Designing ocean ecological systems in the lab

Researchers from MIT have discovered simple rules of assembly of ocean microbiomes that degrade complex polysaccharides in coastal environments. Microbiomes, or microbial communities, are composed of hundreds or thousands of diverse species, making it a challenge to identify the principles that govern their structure and function.

The findings indicate that marine microbiomes can be simplified by grouping species into two types of functional modules. The first type contain polysaccharide specialists that produce the enzymes required to break down the complex sugars. The second type contains species that consume simple metabolic byproducts released by the specialist degraders and are therefore independent of the polysaccharide. This partitioning reveals a simple design for the microbiome: a trophic network in which energy is funneled from degraders to consumers.

“Our work reveals fundamental principles of microbial community assembly that can help us make sense of the vast diversity of microbes in the environment,” states Otto X. Cordero, principal investigator on the research and associate professor in the Department of Civil and Environmental Engineering (CEE). 

Cordero’s co-authors on the paper include CEE research affiliates Tim Enke and Manoshi S. Datta, CEE postdoc Julia Schwartzman, and Computational and Systems Biology Program research affiliate Nathan Cermak, as well as researchers from science and technology university ETH Zurich in Switzerland.

The simple trophic organization revealed by this study allowed Cordero and colleagues to predict microbiome species composition based on the profile of energy resources available to the community. 

“The significance of these discoveries is that we have identified simple rules of assembly, which allows us to predict community composition and rationally design ecological systems in the lab,” emphasizes Cordero. 

In order to investigate the modular organization of the microbial communities, the researchers conducted fieldwork with synthetic marine particles made of polysaccharides that are abundant in marine environments, such as chitin, alginate, agarose and carrageenan, as well as combinations of these substrates.

The team immersed the microscopic particles in natural samples of seawater and studied the colonization dynamics of bacteria using genome sequencing. This analysis allowed the researchers to disentangle the effect of polysaccharide composition on microbiome assembly.

“A promising application of this work is to apply these principles in order to design synthetic communities that degrade complex biological materials, such as those found in agricultural waste and animal feed,” says Cordero. 

from MIT News - Oceanography and ocean engineering http://bit.ly/2UTD6j2

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A steward for ocean research and climate health

The world is continually changing and evolving. But avid hikers and MIT alumni Audrey Buyrn ’58, SM ’63, PhD ’66 her late husband, Alan Phillips ’57, PhD ’61, felt humanity had asked too much from our planet. Anthropogenic activity was pushing the world toward weather and climate extremes, and imperiling the beautiful landscapes and biodiversity they had come to love while experiencing them first-hand on their treks.

“When Alan and I established the Ally of Nature Fund in 2007, it was still possible to be an intelligent skeptic of climate change and to think that catastrophic environmental degradation was far off in space and time. This is no longer possible,” says Buyrn, a sentiment shared with Phillips. “The evidence is in front of our eyes, over and over again from every part of the world.”

Raffaele Ferrari, a Cecil and Ida Green Professor of Oceanography, is one of the MIT researchers investigating this anthropogenic influence on climate. His research focuses on the role that the ocean circulation plays in setting the rate at which the ocean takes up heat and carbon from the atmosphere in present and past climates. Ferrari and his group have demonstrated through theory and observations that small-scale turbulent motions play a crucial role in shaping both the rate and the pathways of this uptake; however, these motions are not properly represented in climate models.

To remedy this, the Ferrari group is contributing to the creation of a new-generation climate model that leverages machine learning and data assimilation techniques to better represent these important small-scale turbulent motions, both in the ocean and atmosphere, so as to close the knowledge gaps and increase certainty in climate predictions compared to existing models. The information produced will help inform decisions to ensure sustainability of the Earth and our environment.

For this work, the School of Science selected Ferrari for the 2019 Ally of Nature Fund Award, bestowed annually to support exploratory projects whose purpose is to prevent, reduce, and repair the impacts of humanity on the natural environment. The fund will be used to expand the Ferrari group’s research, supporting students who are developing basic theories for the role of small-scale ocean turbulence on large-scale circulation in simple, idealized problems — a key step to test the fidelity of the new-generation climate model.

“Professor Ferrari’s oceanographic research impacts how we understand nature and our place in it: from the ocean’s phytoplankton that produce most of the oxygen we breathe, to our predictions about the Earth’s rising temperature and its effects on sea-level rise and food security,” says Michael Sipser, the Donner Professor of Mathematics and dean of the MIT School of Science. “I’m pleased to name him a recipient of the Ally of Nature Fund, as his work has wide-reaching implications in our understanding of the physics and biology of the oceans, and ultimately of our changing climate, which affects us all.”

Through their fund, Buyrn and Phillips have supported the research of other Department of Earth, Atmospheric and Planetary Science (EAPS) professors — including Andrew Babbin, Kristin Bergmann, Tim Cronin, John Marshall, David McGee, and Ron Prinn, in addition to Department of Physics Associate Professor Jeff Gore — on topics ranging from reconstructing and understanding past climates and the evolution of early life on Earth to the physics of our oceans and atmospheres and their impacts on climate.

“Although it is a cliché to say 'more research is needed', more research is needed,” to understand the intricacies of our planet and the value of what could be lost to climate change and anthropogenic degradation, says Buyrn. Together, Ferrari and his EAPS geoscience colleagues are piecing together the history of our planet and its interconnected systems.

“It is not only research in geoscience that needs continued support, but research in many other disciplines, such as chemistry, architecture, civil engineering, molecular biology, and computer sciences,” says Buyrn, that will significantly contribute to the tackling of environmental issues, wholesale. “A mammoth cross-disciplinary attack on environmental problems, including but not limited to climate change, is needed, and MIT — excelling in these areas with experience cooperating and working across fields — is one of the few places that can do it!”

from MIT News - Oceanography and ocean engineering http://bit.ly/2VaIqxY

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Professor Emeritus T. Francis Ogilvie, former ocean engineering department head, dies at 89

Thomas (T.) Francis Ogilvie, professor emeritus of ocean engineering, passed away on March 30, at the age of 89. Ogilvie dedicated most of his career to improving how ocean engineering and naval architecture programs educated students. He served as department head for MIT’s Department of Ocean Engineering — then known as Course 13 — from 1982 to 1994.

Born in Atlantic City in 1929, Ogilvie was surrounded by ocean and boats throughout his childhood. Despite his fascination with boats, he developed an aversion to the water that surrounded him due to a dislike of getting wet. At just 16, Ogilvie enrolled in Cornell University where he studied physics. While at Cornell, he was also appointed to the position of campanologist — or bell-ringer. As bell-ringer, he would climb Cornell’s bell tower and move huge levers to sound the bells over campus, serving as an alarm clock for his fellow students.

After graduating with his bachelor’s degree in physics from Cornell, Ogilvie realized that he could study boats without getting wet. In 1951, he took a job as a physicist at the U.S. Navy’s David Taylor Model Basin (DTMB) in Maryland. While at DTMB, Ogilvie conducted research on the dynamic response of ship structures to explosive loading. He later moved on to study the wave dynamics of ships, submarines, and hydrofoils. During this time, the U.S. Navy acknowledged Ogilvie’s important contributions with a Meritorious Public Service Award in 1955.

Ogilvie received his master’s degree in aeronautical engineering from the University of Maryland in 1957. Three years later, he received his PhD in engineering science from the University of California at Berkeley. After receiving his doctorate, Ogilvie moved to London for eighteen months where he served as a Liaison Scientist for the Office of Naval Research. Upon returning to the U.S., he worked at DTMB for three more years.

In 1967, Ogilvie transitioned into a career in academia. He acted as associate professor of naval architecture and marine engineering at The University of Michigan, where he also taught fluid mechanics. He was eventually named chairman of the Department of Naval Architecture and Marine Engineering at the University of Michigan.

As chairman, Ogilvie made substantial changes to the department. He was responsible for a total restructuring of the undergraduate curriculum and helped develop their graduate program. Thanks in large part to his ability to garner donations from both industry and alumni, Ogilvie was responsible for the modernization of the department’s experimental facilities and the construction of a new building to house the department.

In 1981, he resigned from his role at the University of Michigan, and in 1982 he arrived at MIT as professor and department head of ocean engineering. He served as department head for 12 years.

As with his time in Michigan, Ogilvie made a number of substantial changes to MIT’s Department of Ocean Engineering. He revised the undergraduate program — now known as Course 2-OE — and helped launch several new laboratories. One of the most impactful changes he made as department head was integrating MIT’s Naval Construction and Engineering Program into MIT’s School of Engineering.

Ogilvie was beloved by his colleagues in ocean engineering at MIT. Upon stepping down as department head in 1994, he was honored with the launch of the T. Francis Ogilvie Young Investigator Lectureship in Ocean Engineering. The annual lectureship series was created in recognition of Ogilvie’s contributions to the field of ocean engineering and “with special gratitude for his commitment in mentoring and supporting young faculty and researchers.”

Throughout his career, Ogilvie was recognized with numerous awards and honors. He was invited to serve as visiting professor of naval architecture in Osaka University in Japan and honorary professor of mathematics in Manchester University in the U.K. He was a fellow and served on the executive committee of the Society of Naval Architects and Marine Engineers. In 1989, the society awarded him the William H. Webb Medal “for outstanding contributions to education in naval architecture, marine or ocean engineering.”

In 1996, the year he retired, Ogilvie also received an honorary doctorate from the National Technical University of Athens in celebration of his ship hydrodynamics research.

Ogilvie is survived his daughter, Nancy Ogilvie; his daughter, Beth Ogilvie, and her married partner, Susan Straghalis; and his son, Ken Ogilvie, and his wife, Sue Anderson. Donations may be made in Ogilvie’s name to the ACLU or the Alzheimer's Association.

from MIT News - Oceanography and ocean engineering https://ift.tt/2UrvfYX

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