa) to provide for the community. Sustainability. Preservation. Tradition.

Bridging the gap

Benefits of traditional fishponds extend to research and education. That is how I became involved with He‘eia Fishpond. Last summer I had the opportunity  to intern at C-MORE (Center for Microbial Oceanography: Research and Education), a NSF Science and Technology Center, to work on a research project with Dr. Rosie Alegado looking at the microbial diversity in this coastal ecosystem. As part of my research, I ventured to the fishpond once a week with my two lab mates in order to gather water samples. These water samples were then taken back to the lab, filtered, and subjected to extraction of genomic DNA.

During these visits we got to know the Paepae o He’eia stewards (kia’i loko), learn about the history surrounding the fishpond and see the progress of the various other restoration

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Pictured left to right: Dr. Kiana Frank, Charles Beebe, Kyle Yoshida, and Ka’ena Lee

projects including the removal of mangrove from along the ancient fishpond wall  and invasive limu (algae) from in and around the pond. Our research aimed to complement these restoration efforts. Through a better understanding of the genetic makeup of microbes such as photosynthetic bacteria and microalgae that form the base of the food chain in the fishpond, better management policies could be implemented.

Our weekly visits to the fishpond also enabled us to see, first hand, the outreach efforts of the fishpond stewards. One evening during a 26-hour diurnal experiment in which we worked with Dr. Kiana Frank (who was analyzing microbial communities at different depths within the sediment as well as their sources of respiration and respiration rates), we interacted with a few children who were on the property.  

During the process of water filtration and processing of sediment cores we were surrounded by a group of inquisitive and eager children who wanted to help. Ka‘ena, who was 5 years old, asked, “What are you doing?” as he looked at the filtration apparatus, bewildered. My co-workers and I told him that we were filtering water that we had just collected in order to study the microbes in the fishpond. Ka‘ena looked puzzled and we could see from the confused, yet still-interested look on his face that we needed to add to our answer and perhaps simplify it. I quickly began to think of a way to re-explain this so that he could understand it. Thankfully, my labmate, Mikela, interjected, “Oh, ok! So you know when you’re finished cooking spaghetti noodles and you have to drain out the water?” Ka‘ena nodded. “How do you get rid of the water that you cook your pasta in,” Mikela asked. He described a strainer and Mikela replied in an encouraging tone, “Yes, exactly, a strainer. So what this is [as she pointed to the filtration apparatus with the filter membrane] is like the strainer and the microbes are like the spaghetti noodles that we want to keep.” What a perfect analogy to give to this young child! Ka‘ena beamed at Mikela and responded, “Oh, I see!” We followed Mikela’s lead and continued to answer the other children’s questions in a simplistic, analogous manner. What a treat it was to be able to answer their thought-provoking questions.


Illustration of Oahu fishponds by Robert Dampier, 1825. (Wikipedia Commons)

It was in that moment that I realized how this summer had come full circle: I was working for an organization that, in its very title, seeks to educate. I gleaned from the knowledge of Dr. Alegado and Dr. Frank and in turn was able to pass on that knowledge to these young kids. Not only had I learned more science this summer, but I had formed a deeper appreciation for my culture, for the faithful caretakers at He‘eia fishpond, and for the brilliant scientists (like those at C-MORE) who seek to better understand the environment in which we live. I saw the value of perpetuating knowledge from one generation to the next.

It was then that I understood the necessity of bridging the gap.

Hawaiian fishponds, also known as loko i‘a, were traditional forms of aquaculture that served as a dependable protein source for ancient Hawaiians. The oldest fishpond in Hawai‘i was built about 1200 years ago. By the 1900s there were only 99 of the 360 built in the islands that were operable. 

Leah Shizuru attends the University of Hawaiʻi at Mānoa and will earn a B.S. in Microbiology Spring 2017. As a part-time lifeguard with Ocean Safety, she enjoys spending her free-time outside with her friends and family— surfing, hiking, swimming, paddling, and bodyboarding are just a few of her favorite hobbies. 

Leah would like to thank Yoshimi Rii, Hi’ilei Kawelo, Keli’i Kotubetey, and Dr. Rosie Alegado for their oversight and feedback on this blog post and would also like to thank Dr. Alegado for the opportunity she has to work in her lab.           

Would you like a side of plastic with your fish?

J.Wong-Ala_picContributed by Jennifer Wong-Ala

The aroma of freshly defrosted Alepisaurus ferox (Longnose Lancetfish)  stomach begins to fill the lab as I place my first stomach of the day on the dissection tray. I look at the unopened stomach and begin to see an odd shaped object protruding from the inside. I make my first cut to expose the stomach contents and see the culprit responsible. A white piece of plastic that closely resembles the material paint buckets are made of emerges along with a degraded piece of a black trash bag intertwined with fishing wire. I begin to shake my head and continue to document the rest the of stomach contents.

Plastic pollution has been known to affect large, much-adored marine animals such as sea turtles, monk seals and seabirds. These animals can be strangled, suffocated, or even killed when they ingest plastic debris. Even microscopic organisms such as copepods have been seen to eat microplastics because they closely resemble phytoplankton – microscopic plants in the ocean. Now teams of scientist from the Monterey Bay Aquarium Research Institute (MBARI) and the University of Hawai‘i at Mānoa (UHM) are finding more trash at deeper depths (2000 – 4000 m), where commercially important fish are mistaking plastic debris as food.

But how does plastic even get that deep in the ocean? Aren’t most plastic debris buoyant and stay on the surface? Scientists at MBARI analyzed 1149 video recordings of marine debris from 22 years, looking at videos from remotely operate vehicles (ROVs) in the Monterey Canyon, and found that the largest proportion of the debris observed in the videos was plastic (33%) and metal (23%). Plastic debris was most abundant in undersea canyons at depths of 2000 to 4000 meters. It is thought to have reached those depths by these canyons’ natural sediment transport processes, which exert forces great enough to carry research equipment to the bottoms of these canyons.

Plastic debris can also be passed through the food web in the ocean when deep-sea animals eat other organisms that can live at many depths. For example, plastic debris has been found in the stomachs of the lancetfish which occupy a broad depth range  (0 to 1,000 meters). Lancetfish have been found to ingest plastic from the surface and then travel to deeper depths where it becomes prey to other species such as Opah, Albacore and Yellowfin tuna. The plastic from the Lancetfish has now been passed through the food web and potentially to our dinner plates.


Lancetfish habitat extends to depths where plastic accumulates.

Big steps are already being made in regards to one type of plastic debris called microbeads. This year President Obama signed the Microbead-Free Waters Act of 2015 that will ban the use and sale of products containing microbeads by 2018 and 2019. This was a big step in making a positive impact for our environment, but there is so much more to do.


The author working in the field

Jennifer Wong-Ala transferred from Kapi‘olani Community College to the University of Hawai‘i at Mānoa (UHM) in Fall 2015 as a Junior in the Global Environmental Science Program. She is a NOAA Hollings Scholar, C-MORE Scholar in Dr. Neuheimer’s Lab, Laboratory Technician in Dr. Drazen’s Lab, and is also part of the SOEST Maile Mentoring Bridge. Jenn is interested in computer modeling/analysis of how ocean processes interact with organisms in the ocean and how to best preserve these natural resources. In the future she plans to bring these skills and interests together to conserve marine life in Hawaii. This post was originally written for OCN 320 (Aquatic Pollution), a writing intensive requirement for the GES major.           

Mining, Metals and Megafauna in the Pacific Deep-Sea

DivaAmon Contributed by Diva Amon

I’m a deep-sea biologist with an ethical conundrum: I get to work in one of the most poorly-known habitats on the planet but the only reason I have that privilege is because it will likely be exploited and irreparably altered within the next decade.

We rarely think about where the never-ending stream of resources that we consume comes from. Take for instance the iPhone 6S you upgraded to when nothing was wrong with iPhone 5, or that zero-emission electric car you just bought: do you know where the materials used to make those came from? The demand for metals is increasing worldwide resulting in resources being harvested in ever more remote places, and the next frontier of mining will likely take place in the deep ocean.


Figure 1. Polymetallic nodules of various sizes. Image credit: Diva Amon.

My research takes place in the Clarion-Clipperton Zone (CCZ), an abyssal region (3500-5500 m) in the tropical Pacific Ocean that stretches from Hawaii to Mexico. The CCZ has dense beds of polymetallic nodules: lumps of metallic ore laden with cobalt, copper, nickel and other rare metals that sit like cobbles on a street. It is thought that they form in a similar way to a pearl (accretion) at a rate of a few millimeters per million years. As this entire region is in international waters, it falls under the mandate of the International Seabed Authority (ISA) and so far, there have been 15 mining exploration areas allocated, each up to 75,000 km2 or roughly the size of Panama.

ISA map

Figure 2. Exploration claim areas in the CCZ. Downloaded from the ISA website.

Let’s be honest, nodule mining is going to do some damage. Nodules will be harvested, destroying all animals that rely on this habitat and leaving no possibility for the re-establishment of this community in the future. Machines will also likely disturb and compact large swathes of sediment >5 m wide and 5-20 cm deep, squashing air out of the sediment (removing crucial living space for animals) as well as directly killing any animals residing in or on the sediment. Huge sediment plumes will also be kicked up, which will travel for kilometers before depositing elsewhere, potentially stifling animals and blocking filter-feeding apparatuses. Further entombment of the seafloor will likely occur when tailings are discharged into the water column. Not to mention other possible impacts that include light and noise pollution from machinery, and major changes to the geochemistry of the sediment, food webs (with repercussions for fisheries), and carbon sequestration. The cumulative impacts of these operations aren’t yet understood but will likely be long-standing and ocean-wide.

Oebius mining method

Figure 3. The polymetallic-nodule mining concept taken from Oebius et al 2001.

Despite this looming threat, the CCZ is critically underexplored. We literally do not even know what lives there. The ISA has made it mandatory that contractors undertake a baseline study of the biology living at the seafloor before EIAs and mining can begin.  The ABYSSLINE Project, which I work on, is doing just that in the claim area leased to UK Seabed Resources Ltd (UKSRL). My task is to find out what megafauna (the awesome charismatic animals over 2cm in size) live in the UKSRL claim, how abundant and diverse they are, and what ranges they occupy, not only within the claim but also across the entire CCZ. It’s also crucial to find out whether variations in the megafauna community correlate with nodule presence and other environmental parameters.

Although it is still early days for the project and there are still many more years of work to do, preliminary results show that the UKSRL claim area is rich not only in metals but also in life. Our first expedition sampled a 30 x 30 km area of the UKSRL claim using a remotely operated vehicle and various other pieces of equipment. There was life everywhere: tiny white corals, pink and purple sea cucumbers, bright red shrimp and strange unicellular animals that create sedimented homes the size of your fist.  In this relatively small area, we saw 170 megafauna morphotypes and it’s likely that’s an underestimate! These levels of biodiversity are the highest in the CCZ and are comparable to many other abyssal regions worldwide. We also collected 12 megafauna morphotypes and half of those were new to science including some of the most commonly seen, reiterating how little we know of the abyssal life in this region.


Figure 4. Some of the rare and unique megafauna that call the CCZ home. Image credit: Diva Amon and Craig Smith, University of Hawaii at Manoa. Collage created by Amanda Ziegler.

We’ve seen so many incredible animals in the CCZ and it can suck when you think about what will likely happen in the future. But when I feel that sinking feeling inside, I find the strength to continue by remembering why we are doing this work. We can’t manage what we don’t understand and we can’t protect what we don’t know. If deep-sea mining is to go ahead in the CCZ, high-quality scientific work needs to be done to establish the full extent to which animals will be impacted and how best to mitigate these effects and balance the needs of both society and nature.

Diva Amon is a postdoctoral scholar in the Smith Lab at the Department of Oceanography at the University of Hawaii at Manoa. She is a deep-sea ecologist with a special interest in chemosynthetic habitats and anthropogenic impacts in the deep sea. Her current research is focused on understanding what megafauna inhabit the largely unknown deep sea of the Clarion-Clipperton Zone in the Pacific Ocean, in advance of the mining of this region for polymetallic nodules. She considers herself to be a ‘tropical species’ having been born and raised in Trinidad and Tobago and so has adjusted to life in Hawai’i quickly. You can find her on Twitter as @DivaAmon.  

The art in microbial oceanography – why data visualizations and art are two sides of the same coin

Contributed by Mpvj0vEct_400x400arkus Lindh

When I visited the Museum of Modern Art in New York City this December, I was struck by the similarities between the Jackson Pollock collection and data visualizations of microbial oceanography. It may seem surprising, but the processes of science and art are very similar, if not identical. Some of the major cornerstones of both involve observation, collaboration, research and creativity. Here’s how art can help us appreciate the infinite depth and beauty of biological complexity in the ocean.

In our field of microbial oceanography, we are trying to understand the distribution and function of the smallest plankton in the ocean. Marine microbes have high diversity, short generation times and rapid turnover, and despite their small size, these numerous microorganisms regulate fluxes of energy and chemicals in the ecosystem by processing organic matter. Microbial oceanographers often employ artistic renditions to depict how the very small interact with each other and the environment. For example, in her excellent text on why microbes matter Alice Vislova showed an image by professor Roman Stocker, which illustrates microbial life and organic matter fluxes within a drop of seawater. In particular, illustrations based on ideas by professor Farooq Azam have provided us with a concept of how microbially driven ecosystems work. Azam once drew an illustration on a napkin to convey his ideas to fellow colleagues. This illustration (shown in A, below) has since been used in thousands of classrooms and lectures and is widely known to the oceanography community via his 1998 Science paper ”Microbial control of oceanic carbon flux: The plot thickens” (Science 280: 694-696).


Illustration of the microbial loop, from Azam (1998) “Microbial control of oceanic carbon flux: The plot thickens,” Science 280:694-696 (left), and Jackson Pollock’s No. 31 (right).

Let’s compare Azam’s illustration with Jackson Pollock’s No. 31 (B, above). Ok, now you are probably wondering what Pollock’s drip technique type of painting has to do with a conceptual scientific idea about biological complexity. First, let me quote Pollock when he was explaining the process of his new technique:

New needs need new techniques. And the modern artists have found new ways and means of making their statements… Each age finds it’s own technique. On the floor I’m more at ease…I feel nearer, more part of the painting since this way I can walk around it, work from the four sides and literally be in the painting.

In essence, the process of painting can be analogous to the process of science since we, like artists, use different techniques for different purposes that develop over time. Further, we the scientists are often trying to conceptualize data that are abstract and complex. For example, microbial oceanography deals with multidimensional variation, resulting from differences in ocean circulation, hydrology, and environmental disturbances, and also biological variation.


Jackson Pollock in the process of painting with his “drip” technique.

One of the major challenges for microbial oceanographers today is to understand and predict the consequences of changes in climate for microbially driven ecosystem processes like biogeochemical cycling of elements that are essential to all living organisms. It’s safe to say that the technique of the current age is performed by collecting “big data” from high-throughput sequencing of genes and/or genomes in the ocean. Samples are taken, water is filtered and biomass collected. From the vast complexity of billions of microbes in a liter of seawater, we retrieve gigabytes to terabytes of data. There are several different approaches ranging from amplicon sequencing focusing on specific genes, to annotating microbes taxonomically, to transcriptomics that addresses the expression of particular functional genes. Still, all techniques have the same common tool for understanding results – data visualization. We are working with an ocean canvas that helps us conceptualize microbial dynamics. There are a million ways to visualize data but in the creative process of choosing visualizations, we are constantly learning. In a sense, this is where the science occurs. Hypothesis are born from this artistic process of data visualization. Alternatively, it is in the visualizations that hypotheses are answered. Therefore, regardless of whether your particular field of interest is hypothesis-driven or hypothesis-generating, the art of science is invaluable.

So how do we visualize science? Using computer programs such as R, MATLAB, Excel, or by hand? If you are an ecologist and a deft R programmer, you have probably encountered the Vegan package in R. Vegan is a fantastic resource for microbial ecologists and includes many of the essential analyses to describe alpha and beta diversity as well as population dynamics. I often couple such analyses with the graphical tool ggplot2 , also in R. This tool is very versatile and allows users build essentially any type of plot imaginable. Actually, one of R’s greatest advantages is that it can be used to bring to life virtually any idea for data visualization. Moreover, although ‘help’ functions in R work poorly and are often incomprehensible, there are thousands of online communities with people who are probably doing something similar, from which you can draw inspiration and solutions. Typically I render the art in R and make the finishing touches in Adobe Illustrator. However, often times the process of art begins even before even collecting samples or conducting experiments. By making drawings with a pen and paper, I can take the first step towards a particular analysis I want to make. In the end, few ideas for data visualization are kept, but that does not mean that the process of making the many others was in vain. Rather, it is in this selection process of trial and error that we may learn the most. In fact, I believe that it is in this moment that we as scientists endeavor to push the limits of human knowledge.


Bacterial populations distributed in time and space. Figure by Markus Lindh

 Once the data have been visualized, another process begins: the process of writing. But that, as they say, is a completely different story…

Markus Lindh received his doctoral degree in Ecology at Linneaus University in Sweden. He is interested in how projected climate change could influence the dynamics of particular bacterioplankton populations. He’s also curious about the use of marine bacteria as bio-indicators of environmental change to determine the health status of the sea. He is currently a post-doctoral researcher at the Center for Microbial Oceanography Research and Education at UH Manoa.                                                                                   

Thinking Small: Part I

It isn’t easy to study life forms we can’t see. It’s not easy to talk about them, either. This is the first installment in a series about why and how we (try to) do it anyways.

rsz_11535797_10205060585775774_6958456103789566742_nContributed by Alice Vislova

You can imagine that microbes make tricky research subjects, being invisible to the naked eye, and all. I’m a microbial oceanographer, and, speaking of eyes, I can make people’s eyes glaze over at a party by the mere mention of my research topic by name: microbial metatranscriptomics. No don’t walk away – it only sounds boring because it’s so cutting-edge (wink). We can’t observe the behavior of microbes in the ocean by snorkeling around, but we can get a clue by sequencing RNA in seawater to learn which genes are being expressed. More on that later. For now, I want to discuss why we go to such technological lengths to microbes despite their small size.

The Illumina DNA sequencer is super cool, I promise.

The Illumina DNA sequencer is super cool, I promise.

People are surprised that as an ocean biologist, I study microbes and not something more…visible, like dolphins. It’s true – dolphins are pretty great. But their impact on the planet is nowhere near that of, say, Prochlorococcus – a genus of marine photosynthetic bacteria (cyanobacteria) responsible for at least a quarter of global oxygen production. Microbes can make a big impact despite their individual size because there are so many of them.

But first…what is a microbe, anyway?

Before I got into microbial oceanography as a grad student, I associated microbes mostly with disease. I didn’t know they were such a big deal. In fact, I didn’t even know what they were exactly. So, just to get everybody on the same page: microbes are simply organisms invisible to the naked eye. The vast majority of microbes are single-celled. This diverse group spans all three domains, making up the majority of life on Earth. 

A Bottlenose Dolphin surfs the wake of a research boat. These majestic creatures just can't compete with microbes when it comes to global biogeochemical impact Photo credit: NASA

A Bottlenose Dolphin surfs the wake of a research boat. These majestic creatures just can’t compete with microbes when it comes to global biogeochemical impact
Photo credit: NASA

Microbes – they’re kind of a big deal

Microbes are everywhere. Take a look in the mirror. You’re looking at an aggregate of human and microbial cells – 10 microbial cells to every human cell! We eat, breathe and poop microbes. That dolphin to the left is an aggregate of dolphin and microbial cells! There are a million microbes in a teaspoon of seawater and a billon in that amount of soil. With the water cycle, they rise from oceans and lakes and rain down again. And they’re not just along for the ride. In their vast numbers, microbes seriously impact the environment and organisms they live on, in and around. My aim here is to explain why microbes might matter to us.

s each individual strives to obtain the energy and 

Microbial metabolism affects the chemical composition of the earth.

A great example of both unusual microbial metabolism and symbiosis: 6-foot-tall giant tube worms living on hydrothermal vent fields are mostly bacteria-filled gonads on the inside, processing no mouths or stomachs because they depend exclusively on sulfate-reducing bacteria for energy. Photo credit: NOAA Okeanos Explorer Program, Galapagos Rift Expedition 2011

Great example of both unusual microbial metabolism and symbiosis: 6-foot-tall giant tube worms living on hydrothermal vent fields are mostly bacteria-filled gonads on the inside. Possessing no mouths or stomachs, they depend exclusively on sulfate-reducing bacteria for energy.
Photo credit: NOAA Okeanos Explorer Program, Galapagos Rift Expedition 2011

Like all living things, ourselves included, microbes are chemical factories. Certain molecules go in, enzymes mediate reactions, different molecules come out; this affects the chemistry of the environment. As with the example of photosynthesis by cyanobacteria, although the amount of a certain chemical (oxygen in this case) produced by an individual microbe over time may be small, microbes’ collective impact can have major consequences. In fact, a couple billion years ago in what has been called the Great Oxidation Event, photosynthesis by microbes raised the oxygen concentration in the atmosphere to the point that allowed for something called oxygenic respiration (a.k.a. breathing), while simultaneously wiping out the majority of anaerobic life that had populated the planet at that time.

Furthermore, microbes possess a much more diverse metabolic repertoire than multi-celled organisms. One such example of exotic metabolism is nitrogen fixation. Where animals like ourselves can only obtain nitrogen by eating other living things, diazotrophs possess the ability to incorporate inorganic nitrogen from water or air. Another example: unlike plants and cyanobacteria which obtain energy from sunlight, or the many organisms that get energy from eating those lower on the food chain, some microbes get energy by reducing sulfate emitted from hydrothermal vents. The bottom line – microbial metabolism is diverse and has considerable impacts on our planet.

Microbes are part of a network of interactions between all living things.

The samples I collect in the field just look like water with nothing in it. But in reality, each drop contains a rich hidden world that looks something like this illustration published in Science magazine, an image that has really stuck with me:

From cover of Science, 5 February 2010, used with permission from R. Stocker, J. R. Seymour, G. Gorick

Image from cover of Science, 5 February 2010, used with permission from R. Stocker.

As each individual strives to obtain the energy and particular nutrients it requires, a complex web of ecological relationships is formed. Competition is rampant, especially in the nutrient-poor open ocean around Hawaii, where my research takes place. But collaboration can be found too. For example, take our old friends the diazotrophs. In environments where nitrogen is particularly low, we find nitrogen-fixing bacteria living on or inside diatoms’ silicate shells. This is an example of mutualism, or perhaps commensalism. The bacteria provide a source of organic nitrogen to diatoms, and the diatoms provide protection, or perhaps something else.

Photomicrographs of bacterial symbionts (denoted by arrows) with rectangular host diatoms. Scale bars: 50 μm. Credit: Hilton, J. A., Foster, R. A., Tripp, J., Carter, B. J., Zehr, J. P., and Villareal, T. A. Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nature Communications. 4, April 2013.

Photomicrographs of bacterial symbionts (denoted by arrows) with rectangular host diatoms. Scale bars: 50 μm.
Source: (Hilton et al., 2013)

In fact, it seems that many species of environmental microbes depend on their neighbors for survival. Perhaps this is the reason for the ‘Great Plate Anomaly’ in microbiology – the longstanding mystery of why, despite effort by many researchers, only a fraction of microbes from the environment have been successfully isolated in culture.

Favia pallida (hard coral) with signs of bleaching. Source: Nick Hobgood

Favia pallida (hard coral) with signs of bleaching. Source: Nick Hobgood

The lives of microbes are interdependent not just with one another but also with multi-celled organisms. For example, coral bleaching, the process caused by rising water temperatures and acidification that is decimating reefs around the world, is the loss of single-celled photosynthetic algae that live in and feed the coral. Just last month, NOAA declared a third major global coral bleaching event underway.

So…if you weren’t an avid microbe fan already, hopefully I’ve convinced you that microbes matter. In further installments of the Thinking Small series, we’ll explore some tools we use to study microbes, and what they’ve allowed us to discover.

Stay curious

Alice Vislova is a graduate student at UH Manoa’s Center for Microbial Oceanography Research and Education. She is interested in feedbacks between ecology and evolution. Her current focus is using molecular tools (mostly DNA and RNA sequencing) to study circadian patterns in microbial behavior and life cycles. She’s also the editor of this blog. She welcomes questions and comments at                                                                                                                                   

Works Cited:

Hilton, J. A., Foster, R. A., Tripp, J., Carter, B. J., Zehr, J. P., and Villareal, T. A. Genomic deletions      disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nature         Communications, 4 (2013), p. 1767.

Inspiring community college students to pursue a career in ocean and earth sciences


Contributed by Johanna Wren

Ever wonder what questions community college STEM (Science, Technology, Engineering and Mathematics) students ask when taken on a tour of a research vessel?

“Are all beds the same size?”, posed a five-foot tall student standing next to a 6-foot fellow student, as they inspected the state rooms in the R/V Ka‘imikai-O-Kanaloa.

Or, one of my personal favorites: “Can I drive the boat!?”

Each summer, a score of Kapi‘olani Community College (KCC) students meet every day for six weeks to immerse themselves in math and other STEM subjects as part of the KCC STEM Summer Bridge program, HāKilo II. For the past three summers, C-MORE and SOEST from the University of Hawai‘i at Mānoa have been invited to spend one week with these students, introducing them to ocean and earth science careers through hands-on experiences.

HāKilo II students on a field trip to R/V KOK at Snug Harbor. Photo credit: Heidi Needham.

HāKilo II students on a field trip to R/V KOK at Snug Harbor. Photo credit: Heidi Needham.

The theme throughout the week is Learning by Doing, so we embark on field trips, engage in career exercises, and interact with graduate students and professionals in STEM fields. Our goal is to help the students discover their passions, and urge them to follow those passions in their professional careers. I first got involved with HaKilo II’s SOEST week as a graduate research assistant with the C-MORE Education office in 2013. I have since helped to organize and lead the event each summer, as the intensive week of career exploration has become one of my favorite summer events.

Learning By Doing: Field trips!

“Bet you didn’t know you got a mouthful of critters every time you get in the ocean!” said peer-mentor Dan to a student while looking at what they caught in a plankton tow.

Learning by Doing is done best outside of a classroom, so we take the students on multiple fieldtrips. For example, during these field trips, students figure out how the Hawaiian Islands were formed, and why hillsides and surrounding ocean look the way they do. Seeing first hand – and trying to figure out why – there is coral wedged between layers of basalt high above sea level, turns sea level rise from an abstract concept into a tangible one. Learning by doing, seeing and feeling is so much more powerful than being told how the world works.

Student and instructor during a geology field trip, talking about the formation of O‘ahu and sea level change at Lāna‘i lookout. Photo credit: Johanna Wren

Student and instructor during a geology field trip, talking about the formation of O‘ahu and sea level change at Lāna‘i lookout. Photo credit: Johanna Wren

Even though we have visited some of the same sites every year, there are always new things to discover, and students never fail to impress and surprise me with their curiosity and insightfulness. I really enjoy showing students what lives in the clear and seemingly empty waters near the beach. After conducting a plankton tow, while looking at the copepods and other animals in the water, students often wonder if they swallow all of those animals when they go swimming. It’s really nice to see even the most intractable student, who wouldn’t part from her smartphone for more than a minute, get excited about the land and sea around her.

Learning By Doing: Experience as a near-peer mentor

“Let’s ask Daren, he knows everything.” – A commonly overheard statement by a group of students when they ran into a problem they couldn’t solve.

Spending a summer studying subjects that often take students outside of their comfort zone can be intimidating and scary to many. At the same time, there is nothing more inspiring than connecting with an individual you identify with, who shares your background or interest. This is where the near-peer mentors like Dan and Daren come in. Each year, a handful of senior KCC students, many of whom participated in HāKilo II in previous years, act as peer-mentors and play a pivotal role in inspiring and engaging students. Students can identify with a mentor who went through the program just last year, and who comes from a similar cultural and/or academic background. The students are less reserved with their questions, and the peer-mentors themselves develop into teachers with enthusiasm and confidence.

Students in HāKilo II learning about seagliders, and how to combine an interest in engineering with a love for the ocean, from Sarah Searson. Photo credit: Johanna Wren

Students in HāKilo II learning about seagliders, and how to combine an interest in engineering with a love for the ocean, from Sarah Searson, a sea-going marine technician. Photo credit: Johanna Wren

I especially like witnessing the progression from student one year to peer-mentor the following year. Watching them go from shy and unsure students to outgoing, empowered, and confident in their new role as peer-mentor is motivating. And what I always find remarkable is how humble the peer-mentors are: they all have an ‘if I can do it, you can do it’ attitude. Peer-mentors take on the roles of a leader, educator, and mentor, and they not only inspire the students, they inspire me as well.

Learning by Doing: Networking with people paid to pursue their passion

“Man, that’s the closest I’ve been to an astronaut!” said one student after talking to a geology professor working on the Curiosity Mission with NASA.

Instead of reciting statistics and course requirements, which often become overwhelming, we introduce the students to career professionals in a variety of fields, from surf forecasters to ocean engineers. Students “talk story” with 20 different professionals, hearing – and often seeing – firsthand what that career entails and what kind of education they need to get there.

HāKilo II students talking with a career professional, Kimball Millikan, about wave buoys and ocean engineering. Photo credit: Johanna Wren.

HāKilo II students talking with a career professional, Kimball Millikan, about wave buoys and ocean engineering. Photo credit: Johanna Wren.

Once students realize that many of the professionals they talked to get paid to surf, dive or hike (common hobbies among the students), their enthusiasm skyrockets. The type of questions they ask changes from general (e.g. “What kind of degree do you have?”) to specific (e.g. “What subject would you recommend that I focus on to get your job?”). The dedication that the professionals show not only to their profession but also to sharing their passion with young scientists is profound. At the end of the week, we ask the professionals to give one take home message to the students, and it is universally: “You work too much not to love what you do.”

The best part about this program for me each year is when students discover that their interests don’t have to stay hobbies, but that they can become their careers. A few weeks ago, I ran into one of the students who participated in HāKilo II two years ago and was a peer-mentor last year. When I first met her in 2013 she intended to major in Nursing. Since then, she has changed her focus, transferred to UH Mānoa’s Dept. of Oceanography Global Environmental Sciences program, and participated in marine biology and oceanography summer research experiences both in the U.S. and abroad. She is a true inspiration and role model, and I’m so honored to have had a small part in helping her find her passion.

Johanna Wren is a PhD candidate in the Department of Oceanography in the Toonen-Bowen (ToBo) Lab at Hawai‘i Institute of Marine Biology (HIMB) at the University of Hawai‘i at Mānoa. Her research focuses on larval dispersal and population connectivity of reef fish using a biophysical modeling approach. She is interested in identifying biophysical drivers around the Hawaiian Islands that shape the connectivity patterns seen in reef fish communities today.


Climate Science for Marshallese High School Teachers



Contributed by Michelle Tigchelaar

As a climate modeler, I mostly experience climate change through graphs and figures, scientific papers and the long-term projections of the Intergovernmental Panel on Climate Change report. At times the reality of climate change becomes more tangible, like when we went on a field trip to Mauna Loa and were presented with a 400 ppm CO2 air sample — the Keeling curve in action! But it wasn’t until I visited the Marshall Islands this June to contribute to the 2015 Climate Science Teaching Institute, that the painful truth of a changing climate truly hit home.

Majuro Atoll from above. Photo credit: M. Tigchelaar

Majuro Atoll from above. Photo credit: M. Tigchelaar

At an average elevation of 2 m above sea level, the narrow atoll islands of the Republic of the Marshall Islands (RMI) and its population of 68,000 are at risk of near-constant inundation by the end of this century. Not much further down the road, the islands could disappear entirely. The injustice of this is enormous. Not only did the Marshallese do very little to contribute to the leading causes of climate change, they also do not have the resources that richer (i.e., more polluting) countries have to deal with its consequences. Recently, the RMI Ministry of Education added climate change education to the mandatory curriculum, so that its citizens will be better informed about what is happening to their islands and the world around them. In this context, COSEE Island Earth – with support from PREL and NSF Ocean Sciences – organized a workshop for high school teachers so that they will be equipped with knowledge and activities to use in their classrooms. I had the honor of teaching the physical climate science part of this workshop.

Teaching at this workshop proved to be challenging, for unexpected reasons. For starters, it was difficult to figure out what material to present on. How was I to  condense all the complexities of the climate system and climate change science into a few lectures that are understandable, relevant and comprehensive? Many of the attendants of our workshop were general science or biology teachers, so they had little prior knowledge of how the climate system works. Furthermore, while English is an official language of the Marshall Islands, most teachers were more comfortable in their own language — which was often, but not always, Marshallese (many teachers in the RMI come from other Pacific Islands such as Fiji, Micronesia or the Philippines). We also encountered cultural differences between teachers in the US and the Marshall Islands, with the latter seeming less vocal when questions arose. By starting with the material at the very beginning, building slowly, repeating key points and leaving ample room for questions, I hoped I was able to adequately convey the material.

Teaching about sea level rise projections at the College of the Marshall Islands. Photo credit: Dr. Judy Lemus.

Teaching about sea level rise projections at the College of the Marshall Islands. Photo credit: Dr. Judy Lemus.

In the US, decades of research and coordination have resulted in the availability of a wealth of papers, reports and websites that present scientists and the general public with detailed information about past climate measurements and future climate projections (think for instance of the National Climate Assessment or NOAA’s El Niño Portal). By comparison, a lot less is known about climate variability and change in Pacific Island nations, so I had a hard time finding easily digestible information to share with the teachers. Fortunately, the international research community is slowly starting to pay more attention to this region of the globe. I was thankful for the help of Drs. Mark Merrifield and Phil Thompson from the UH Sea Level Center, who shared and explained their work on sea level rise in the Pacific Islands. More importantly, some great local organizations were able to present at the workshop as well. By involving local organizations, we were able to facilitate the creation of (hopefully) lasting connections, so that exchange of climate knowledge can also happen outside of this workshop and in years to come.

SeaGrant’s Karl Fellenius showing the class instrumentation from the Pacific Islands Ocean Observing System (PacIOOS) that is moored in the harbor of Majuro. Photo credit: M. Tigchelaar

SeaGrant’s Karl Fellenius showing the class instrumentation from the Pacific Islands Ocean Observing System (PacIOOS) that is moored in the harbor of Majuro. Photo credit: M. Tigchelaar

During the workshop, one of our aims was to come up with activities that teachers can easily reproduce in their classrooms. On my end, I demonstrated: 1. how to create El Niño in a tank (with food coloring and a blow dryer); 2. why sea level rises due to thermal expansion and the melting of land-, but not sea-, ice (with water, clay, ice and a heat lamp); 3. where and by how much sea level is expected to rise in the future (using the online NOAA sea level rise viewer); 4. how moon phases work (with styrofoam balls and a lamp); and 5. how to measure humidity and demonstrate convection (again using ice and food coloring and thermometers). We thought we had done a pretty decent job at coming up with accessible activities, until we learned that some schools do not have the resources we expected them to have. For instance, some schools on the more remote islands of the nation only have one computer, or no steady electricity source. One teacher told us that they don’t usually have access to ice, except for when a fishing boat stops in port! Luckily we had brought supplies with us to hand out to the teachers, so that they could at least do some of the activities.

Demonstrating why we see different phases of the moon. Photo credit: M. Tigchelaar

Demonstrating why we see different phases of the moon. Photo credit: M. Tigchelaar

All these challenges aside, I left the workshop with many positive impressions. One would think that the prospect of a disappearing homeland and the terrible injustices of climate change and socio-economic inequality would leave a community despondent and angry. Perhaps a lesser people would be. But I found the Marshallese teachers to be eager to learn and open-hearted. Many of them went to great lengths to attend this workshop, and all appeared to be incredibly thankful for the opportunity and excited to teach the material to their students — with whatever resources they have. I was particularly inspired by one teacher, an older gentleman from Januit. He truly grasped that dealing with climate change in these remote islands is not only an issue for international politicians, but also an opportunity for islanders to increase resiliency and battle poverty by taking better care of reefs, land and people. When these kinds of insights enter into school curricula, that is the power of education. So in the end, while I hope that the Marshallese high school teachers were able to learn from me and my knowledge of climate change, I am also grateful for all that they taught me.

Michelle Tigchelaar is a PhD candidate in the Department of Oceanography at the University of Hawai’i at Mānoa. Her research focuses on modeling the response of the climate system to long-term forcing over the past 800,000 years. She also enjoys putting science to good use and being a student activist.