microbial

Center for Microbial Oceanography: Research and Education C-MORE Center Links Marine Microbes to Ecological Processes

Established in August 2006, C-MORE is focused on a comprehensive understanding of the diverse communities of microbes in the sea: what their genes code for, how they work together to control the flux of energy and matter in the ocean, and how all of this may change in the future.

32 CENTER FOR MICROBIAL OCEANOGRAPHY: RESEARCH AND EDUCATION • TEAM SCIENCE Located at the University of Hawaii, the center is focused on “linking genomes to biomes.” So how do you connect the narrow focus of molecular genetics to the broad focus of ecology? With the “three Cs”: collaboration, cooperation, and communication. The ultimate goal of C-MORE is to achieve a new understanding of the role of microbes in global ocean processes. C-MORE represents a sustained effort to understand how the genetics of individual microbial cells are connected with the behavior of populations, and furthermore, to understand the roles different populations play in ocean biogeochemistry, and ultimately, in global ocean processes, including climate change. Research at C-MORE depends on cooperation and collaboration among individuals whose diverse expertise includes microbial genetics, population ecology, biogeochemistry, satellite-based oceanography, ocean ecosystem modeling, engineering and instrument development, and many other disciplines. Each component of C-MORE research contributes to the “genomes to biomes” goal. The center is headquartered at the University of Hawaii, led by center director David Karl. Investigators also are located at the Institute of Technology, Woods Hole Oceanographic Institute, Monterey Bay Aquarium Research Institute, the University of California, Santa Cruz (UCSC), and Oregon State University. Many of C-MORE’s researchers have been working together for more than 10 years, notes C-MORE research coordinator Edward DeLong of MIT. “In the end, the thing that will really make everything work together in a sustained way is a deep level of trust. And I think because we are all friends, colleagues, and scientific collaborators—and have been so over a good amount of time—we have already established that,” he says. C-MORE researchers communicate daily through email, telephone, in-person conferences and teleconferences, aided by the state of the art communications capability of C-MORE Hale (“the house of C-MORE”), a new University of Hawaii building dedicated to the Center. Microorganisms dominate the living biomass in the world’s oceans, and just like humans, they contain genes which allow particular types of activities to occur, such as taking up different types of nutrients or performing photosynthesis. Because of the enormous diversity of different types of microorganisms in the ocean, and the fact that we cannot isolate most of them, an understanding of their genetic composition and capabilities comes from analysis of all gene sequences in seawater collected at different locations, a research approach known as . Samples collected from several locations during a C-MORE cruise between American Samoa and Hawaii have been analyzed by Jonathan Zehr, Karl, and colleagues. This region has several distinct types of oceanic habitats. Over a million fragments of genes were analyzed from these samples using a high throughput DNA sequencing technology. In another approach, MIT researcher Sallie W. Chisholm and colleagues have examined the genetic inventory of microbial cells. Chisholm’s group uses a flow cytometer to sort individual cells based on their characteristic fluorescence as they pass through a laser beam. Each cell’s genome--the DNA that encodes all of the genes that define the cell’s ecological niche--is amplified in a way that provides enough DNA for genome sequencing. The approach can be focused on particular groups of microbes to understand their intrinsic diversity, or to look at the broad diversity of microbes. Along with metagenomics, this approach has uncovered an astounding diversity of metabolic pathways in uncultured –providing an unprecedented window into marine microbial diversity. C-MORE scientists also study specific components of microbial communities. Above left: The Kilo Moana Matthew Church of the University of Hawaii and colleagues examined processes Top: C-MORE Hale controlling the growth, diversity, and carbon removal of diatoms, among the most Bottom: Micrograph of oceanic productive and wide spread of marine photosynthetic organisms. microbes. Photo: Courtesy of Ed DeLong

TEAM SCIENCE • CENTER FOR MICROBIAL OCEANOGRAPHY: RESEARCH AND EDUCATION 33 Science at a Distance C-MORE develops sea-going sensors for marine microbial research Traditional marine investigations The instrument has been While Center investigators all too often have required applied in the field on a variety utilize the ESP in an open transporting samples to a of platforms including coastal ocean setting to study microbial laboratory for subsequent testing. moorings, a coastal pier, an open mediated cycling of nutrients What researchers really need is ocean drifter, research ships, and energy, other academic and a sea-going instrument that could and a benthic lander rated to a government groups are currently automate molecular analyses so depth of 4,000 meters for use on evaluating the utility of the that specific organisms, genes, deep-sea cable observatories. It machine as a tool for augmenting and gene products could be supports two-way communications water quality monitoring networks analyzed easily in real time. for transmitting results and for ocean and freshwater C-MORE partners have given downloading new instructions so systems. C-MORE, through life to this vision through the that its mode of operation can be the Monterey Bay Aquarium development of the Environmental altered remotely. Research Institute, is loaning Sample Processor (ESP). The ESP “For the first time, ocean- ESP instrumentation necessary employs DNA and protein probe observing systems that allow to conduct these tests as one arrays along with the method of investigators to carry out element of the Center’s broader The Environmental Sample quantitative polymerase chain interactive experiments and test technology transfer portfolio. Processor (ESP), suspended reaction (PCR) to analyze a wide hypotheses remotely from a below a surface float, drifts in the variety of marine species and molecular biological perspective open ocean with the R/V Western Flyer nearby. Photo: Philip Sammet samples. are being realized,” says C-MORE copyright 2010 MBARI. researcher Chris Scholin.

A Conversation with the Director David Karl

Microbial oceanography is a So I was thinking about going needed to make real progress field full of surprises. It seems into some other field that might in microbial oceanography. We every time scientists think they be more pioneering and more have not been disappointed. have it all figured out, they find cutting-edge. Based on the extensive out there’s more to learn. “Well, the year that I laboratory experiments, field When C-MORE director graduated, a group of scientists observations, and ecosystem David Karl graduated with a who are now part of our center modeling conducted across Ph.D. in 1978, he was ready discovered the second-most the C-MORE institutions we to leave the field because he abundant group of organisms are beginning to re-write the thought that we knew all there in the sea—before that, we textbooks, but much more work was to know about the ocean. didn’t even know about these needs to be done. “We’d been studying this for organisms. A decade later in “New discoveries are a hundred years. There were 1988, the most abundant group likely as we move forward University of Hawaii undergraduate clever and intelligent people in of plants in the ocean was with the center. The next five students deploying instruments for the field and we had books and discovered. years should be a thrilling spectral analysis observations. we had paradigms and we had “We established C-MORE experience.” models. And I thought all that in 2006 because we thought there was left was to dot the i’s that a comprehensive, and cross the t’s—and I didn’t interdisciplinary, and like to do that kind of stuff. collaborative approach was

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