From The Doerr School of Sustainability At Stanford University: “You are stuck with your same old genome but corals are not”

From The Doerr School of Sustainability

At

Stanford University

1.20.23 [Just today in social media.]

Dr. Elora López-Nandam sampling corals for a study of mutations and how they may help corals adapt quickly. Photo by Dan Griffin.

Some corals live to be hundreds and even thousands of years old. They were born with genes that were successful back in their parent’s generation, so how can these old corals still be successful now? Especially in a changing climate? It’s possible that the generation and the filtering of mutations that occur in different parts of a big coral act as a proving ground for adaptive genetics for the future. The new study from Stanford, Hopkins Marine Station and the California Academy of Sciences shows a novel way that some very ancient animals might be surviving.

You got your entire set of genes– good or bad – from your parents, and those are the only genes you will have for your entire life. Those genes are also the only ones you will pass along to your children. Of course, there are a few exceptions – like mutations that happen in sperm or egg cells that you might pass along to the next generation. And a growing chorus of technologies is poised to alter harmful mutations in human genes that make life difficult, such as recent success in altering the genes in lung cells that cause cystic fibrosis. Nearly every animal must make a living with a set of genes that remains virtually unchanged during their lifetime, but a recent study of tropical reef building corals shows something different. These very long-lived animals are constantly changing and testing their genes – and some of these changes make it into the next generation. In this way a centuries-old coral might be a cauldron of genetic innovation, and it might help prepare them for climate change.

The new data come from the PhD work of Elora López-Nandam and her colleagues in Steve Palumbi’s lab at Hopkins Marine Station at Stanford University, published this week in the Proceedings of the Royal Society [below]. With help from the Chan Zuckerberg BioHub, López-Nandam looked very carefully at genomes of corals by taking samples from different branches of these tree-like animals. Full genome sequences showed hundreds of places in each individual branch where the DNA was slightly different – these differences represent localized mutations in these branches. Then she and collaborator Rebecca Albright used a new facility at the California Academy of Sciences to spawn these same corals and look at which of the mutations were passed to the gametes. Much to their surprise, because it does not happen this way in humans or most animals, many of the mutations in the normal tissues of the corals were passed on to the gametes. This means that mutations that occur during the growth of corals can then jump to offspring in the next generation.

A large, circular coral from the island of Palau in the West Pacific, photo by D. Griffin.

But passing mutations on to your offspring can burden them with potentially bad genes. This is why most animals do not pass along the mutations that occur in their normal tissues like skin. The López-Nandam study shows that corals reduce this problem by filtering mutations before being delivered into the next generation. By examining where each mutation appears in the genome, the authors could find the changes that alter a protein sequence and ones that did not. Random mutations change protein genes at well-known rates, and these mutations are often the deleterious ones that cause genetic disease. The López-Nandam study found that the mutations that made it into the next coral generation had far fewer protein changes. This means that the corals were somehow filtering out the most likely deleterious mutations, and passing on changes that did not hurt the coral cells or that potentially benefited them.

Overall, this study agrees with previous studies that found mutations in the tissues of large, long-lived corals are evolutionarily important. These mutations can add to the genetic diversity of coral populations and increase their ability to adapt to new conditions. In most animals this process also happens when offspring inherit new mutations that happen in the eggs and sperm of their parents, but takes many generations. The López-Nandam study goes a step further and shows that this adaptive process can happen within a single coral colony in a single generation: mutations are filtered to remove the harmful ones, potentially giving rise to patches of coral with new adaptive alleles…maybe even new mutations that can help counteract some of the stresses of climate-induced heat waves.

Proceedings of the Royal Society
From the science paper

See the full article here .

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Doerr School of Sustainability campus

The Stanford Doerr School of Sustainability draws on a deep understanding of Earth, climate, and society to create solutions at a global scale, in collaboration with partners worldwide. Together, we strive to create a future where humans and nature thrive in concert and in perpetuity.

The Stanford Doerr School of Sustainability is a school at Stanford University focusing on climate change and sustainability.

It opened on September 1, 2022, as Stanford’s first new school since the School of Humanities and Sciences in 1948. It will be one of the largest climate change–related schools in the United States.

Arun Majumdar will be the school’s first dean. Initially, the school will have 90 faculty members. It has plans to add 60 more faculty members over 10 years and construct two new buildings adjacent to the existing Green Earth Sciences and Jerry Yang and Akiko Yamazaki Environment and Energy buildings. It will incorporate the academic departments and interdisciplinary programs of the School of Earth, Energy & Environmental Sciences, Woods Institute for the Environment, and Precourt Institute for Energy and will award both undergraduate and graduate degrees. The school will also include the Hopkins Marine Station and a startup accelerator. Despite being Stanford’s newest school, it will include the university’s oldest academic department, geology. The Department of Civil & Environmental Engineering will be a joint department within the School of Sustainability and the School of Engineering.

Stanford has raised $1.69 billion for the establishment of the school, including $1.1 billion from venture capitalist John Doerr and his wife Ann, after whom the school is named. The Doerrs’ gift was the largest ever given to a university for the establishment of a new school and the second largest gift to an academic institution; it makes the Doerrs the top funders of climate change research and scholarship. Other donors include Yahoo! cofounders Jerry Yang and David Filo and their spouses, Akiko Yamazaki and Angela Filo. The Doerr School has also received funding from ExxonMobil, TotalEnergies, Shell, Saudi Aramco, Petrobras, and many other oil and gas companies via the Doerr School’s industry affiliates program and the Precourt Institute. Dean Majumdar has indicated that the Doerr School is open to continuing to accept funding from and to work with fossil fuel companies, drawing criticism from Stanford students, faculty, staff, and alumni.

Stanford University campus

Leland and Jane Stanford founded Stanford University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members.

Stanford University, officially Leland Stanford Junior University, is a private research university located in Stanford, California. Stanford was founded in 1885 by Leland and Jane Stanford in memory of their only child, Leland Stanford Jr., who had died of typhoid fever at age 15 the previous year. Stanford is consistently ranked as among the most prestigious and top universities in the world by major education publications. It is also one of the top fundraising institutions in the country, becoming the first school to raise more than a billion dollars in a year.

Leland Stanford was a U.S. senator and former governor of California who made his fortune as a railroad tycoon. The school admitted its first students on October 1, 1891, as a coeducational and non-denominational institution. Stanford University struggled financially after the death of Leland Stanford in 1893 and again after much of the campus was damaged by the 1906 San Francisco earthquake. Following World War II, provost Frederick Terman supported faculty and graduates’ entrepreneurialism to build self-sufficient local industry in what would later be known as Silicon Valley.

The university is organized around seven schools: three schools consisting of 40 academic departments at the undergraduate level as well as four professional schools that focus on graduate programs in law, medicine, education, and business. All schools are on the same campus. Students compete in 36 varsity sports, and the university is one of two private institutions in the Division I FBS Pac-12 Conference. It has gained 126 NCAA team championships, and Stanford has won the NACDA Directors’ Cup for 24 consecutive years, beginning in 1994–1995. In addition, Stanford students and alumni have won 270 Olympic medals including 139 gold medals.

As of October 2020, 84 Nobel laureates, 28 Turing Award laureates, and eight Fields Medalists have been affiliated with Stanford as students, alumni, faculty, or staff. In addition, Stanford is particularly noted for its entrepreneurship and is one of the most successful universities in attracting funding for start-ups. Stanford alumni have founded numerous companies, which combined produce more than $2.7 trillion in annual revenue, roughly equivalent to the 7th largest economy in the world (as of 2020). Stanford is the alma mater of one president of the United States (Herbert Hoover), 74 living billionaires, and 17 astronauts. It is also one of the leading producers of Fulbright Scholars, Marshall Scholars, Rhodes Scholars, and members of the United States Congress.

Stanford University was founded in 1885 by Leland and Jane Stanford, dedicated to Leland Stanford Jr, their only child. The institution opened in 1891 on Stanford’s previous Palo Alto farm.

Jane and Leland Stanford modeled their university after the great eastern universities, most specifically Cornell University. Stanford opened being called the “Cornell of the West” in 1891 due to faculty being former Cornell affiliates (either professors, alumni, or both) including its first president, David Starr Jordan, and second president, John Casper Branner. Both Cornell and Stanford were among the first to have higher education be accessible, nonsectarian, and open to women as well as to men. Cornell is credited as one of the first American universities to adopt this radical departure from traditional education, and Stanford became an early adopter as well.

Despite being impacted by earthquakes in both 1906 and 1989, the campus was rebuilt each time. In 1919, The Hoover Institution on War, Revolution and Peace was started by Herbert Hoover to preserve artifacts related to World War I. The Stanford Medical Center, completed in 1959, is a teaching hospital with over 800 beds. The DOE’s SLAC National Accelerator Laboratory (originally named the Stanford Linear Accelerator Center), established in 1962, performs research in particle physics.

DOE’s SLAC National Accelerator Laboratory campus with world’s first x-ray laser- the Linac Coherent Light Source (LCLS) unveiled in 2009.

Land

Most of Stanford is on an 8,180-acre (12.8 sq mi; 33.1 km^2) campus, one of the largest in the United States. It is located on the San Francisco Peninsula, in the northwest part of the Santa Clara Valley (Silicon Valley) approximately 37 miles (60 km) southeast of San Francisco and approximately 20 miles (30 km) northwest of San Jose. In 2008, 60% of this land remained undeveloped.

Stanford’s main campus includes a census-designated place within unincorporated Santa Clara County, although some of the university land (such as the Stanford Shopping Center and the Stanford Research Park) is within the city limits of Palo Alto. The campus also includes much land in unincorporated San Mateo County (including the SLAC National Accelerator Laboratory and the Jasper Ridge Biological Preserve), as well as in the city limits of Menlo Park (Stanford Hills neighborhood), Woodside, and Portola Valley.

Non-central campus

Stanford currently operates in various locations outside of its central campus.

On the founding grant:

Jasper Ridge Biological Preserve is a 1,200-acre (490 ha) natural reserve south of the central campus owned by the university and used by wildlife biologists for research.

SLAC National Accelerator Laboratory is a facility west of the central campus operated by the university for the Department of Energy. It contains the longest linear particle accelerator in the world, 2 miles (3.2 km) on 426 acres (172 ha) of land. Golf course and a seasonal lake: The university also has its own golf course and a seasonal lake (Lake Lagunita, actually an irrigation reservoir), both home to the vulnerable California tiger salamander. As of 2012 Lake Lagunita was often dry and the university had no plans to artificially fill it.

Off the founding grant:

Hopkins Marine Station, in Pacific Grove, California, is a marine biology research center owned by the university since 1892., in Pacific Grove, California, is a marine biology research center owned by the university since 1892.
Study abroad locations: unlike typical study abroad programs, Stanford itself operates in several locations around the world; thus, each location has Stanford faculty-in-residence and staff in addition to students, creating a “mini-Stanford”.

Redwood City campus for many of the university’s administrative offices located in Redwood City, California, a few miles north of the main campus. In 2005, the university purchased a small, 35-acre (14 ha) campus in Midpoint Technology Park intended for staff offices; development was delayed by The Great Recession. In 2015 the university announced a development plan and the Redwood City campus opened in March 2019.

The Bass Center in Washington, DC provides a base, including housing, for the Stanford in Washington program for undergraduates. It includes a small art gallery open to the public.

China: Stanford Center at Peking University, housed in the Lee Jung Sen Building, is a small center for researchers and students in collaboration with Beijing University [北京大学](CN) (Kavli Institute for Astronomy and Astrophysics at Peking University(CN) (KIAA-PKU).

Administration and organization

Stanford is a private, non-profit university that is administered as a corporate trust governed by a privately appointed board of trustees with a maximum membership of 38. Trustees serve five-year terms (not more than two consecutive terms) and meet five times annually.[83] A new trustee is chosen by the current trustees by ballot. The Stanford trustees also oversee the Stanford Research Park, the Stanford Shopping Center, the Cantor Center for Visual Arts, Stanford University Medical Center, and many associated medical facilities (including the Lucile Packard Children’s Hospital).

The board appoints a president to serve as the chief executive officer of the university, to prescribe the duties of professors and course of study, to manage financial and business affairs, and to appoint nine vice presidents. The provost is the chief academic and budget officer, to whom the deans of each of the seven schools report. Persis Drell became the 13th provost in February 2017.

As of 2018, the university was organized into seven academic schools. The schools of Humanities and Sciences (27 departments), Engineering (nine departments), and Earth, Energy & Environmental Sciences (four departments) have both graduate and undergraduate programs while the Schools of Law, Medicine, Education and Business have graduate programs only. The powers and authority of the faculty are vested in the Academic Council, which is made up of tenure and non-tenure line faculty, research faculty, senior fellows in some policy centers and institutes, the president of the university, and some other academic administrators, but most matters are handled by the Faculty Senate, made up of 55 elected representatives of the faculty.

The Associated Students of Stanford University (ASSU) is the student government for Stanford and all registered students are members. Its elected leadership consists of the Undergraduate Senate elected by the undergraduate students, the Graduate Student Council elected by the graduate students, and the President and Vice President elected as a ticket by the entire student body.

Stanford is the beneficiary of a special clause in the California Constitution, which explicitly exempts Stanford property from taxation so long as the property is used for educational purposes.

Endowment and donations

The university’s endowment, managed by the Stanford Management Company, was valued at $27.7 billion as of August 31, 2019. Payouts from the Stanford endowment covered approximately 21.8% of university expenses in the 2019 fiscal year. In the 2018 NACUBO-TIAA survey of colleges and universities in the United States and Canada, only Harvard University, the University of Texas System, and Yale University had larger endowments than Stanford.

In 2006, President John L. Hennessy launched a five-year campaign called the Stanford Challenge, which reached its $4.3 billion fundraising goal in 2009, two years ahead of time, but continued fundraising for the duration of the campaign. It concluded on December 31, 2011, having raised a total of $6.23 billion and breaking the previous campaign fundraising record of $3.88 billion held by Yale. Specifically, the campaign raised $253.7 million for undergraduate financial aid, as well as $2.33 billion for its initiative in “Seeking Solutions” to global problems, $1.61 billion for “Educating Leaders” by improving K-12 education, and $2.11 billion for “Foundation of Excellence” aimed at providing academic support for Stanford students and faculty. Funds supported 366 new fellowships for graduate students, 139 new endowed chairs for faculty, and 38 new or renovated buildings. The new funding also enabled the construction of a facility for stem cell research; a new campus for the business school; an expansion of the law school; a new Engineering Quad; a new art and art history building; an on-campus concert hall; a new art museum; and a planned expansion of the medical school, among other things. In 2012, the university raised $1.035 billion, becoming the first school to raise more than a billion dollars in a year.

Research centers and institutes

DOE’s SLAC National Accelerator Laboratory
Stanford Research Institute, a center of innovation to support economic development in the region.
Hoover Institution, a conservative American public policy institution and research institution that promotes personal and economic liberty, free enterprise, and limited government.
Hasso Plattner Institute of Design, a multidisciplinary design school in cooperation with the Hasso Plattner Institute of University of Potsdam [Universität Potsdam](DE) that integrates product design, engineering, and business management education).
Martin Luther King Jr. Research and Education Institute, which grew out of and still contains the Martin Luther King Jr. Papers Project.
John S. Knight Fellowship for Professional Journalists
Center for Ocean Solutions
Together with UC Berkeley and UC San Francisco, Stanford is part of the Biohub, a new medical science research center founded in 2016 by a $600 million commitment from Facebook CEO and founder Mark Zuckerberg and pediatrician Priscilla Chan.

Discoveries and innovation

Natural sciences

Biological synthesis of deoxyribonucleic acid (DNA) – Arthur Kornberg synthesized DNA material and won the Nobel Prize in Physiology or Medicine 1959 for his work at Stanford.
First Transgenic organism – Stanley Cohen and Herbert Boyer were the first scientists to transplant genes from one living organism to another, a fundamental discovery for genetic engineering. Thousands of products have been developed on the basis of their work, including human growth hormone and hepatitis B vaccine.
Laser – Arthur Leonard Schawlow shared the 1981 Nobel Prize in Physics with Nicolaas Bloembergen and Kai Siegbahn for his work on lasers.
Nuclear magnetic resonance – Felix Bloch developed new methods for nuclear magnetic precision measurements, which are the underlying principles of the MRI.

Computer and applied sciences

ARPANET – Stanford Research Institute, formerly part of Stanford but on a separate campus, was the site of one of the four original ARPANET nodes.

Internet—Stanford was the site where the original design of the Internet was undertaken. Vint Cerf led a research group to elaborate the design of the Transmission Control Protocol (TCP/IP) that he originally co-created with Robert E. Kahn (Bob Kahn) in 1973 and which formed the basis for the architecture of the Internet.

Frequency modulation synthesis – John Chowning of the Music department invented the FM music synthesis algorithm in 1967, and Stanford later licensed it to Yamaha Corporation.

Google – Google began in January 1996 as a research project by Larry Page and Sergey Brin when they were both PhD students at Stanford. They were working on the Stanford Digital Library Project (SDLP). The SDLP’s goal was “to develop the enabling technologies for a single, integrated and universal digital library” and it was funded through the National Science Foundation, among other federal agencies.

Klystron tube – invented by the brothers Russell and Sigurd Varian at Stanford. Their prototype was completed and demonstrated successfully on August 30, 1937. Upon publication in 1939, news of the klystron immediately influenced the work of U.S. and UK researchers working on radar equipment.

RISC – ARPA funded VLSI project of microprocessor design. Stanford and University of California- Berkeley are most associated with the popularization of this concept. The Stanford MIPS would go on to be commercialized as the successful MIPS architecture, while Berkeley RISC gave its name to the entire concept, commercialized as the SPARC. Another success from this era were IBM’s efforts that eventually led to the IBM POWER instruction set architecture, PowerPC, and Power ISA. As these projects matured, a wide variety of similar designs flourished in the late 1980s and especially the early 1990s, representing a major force in the Unix workstation market as well as embedded processors in laser printers, routers and similar products.
SUN workstation – Andy Bechtolsheim designed the SUN workstation for the Stanford University Network communications project as a personal CAD workstation, which led to Sun Microsystems.

Businesses and entrepreneurship

Stanford is one of the most successful universities in creating companies and licensing its inventions to existing companies; it is often held up as a model for technology transfer. Stanford’s Office of Technology Licensing is responsible for commercializing university research, intellectual property, and university-developed projects.

The university is described as having a strong venture culture in which students are encouraged, and often funded, to launch their own companies.

Companies founded by Stanford alumni generate more than $2.7 trillion in annual revenue, equivalent to the 10th-largest economy in the world.

Some companies closely associated with Stanford and their connections include:

Hewlett-Packard, 1939, co-founders William R. Hewlett (B.S, PhD) and David Packard (M.S).
Silicon Graphics, 1981, co-founders James H. Clark (Associate Professor) and several of his grad students.
Sun Microsystems, 1982, co-founders Vinod Khosla (M.B.A), Andy Bechtolsheim (PhD) and Scott McNealy (M.B.A).
Cisco, 1984, founders Leonard Bosack (M.S) and Sandy Lerner (M.S) who were in charge of Stanford Computer Science and Graduate School of Business computer operations groups respectively when the hardware was developed.[163]
Yahoo!, 1994, co-founders Jerry Yang (B.S, M.S) and David Filo (M.S).
Google, 1998, co-founders Larry Page (M.S) and Sergey Brin (M.S).
LinkedIn, 2002, co-founders Reid Hoffman (B.S), Konstantin Guericke (B.S, M.S), Eric Lee (B.S), and Alan Liu (B.S).
Instagram, 2010, co-founders Kevin Systrom (B.S) and Mike Krieger (B.S).
Snapchat, 2011, co-founders Evan Spiegel and Bobby Murphy (B.S).
Coursera, 2012, co-founders Andrew Ng (Associate Professor) and Daphne Koller (Professor, PhD).

Student body

Stanford enrolled 6,996 undergraduate and 10,253 graduate students as of the 2019–2020 school year. Women comprised 50.4% of undergraduates and 41.5% of graduate students. In the same academic year, the freshman retention rate was 99%.

Stanford awarded 1,819 undergraduate degrees, 2,393 master’s degrees, 770 doctoral degrees, and 3270 professional degrees in the 2018–2019 school year. The four-year graduation rate for the class of 2017 cohort was 72.9%, and the six-year rate was 94.4%. The relatively low four-year graduation rate is a function of the university’s coterminal degree (or “coterm”) program, which allows students to earn a master’s degree as a 1-to-2-year extension of their undergraduate program.

As of 2010, fifteen percent of undergraduates were first-generation students.

Athletics

As of 2016 Stanford had 16 male varsity sports and 20 female varsity sports, 19 club sports and about 27 intramural sports. In 1930, following a unanimous vote by the Executive Committee for the Associated Students, the athletic department adopted the mascot “Indian.” The Indian symbol and name were dropped by President Richard Lyman in 1972, after objections from Native American students and a vote by the student senate. The sports teams are now officially referred to as the “Stanford Cardinal,” referring to the deep red color, not the cardinal bird. Stanford is a member of the Pac-12 Conference in most sports, the Mountain Pacific Sports Federation in several other sports, and the America East Conference in field hockey with the participation in the inter-collegiate NCAA’s Division I FBS.

Its traditional sports rival is the University of California, Berkeley, the neighbor to the north in the East Bay. The winner of the annual “Big Game” between the Cal and Cardinal football teams gains custody of the Stanford Axe.

Stanford has had at least one NCAA team champion every year since the 1976–77 school year and has earned 126 NCAA national team titles since its establishment, the most among universities, and Stanford has won 522 individual national championships, the most by any university. Stanford has won the award for the top-ranked Division 1 athletic program—the NACDA Directors’ Cup, formerly known as the Sears Cup—annually for the past twenty-four straight years. Stanford athletes have won medals in every Olympic Games since 1912, winning 270 Olympic medals total, 139 of them gold. In the 2008 Summer Olympics, and 2016 Summer Olympics, Stanford won more Olympic medals than any other university in the United States. Stanford athletes won 16 medals at the 2012 Summer Olympics (12 gold, two silver and two bronze), and 27 medals at the 2016 Summer Olympics.

Traditions

The unofficial motto of Stanford, selected by President Jordan, is Die Luft der Freiheit weht. Translated from the German language, this quotation from Ulrich von Hutten means, “The wind of freedom blows.” The motto was controversial during World War I, when anything in German was suspect; at that time the university disavowed that this motto was official.
Hail, Stanford, Hail! is the Stanford Hymn sometimes sung at ceremonies or adapted by the various University singing groups. It was written in 1892 by mechanical engineering professor Albert W. Smith and his wife, Mary Roberts Smith (in 1896 she earned the first Stanford doctorate in Economics and later became associate professor of Sociology), but was not officially adopted until after a performance on campus in March 1902 by the Mormon Tabernacle Choir.
“Uncommon Man/Uncommon Woman”: Stanford does not award honorary degrees, but in 1953 the degree of “Uncommon Man/Uncommon Woman” was created to recognize individuals who give rare and extraordinary service to the University. Technically, this degree is awarded by the Stanford Associates, a voluntary group that is part of the university’s alumni association. As Stanford’s highest honor, it is not conferred at prescribed intervals, but only when appropriate to recognize extraordinary service. Recipients include Herbert Hoover, Bill Hewlett, Dave Packard, Lucile Packard, and John Gardner.
Big Game events: The events in the week leading up to the Big Game vs. UC Berkeley, including Gaieties (a musical written, composed, produced, and performed by the students of Ram’s Head Theatrical Society).
“Viennese Ball”: a formal ball with waltzes that was initially started in the 1970s by students returning from the now-closed Stanford in Vienna overseas program. It is now open to all students.
“Full Moon on the Quad”: An annual event at Main Quad, where students gather to kiss one another starting at midnight. Typically organized by the Junior class cabinet, the festivities include live entertainment, such as music and dance performances.
“Band Run”: An annual festivity at the beginning of the school year, where the band picks up freshmen from dorms across campus while stopping to perform at each location, culminating in a finale performance at Main Quad.
“Mausoleum Party”: An annual Halloween Party at the Stanford Mausoleum, the final resting place of Leland Stanford Jr. and his parents. A 20-year tradition, the “Mausoleum Party” was on hiatus from 2002 to 2005 due to a lack of funding, but was revived in 2006. In 2008, it was hosted in Old Union rather than at the actual Mausoleum, because rain prohibited generators from being rented. In 2009, after fundraising efforts by the Junior Class Presidents and the ASSU Executive, the event was able to return to the Mausoleum despite facing budget cuts earlier in the year.
Former campus traditions include the “Big Game bonfire” on Lake Lagunita (a seasonal lake usually dry in the fall), which was formally ended in 1997 because of the presence of endangered salamanders in the lake bed.

Award laureates and scholars

Stanford’s current community of scholars includes:

19 Nobel Prize laureates (as of October 2020, 85 affiliates in total)
171 members of the National Academy of Sciences
109 members of National Academy of Engineering
76 members of National Academy of Medicine
288 members of the American Academy of Arts and Sciences
19 recipients of the National Medal of Science
1 recipient of the National Medal of Technology
4 recipients of the National Humanities Medal
49 members of American Philosophical Society
56 fellows of the American Physics Society (since 1995)
4 Pulitzer Prize winners
31 MacArthur Fellows
4 Wolf Foundation Prize winners
2 ACL Lifetime Achievement Award winners
14 AAAI fellows
2 Presidential Medal of Freedom winners

From “Astronomy Magazine” : “How lunar cycles guide the spawning of corals and worms and more”

From “Astronomy Magazine”

3.2.23
Virat Markandeya

Many sea creatures release eggs and sperm into the water on just the right nights of the month. Researchers are starting to understand the biological rhythms that sync them to phases of the Moon.

Many species of coral release their bundles of sperm and eggs during a particular phase in the lunar cycle, as shown here for coral in the Red Sea. The fantastic show — as well as reproductive events in other marine creatures — requires a biological clock with tight coupling to lunar cycles. TOM SHLESINGER.

It’s evening at the northern tip of the Red Sea, in the Gulf of Aqaba, and Tom Shlesinger readies to take a dive. During the day, the seafloor is full of life and color; at night it looks much more alien. Shlesinger is waiting for a phenomenon that occurs once a year for a plethora of coral species, often several nights after the Full Moon.

Guided by a flashlight, he spots it: coral releasing a colorful bundle of eggs and sperm, tightly packed together. “You’re looking at it and it starts to flow to the surface,” Shlesinger says. “Then you raise your head, and you turn around, and you realize: All the colonies from the same species are doing it just now.”

Some coral species release bundles of a pinkish- purplish color, others release ones that are yellow, green, white or various other hues. “It’s quite a nice, aesthetic sensation,” says Shlesinger, a marine ecologist at Tel Aviv University and the Interuniversity Institute for Marine Sciences in Eilat, Israel, who has witnessed the show during many years of diving. Corals usually spawn in the evening and night within a tight time window of 10 minutes to half an hour. “The timing is so precise, you can set your clock by the time it happens,” Shlesinger says.

Moon-controlled rhythms in marine critters have been observed for centuries. There is calculated guesswork, for example, that in 1492 Christopher Columbus encountered a kind of glowing marine worm engaged in a lunar-timed mating dance, like the “flame of a small candle alternately raised and lowered” [PLOS ONE (below)] Diverse animals such as sea mussels, corals, polychaete worms and certain fishes are thought to synchronize their reproductive behavior by the Moon. The crucial reason is that such animals — for example, over a hundred coral species [Marine Biology (below)] at the Great Barrier Reef — release their eggs before fertilization takes place, and synchronization maximizes the probability of an encounter between eggs and sperm.

How does it work? That has long been a mystery, but researchers are getting closer to understanding. They have known for at least 15 years that corals, like many other species, contain light-sensitive proteins called cryptochromes, and have recently reported that in the stony coral, Dipsastraea speciosa, a period of darkness between sunset and moonrise appears key [PNAS (below)] for triggering spawning some days later.

PNAS 2021

Fig. 1.

Spawning day of D. speciosa in the field manipulation experiment. (A) Study location at Lyudao (Green Island), Taiwan. The white dot indicates Gonggan, where D. speciosa fragments were collected and the field observation and experiment were conducted. (B) An egg trap in a transparent plastic bag and (C) an egg trap in an aluminum foil bag. (D) Spawning in natural populations of D. speciosa (>10 colonies) at the study location and (E) spawning of D. speciosa fragments under the moonlight-blocking treatment commencing at 3 d before the full moon (panel 1), 1 d before the full moon (panel 2), and 1 d after the full moon (panel 3). Black bars indicate major spawning (>hundreds of eggs), and white bars indicate minor spawning (several eggs) in four replicate fragments. Note that “NA” indicates no observation. Different letters in the panels in E indicate significant differences between the treatments (ANOVA and Tukey HSD test; P < 0.001). For detailed results of statistical analysis, refer to SI Appendix, Table S2.

Fig. 2.

Spawning day of D. speciosa under different moonlight exposure days. (A) The design of one experimental unit, including four replicate tank systems for each experimental treatment. (B) D. speciosa fragments were exposed to three experimental moonlight (dim light [∼0.3 lx]) conditions with different exposure days at nighttime (18:30 to 05:00): no light treatment (panel 1), 2-d exposure treatment (panel 2), and 4-d exposure treatment (panel 3). Black bars indicate major spawning (>hundreds of eggs), and white bars indicate minor spawning (several eggs) in four replicate fragments. Different letters in the panels indicate significant differences between the treatments (ANOVA and Tukey HSD test; P ≤ 0.001). For detailed results of statistical analysis, refer to SI Appendix, Table S2.

Marine Biology 1986

PLOS ONE 2018

Fig 1

Bioluminescent display of Odontosyllis enopla.
During the breeding period, female Odontosyllis enopla swim in slow circles secreting a bright bluish-green luminous mucus while releasing gametes. Photo credit: Dr. James B. Wood.

Fig 2

Multiple sequence alignment of the Odontosyllis enopla luciferase gene with that of the Japanese syllid O. undecimdonta.
The Odontosyllis enopla luciferase gene (329 amino acids in length) is aligned with the four putative luciferase transcripts (isoforms) of O. undecimdonta. The alignment was generated using default parameters and the L-INS-i iterative refinement method within MAFFT (v7.402). Ou: O. undecimdonta. Oe1: O. enopla Individual 1.

Fig 3

An unrooted maximum likelihood-based phylogenetic tree showing the relationship of both orthologs and paralogs of the luciferase gene for Odontosyllis enopla and O. undecimdonta.

The four transcripts (isoforms) found by Schultz et al. [44*] are in orange. ‘O_undecimdonta_DN31989’ (green) is identical to one of the four isoforms but has a different name because it is based on our Trinity assembly. The two additional green terminals are paralogs of the O. undecimdonta luciferase that were not reported by Schultz et al. [44]. For O. enopla, orthologs are shown in purple and the paralogs in blue. O_enopla_1: Individual 1, O_enopla_2: Individual 2, O_enopla_3: Individual 3. The ML tree was constructed using a MUSCLE-based amino acid alignment and the following parameters: WAG + gamma + I model; aLRT-based support values.
*References in the science paper

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Astronomy is a magazine about the science and hobby of Astronomy. Based near Milwaukee in Waukesha, Wisconsin, it is produced by Kalmbach Publishing. Astronomy’s readers include those interested in astronomy and those who want to know about sky events, observing techniques, astrophotography, and amateur astronomy in general.

Astronomy was founded in 1973 by Stephen A. Walther, a graduate of The University of Wisconsin–Stevens Point and amateur astronomer. The first issue, August 1973, consisted of 48 pages with five feature articles and information about what to see in the sky that month. Issues contained astrophotos and illustrations created by astronomical artists. Walther had worked part time as a planetarium lecturer at The University of Wisconsin–Milwaukee and developed an interest in photographing constellations at an early age. Although even in childhood he was interested to obsession in Astronomy, he did so poorly in mathematics that his mother despaired that he would ever be able to earn a living. However, he graduated in Journalism from the University of Wisconsin Stevens Point, and as a senior class project he created a business plan for a magazine for amateur astronomers. With the help of his brother David, he was able to bring the magazine to fruition. He died in 1977.

From The National Science Foundation: “Scientists discover immense biodiversity in high-temperature and deep-sea microorganism communities”

From The National Science Foundation

3.7.23

High-temperature venting on the caldera wall of Brothers Volcano produces black smoker chimneys.
Credit: New Zealand-American Submarine Ring of Fire Exploration.

Researchers sequence microbial genomes to learn more about diversity and interconnections.

A new study by researchers at Portland State University and the University of Wisconsin finds that a rich diversity of microorganisms lives in interdependent communities in high -temperature geothermal environments in the deep sea.

The study, published in the journal Microbiome [below], was led by Anna-Louise Reysenbach at PSU.

When the 350-400 degree C fluid exiting the Earth’s crust through deep-sea hydrothermal vents mixes with seawater, it creates large, porous rocks often referred to as chimneys or hydrothermal deposits. These chimneys are colonized by microbes that thrive in high-temperature environments.

Reysenbach has collected chimneys from deep-sea hydrothermal vents in the world’s oceans. Her lab uses genetic fingerprinting and cultivation techniques to study the microbial diversity of the communities associated with these rocks.

In the U.S. National Science Foundation-supported study, Reysenbach and the team were able to take advantage of advances in molecular biology techniques to sequence the entire genomes of the microbes in these communities to learn more about their diversity and interconnected ecosystems.

“This research demonstrates the incredible diversity of microbial communities in the extreme environments of deep-sea hydrothermal vents throughout the ocean basins,” says Gail Christeson, a program director in NSF’s Division of Ocean Sciences.

The team constructed genomes of 3,635 bacteria and archaea from 40 rock communities. The diversity was staggering, according to the scientists, and greatly expands what is known about how many different types of bacteria and archaea exist.

The researchers discovered at least 500 new genera (the level of taxonomic organization above species) and have evidence for two new phyla (five levels up from species). The team also found evidence of microbial diversity hotspots. Samples from the deep-sea Brothers Volcano near New Zealand, for example, were enriched with microorganisms, many endemic to that volcano.

“That biodiversity was just so huge,” says Reysenbach. “At one volcano there was so much new diversity that we hadn’t seen elsewhere.” The finding suggests that the increased complexity of the subsurface rocks of a volcano makes them more likely to house diverse microbial species compared to deep-sea hydrothermal vents.

Microbiome

Fig. 1

Maximum-likelihood phylogenomic tree of bacterial metagenome-assembled genomes, constructed using 120 bacterial marker genes in GTDB-Tk. Major taxonomic groups are highlighted, and the number of MAGs in each taxon is shown in parentheses. See Table S2 for details. Bacterial lineages are shown at the phylum classification, except for the Proteobacteria which are split into their component classes. The inner ring displays quality (green: high quality, > 90% completion, < 5% contamination; purple: medium quality, ≥ 50% completion, ≤ 10% contamination), while the outer ring shows normalized read coverage up to 200x. The scale bar indicates 0.1 amino acid substitutions per site, and filled circles are shown for SH-like support values ≥ 80%. The tree was artificially rooted with the Patescibacteria using iTOL. The Newick format tree used to generate this figure is available in Data S4, and the formatted tree is available online at https://itol.embl.de/shared/alrlab

Fig. 2

Maximum-likelihood phylogenomic reconstruction of deep-sea hydrothermal vent archaeal metagenome-assembled genomes generated in GTDB-Tk. The tree was generated with 122 archaeal marker genes. Taxa are shown at the phylum level, except for the Thermoproteota, Asgardarchaeota, Halobacteriota, and Methanobacteriota, shown at the class level. The number of MAGs in each highlighted taxon is shown in parentheses. See Table S2 for details. Quality is shown on the inner ring (green: high quality, purple: medium quality, with one manually curated Nanoarchaeota MAG below the 50% completion threshold also displayed as medium quality), while the outer ring displays normalized read coverage up to 200x. SH-like support values ≥ 80% are indicated with filled circles, and the scale bar represents 0.1 amino acid substitutions per site. The tree was artificially rooted with the Iainarchaeota, Micrarchaeota, SpSt-1190, Undinarchaeota, Nanohaloarchaeota, EX4484-52, Aenigmarchaeota, Aenigmarchaeota_A, and Nanoarchaeota using iTOL. The tree used to create this figure is available in Newick format (Data S5), and the formatted tree is publicly available on iTOL at https://itol.embl.de/shared/alrlab

For further images see the science paper.

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The National Science Foundation is an independent federal agency created by Congress in 1950 “to promote the progress of science; to advance the national health, prosperity, and welfare; to secure the national defense…we are the funding source for approximately 24 percent of all federally supported basic research conducted by America’s colleges and universities. In many fields such as mathematics, computer science and the social sciences, The National Science Foundation is the major source of federal backing.

We fulfill our mission chiefly by issuing limited-term grants — currently about 12,000 new awards per year, with an average duration of three years — to fund specific research proposals that have been judged the most promising by a rigorous and objective merit-review system. Most of these awards go to individuals or small groups of investigators. Others provide funding for research centers, instruments and facilities that allow scientists, engineers and students to work at the outermost frontiers of knowledge.

The National Science Foundation ‘s goals — discovery, learning, research infrastructure and stewardship — provide an integrated strategy to advance the frontiers of knowledge, cultivate a world-class, broadly inclusive science and engineering workforce and expand the scientific literacy of all citizens, build the nation’s research capability through investments in advanced instrumentation and facilities, and support excellence in science and engineering research and education through a capable and responsive organization. We like to say that The National Science Foundation is “where discoveries begin.”

Many of the discoveries and technological advances have been truly revolutionary. In the past few decades, The National Science Foundation -funded researchers have won some 236 Nobel Prizes as well as other honors too numerous to list. These pioneers have included the scientists or teams that discovered many of the fundamental particles of matter, analyzed the cosmic microwaves left over from the earliest epoch of the universe, developed carbon-14 dating of ancient artifacts, decoded the genetics of viruses, and created an entirely new state of matter called a Bose-Einstein condensate.

The National Science Foundation also funds equipment that is needed by scientists and engineers but is often too expensive for any one group or researcher to afford. Examples of such major research equipment include giant optical and radio telescopes, Antarctic research sites, high-end computer facilities and ultra-high-speed connections, ships for ocean research, sensitive detectors of very subtle physical phenomena and gravitational wave observatories.

Another essential element in The National Science Foundation ‘s mission is support for science and engineering education, from pre-K through graduate school and beyond. The research we fund is thoroughly integrated with education to help ensure that there will always be plenty of skilled people available to work in new and emerging scientific, engineering and technological fields, and plenty of capable teachers to educate the next generation.

No single factor is more important to the intellectual and economic progress of society, and to the enhanced well-being of its citizens, than the continuous acquisition of new knowledge. The National Science Foundation is proud to be a major part of that process.

Specifically, the Foundation’s organic legislation authorizes us to engage in the following activities:

Initiate and support, through grants and contracts, scientific and engineering research and programs to strengthen scientific and engineering research potential, and education programs at all levels, and appraise the impact of research upon industrial development and the general welfare.

Award graduate fellowships in the sciences and in engineering.

Foster the interchange of scientific information among scientists and engineers in the United States and foreign countries.

Foster and support the development and use of computers and other scientific methods and technologies, primarily for research and education in the sciences.

Evaluate the status and needs of the various sciences and engineering and take into consideration the results of this evaluation in correlating our research and educational programs with other federal and non-federal programs.

Provide a central clearinghouse for the collection, interpretation and analysis of data on scientific and technical resources in the United States, and provide a source of information for policy formulation by other federal agencies.

Determine the total amount of federal money received by universities and appropriate organizations for the conduct of scientific and engineering research, including both basic and applied, and construction of facilities where such research is conducted, but excluding development, and report annually thereon to the President and the Congress.

Initiate and support specific scientific and engineering activities in connection with matters relating to international cooperation, national security and the effects of scientific and technological applications upon society.

Initiate and support scientific and engineering research, including applied research, at academic and other nonprofit institutions and, at the direction of the President, support applied research at other organizations.

Recommend and encourage the pursuit of national policies for the promotion of basic research and education in the sciences and engineering. Strengthen research and education innovation in the sciences and engineering, including independent research by individuals, throughout the United States.

Support activities designed to increase the participation of women and minorities and others underrepresented in science and technology.

At present, The National Science Foundation has a total workforce of about 2,100 at its Alexandria, VA, headquarters, including approximately 1,400 career employees, 200 scientists from research institutions on temporary duty, 450 contract workers and the staff of the NSB office and the Office of the Inspector General.

The National Science Foundation is divided into the following seven directorates that support science and engineering research and education: Biological Sciences, Computer and Information Science and Engineering, Engineering, Geosciences, Mathematical and Physical Sciences, Social, Behavioral and Economic Sciences, and Education and Human Resources. Each is headed by an assistant director and each is further subdivided into divisions like materials research, ocean sciences and behavioral and cognitive sciences.

Within The National Science Foundation ‘s Office of the Director, the Office of Integrative Activities also supports research and researchers. Other sections of The National Science Foundation are devoted to financial management, award processing and monitoring, legal affairs, outreach and other functions. The Office of the Inspector General examines the foundation’s work and reports to the NSB and Congress.

Each year, The National Science Foundation supports an average of about 200,000 scientists, engineers, educators and students at universities, laboratories and field sites all over the United States and throughout the world, from Alaska to Alabama to Africa to Antarctica. You could say that The National Science Foundation support goes “to the ends of the earth” to learn more about the planet and its inhabitants, and to produce fundamental discoveries that further the progress of research and lead to products and services that boost the economy and improve general health and well-being.

As described in our strategic plan, The National Science Foundation is the only federal agency whose mission includes support for all fields of fundamental science and engineering, except for medical sciences. The National Science Foundation is tasked with keeping the United States at the leading edge of discovery in a wide range of scientific areas, from astronomy to geology to zoology. So, in addition to funding research in the traditional academic areas, the agency also supports “high risk, high pay off” ideas, novel collaborations and numerous projects that may seem like science fiction today, but which the public will take for granted tomorrow. And in every case, we ensure that research is fully integrated with education so that today’s revolutionary work will also be training tomorrow’s top scientists and engineers.

Unlike many other federal agencies, The National Science Foundation does not hire researchers or directly operate our own laboratories or similar facilities. Instead, we support scientists, engineers and educators directly through their own home institutions (typically universities and colleges). Similarly, we fund facilities and equipment such as telescopes, through cooperative agreements with research consortia that have competed successfully for limited-term management contracts.

The National Science Foundation ‘s job is to determine where the frontiers are, identify the leading U.S. pioneers in these fields and provide money and equipment to help them continue. The results can be transformative. For example, years before most people had heard of “nanotechnology,” The National Science Foundation was supporting scientists and engineers who were learning how to detect, record and manipulate activity at the scale of individual atoms — the nanoscale. Today, scientists are adept at moving atoms around to create devices and materials with properties that are often more useful than those found in nature.

Dozens of companies are gearing up to produce nanoscale products. The National Science Foundation is funding the research projects, state-of-the-art facilities and educational opportunities that will teach new skills to the science and engineering students who will make up the nanotechnology workforce of tomorrow.

At the same time, we are looking for the next frontier.

The National Science Foundation ‘s task of identifying and funding work at the frontiers of science and engineering is not a “top-down” process. The National Science Foundation operates from the “bottom up,” keeping close track of research around the United States and the world, maintaining constant contact with the research community to identify ever-moving horizons of inquiry, monitoring which areas are most likely to result in spectacular progress and choosing the most promising people to conduct the research.

The National Science Foundation funds research and education in most fields of science and engineering. We do this through grants and cooperative agreements to more than 2,000 colleges, universities, K-12 school systems, businesses, informal science organizations and other research organizations throughout the U.S. The Foundation considers proposals submitted by organizations on behalf of individuals or groups for support in most fields of research. Interdisciplinary proposals also are eligible for consideration. Awardees are chosen from those who send us proposals asking for a specific amount of support for a specific project.

Proposals may be submitted in response to the various funding opportunities that are announced on the The National Science Foundation website. These funding opportunities fall into three categories — program descriptions, program announcements and program solicitations — and are the mechanisms The National Science Foundation uses to generate funding requests. At any time, scientists and engineers are also welcome to send in unsolicited proposals for research and education projects, in any existing or emerging field. The Proposal and Award Policies and Procedures Guide (PAPPG) provides guidance on proposal preparation and submission and award management. At present, The National Science Foundation receives more than 42,000 proposals per year.

To ensure that proposals are evaluated in a fair, competitive, transparent and in-depth manner, we use a rigorous system of merit review. Nearly every proposal is evaluated by a minimum of three independent reviewers consisting of scientists, engineers and educators who do not work at NSF or for the institution that employs the proposing researchers. The National Science Foundation selects the reviewers from among the national pool of experts in each field and their evaluations are confidential. On average, approximately 40,000 experts, knowledgeable about the current state of their field, give their time to serve as reviewers each year.

The reviewer’s job is to decide which projects are of the very highest caliber. The National Science Foundation ‘s merit review process, considered by some to be the “gold standard” of scientific review, ensures that many voices are heard and that only the best projects make it to the funding stage. An enormous amount of research, deliberation, thought and discussion goes into award decisions.

The National Science Foundation program officer reviews the proposal and analyzes the input received from the external reviewers. After scientific, technical and programmatic review and consideration of appropriate factors, the program officer makes an “award” or “decline” recommendation to the division director. Final programmatic approval for a proposal is generally completed at The National Science Foundation ‘s division level. A principal investigator (PI) whose proposal for The National Science Foundation support has been declined will receive information and an explanation of the reason(s) for declination, along with copies of the reviews considered in making the decision. If that explanation does not satisfy the PI, he/she may request additional information from the cognizant The National Science Foundation program officer or division director.

If the program officer makes an award recommendation and the division director concurs, the recommendation is submitted to The National Science Foundation’s Division of Grants and Agreements (DGA) for award processing. A DGA officer reviews the recommendation from the program division/office for business, financial and policy implications, and the processing and issuance of a grant or cooperative agreement. DGA generally makes awards to academic institutions within 30 days after the program division/office makes its recommendation.

From The Rosenstiel School of Marine and Atmospheric and Earth Science At The University of Miami: “Unique hybrid reefs deployed off Miami Beach”

From The Rosenstiel School of Marine and Atmospheric and Earth Science

At

The University of Miami

3.2.23
Robert C. Jones Jr.
Janette Neuwahl Tannen
Underwater photos: Emily Esplandiu/University of Miami
Platform photos: Joshua Prezant/University of Miami

Hybrid reef structures are seen before being lowered into waters off North Miami Beach. Photos: Aerial photos courtesy of Camera Copters.

The 18-foot-long structures-including fascinating honeycomb-shaped tubes-are part of an effort by University of Miami researchers and scientists to help restore damaged coral reefs and protect coastal environments.

The first piece of a series of concrete structures was lowered into the water off the coast of Miami Beach on Wednesday morning, a massive crane on the deck of a floating barge hoisting the unit into the air and sinking it to the seabed.

During the next six hours, crewmembers aboard the barge would repeat that process until the structures, some stacked on top of each other, were settled on the seafloor, 14 feet below the surface.

To casual observers onshore, the daylong operation might have seemed routine. But this maritime activity was hardly run-of-the-mill.

In a project that could pave the way for greater efforts to protect coastlines from sea level rise and storm surge and serve as an innovative base structure to develop thriving coral reefs, a team of researchers and scientists from the University of Miami sunk 27 interlocking concrete structures that will form two hybrid reef units 1,000 feet offshore of North Beach Oceanside Park, at the northern edge of Miami Beach.

The units are the centerpiece of a project called Engineering Coastal Resilience Through Hybrid Reef Restoration, or ECoREEF, which combines cement- and nature-based strategies to foster coastal resilience. Supported by the University’s Laboratory for Integrative Knowledge (U-LINK) and the City of Miami Beach, the project was developed at a time when coral reefs are struggling to survive. A recent study [One Earth (below)]indicates that half of the world’s living coral reefs have died since the 1950s. Meanwhile, other research has shown that healthy and complex coral reefs are able to buffer up to 97 percent of the energy from waves and can also reduce flooding frequency.

One of the SEAHIVE units is lowered into the ocean off northern Miami Beach.

“Coral reefs are disappearing at alarming rates throughout the world as a result of disease and warming oceans so our reefs have lost a lot of the structure. They need to reduce wave energy,” said ECoREEF lead investigator, Diego Lirman, an associate professor of marine biology and ecology at the University’s Rosenstiel School of Marine, Atmospheric, and Earth Science. “By placing these [hybrid] reefs near the shoreline and planting stress-tolerant corals on them scientists hope to recover some of the lost services provided by healthy reefs, such as coastal protection, and to build a habitat for organisms like fish and lobsters.”

One Earth

Figure 1. Global coral reef cover trends

Coral cover
Overall, historical coral coverage was estimated to range from 58% to 70% in coral reef systems worldwide.8
There has been approximately a 50% decline in coral reef cover globally from 1957–2007 (Figure 1A). There were only a few observations in the early part of the time series, which originated from the western Indian Ocean, indicating high uncertainty around what the average coral cover was during the mid-20th century. The effects of climate change worldwide started prior to this period, suggesting that the historical baseline could have been higher (Figures S1 and S2). The average decadal rate of loss in coral coverage during the study period ranged from 4.7% to 6.8% (Figure 1A). Most regions had relatively low sampling effort, except for countries in the western central Atlantic and the western central Pacific (Figure S1). Most countries showed declines in coral cover, although some countries in the Caribbean (Barbados, Cuba, Panama) and the western Pacific (Japan, Malaysia, Philippines, Thailand) showed increases based on available survey data (Figure 1B).

Figure 2. Global coral-reef-associated biodiversity

Biodiversity
Countries with the greatest coral-reef-associated biodiversity were typically found in the Pacific, although there was no clear separation among ocean basins (Figure 2A). We examined the species-area relationship43
for coral-reef-associated organisms by the main taxonomic groups (macroalgae, macroinvertebrates, and fish). Regression (log-log linear) between the estimated area of coral and total species richness among exclusive economic zones (EEZs) (n = 94) showed a positive relationship with a slope of 0.30 (p = 4.98e-07) and an intercept of 1.58 (p = 1.04e-08), with a Spearman coefficient of 0.63 (Figure 2B). Macroinvertebrates had a slope of 0.40, an intercept of 0.03 (p = 7.79e-06; p = 0.93, respectively), and a Spearman coefficient of 0.52. Fish had a slope of 0.30, an intercept of 0.70 (p = 2.88e-06; p = 0.01, respectively), and a Spearman coefficient of 0.52. Mammals had a slope of 0.09, an intercept of 0.95 (p = 0.01; p = 5.51e-09), and a Spearman coefficient of 0.28. We also subset EEZs that had a latitudinal centroid of coral reef area within the tropics and found that the species-area relationship increased for all groups, with a Spearman coefficient of 0.74.

For further illustrations see the science paper.

See the full article here.

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Stem Education Coalition

The Rosenstiel School of Marine and Atmospheric and Earth Science is an academic and research institution for the study of oceanography and the atmospheric sciences within the University of Miami. It is located on a 16-acre (65,000 m^²) campus on Virginia Key in Miami, Florida. It is the only subtropical applied and basic marine and atmospheric research institute in the continental United States.

Up until 2008, RSMAS was solely a graduate school within the University of Miami, while it jointly administrated an undergraduate program with UM’s College of Arts and Sciences. In 2008, the Rosenstiel School has taken over administrative responsibilities for the undergraduate program, granting Bachelor of Science in Marine and Atmospheric Science (BSMAS) and Bachelor of Arts in Marine Affairs (BAMA) baccalaureate degree. Master’s, including a Master of Professional Science degree, and doctorates are also awarded to RSMAS students by the UM Graduate School.

The Rosenstiel School’s research includes the study of marine life, particularly Aplysia and coral; climate change; air-sea interactions; coastal ecology; and admiralty law. The school operates a marine research laboratory ship, and has a research site at an inland sinkhole. Research also includes the use of data from weather satellites and the school operates its own satellite downlink facility. The school is home to the world’s largest hurricane simulation tank.

The University of Miami is a private research university in Coral Gables, Florida. As of 2020, the university enrolled approximately 18,000 students in 12 separate colleges and schools, including the Leonard M. Miller School of Medicine in Miami’s Health District, a law school on the main campus, and the Rosenstiel School of Marine and Atmospheric Science focused on the study of oceanography and atmospheric sciences on Virginia Key, with research facilities at the Richmond Facility in southern Miami-Dade County.

The university offers 132 undergraduate, 148 master’s, and 67 doctoral degree programs, of which 63 are research/scholarship and 4 are professional areas of study. Over the years, the university’s students have represented all 50 states and close to 150 foreign countries. With more than 16,000 full- and part-time faculty and staff, The University of Miami is a top 10 employer in Miami-Dade County. The University of Miami’s main campus in Coral Gables has 239 acres and over 5.7 million square feet of buildings.

The University of Miami is classified among “R1: Doctoral Universities – Very high research activity”. The University of Miami research expenditure in FY 2019 was $358.9 million. The University of Miami offers a large library system with over 3.9 million volumes and exceptional holdings in Cuban heritage and music.

The University of Miami also offers a wide range of student activities, including fraternities and sororities, and hundreds of student organizations. The Miami Hurricane, the student newspaper, and WVUM, the student-run radio station, have won multiple collegiate awards. The University of Miami’s intercollegiate athletic teams, collectively known as the Miami Hurricanes, compete in Division I of the National Collegiate Athletic Association. The University of Miami’s football team has won five national championships since 1983 and its baseball team has won four national championships since 1982.

Research

The University of Miami is classified among “R1: Doctoral Universities – Very high research activity”. In fiscal year 2016, The University of Miami received $195 million in federal research funding, including $131.3 million from the Department of Health and Human Services and $14.1 million from the National Science Foundation. Of the $8.2 billion appropriated by Congress in 2009 as a part of the stimulus bill for research priorities of The National Institutes of Health, the Miller School received $40.5 million. In addition to research conducted in the individual academic schools and departments, Miami has the following university-wide research centers:

The Center for Computational Science
The Institute for Cuban and Cuban-American Studies (ICCAS)
Leonard and Jayne Abess Center for Ecosystem Science and Policy
The Miami European Union Center: This group is a consortium with Florida International University (FIU) established in fall 2001 with a grant from the European Commission through its delegation in Washington, D.C., intended to research economic, social, and political issues of interest to the European Union.
The Sue and Leonard Miller Center for Contemporary Judaic Studies
John P. Hussman Institute for Human Genomics – studies possible causes of Parkinson’s disease, Alzheimer’s disease and macular degeneration.
Center on Research and Education for Aging and Technology Enhancement (CREATE)
Wallace H. Coulter Center for Translational Research

The Miller School of Medicine receives more than $200 million per year in external grants and contracts to fund 1,500 ongoing projects. The medical campus includes more than 500,000 sq ft (46,000 m^2) of research space and the The University of Miami Life Science Park, which has an additional 2,000,000 sq ft (190,000 m^2) of space adjacent to the medical campus. The University of Miami’s Interdisciplinary Stem Cell Institute seeks to understand the biology of stem cells and translate basic research into new regenerative therapies.

As of 2008, The Rosenstiel School of Marine and Atmospheric Science receives $50 million in annual external research funding. Their laboratories include a salt-water wave tank, a five-tank Conditioning and Spawning System, multi-tank Aplysia Culture Laboratory, Controlled Corals Climate Tanks, and DNA analysis equipment. The campus also houses an invertebrate museum with 400,000 specimens and operates the Bimini Biological Field Station, an array of oceanographic high-frequency radar along the US east coast, and the Bermuda aerosol observatory. The University of Miami also owns the Little Salt Spring, a site on the National Register of Historic Places, in North Port, Florida, where RSMAS performs archaeological and paleontological research.

The University of Miami built a brain imaging annex to the James M. Cox Jr. Science Center within the College of Arts and Sciences. The building includes a human functional magnetic resonance imaging (fMRI) laboratory, where scientists, clinicians, and engineers can study fundamental aspects of brain function. Construction of the lab was funded in part by a $14.8 million in stimulus money grant from the National Institutes of Health.

In 2016 the university received $161 million in science and engineering funding from the U.S. federal government, the largest Hispanic-serving recipient and 56th overall. $117 million of the funding was through the Department of Health and Human Services and was used largely for the medical campus.

The University of Miami maintains one of the largest centralized academic cyber infrastructures in the country with numerous assets. The Center for Computational Science High Performance Computing group has been in continuous operation since 2007. Over that time the core has grown from a zero HPC cyberinfrastructure to a regional high-performance computing environment that currently supports more than 1,200 users, 220 TFlops of computational power, and more than 3 Petabytes of disk storage.

From The Georgia Institute of Technology: “Machine Learning Predicts Biodiversity and Resilience in the Coral Triangle”

From The Georgia Institute of Technology

2.9.23
Catherine Barzler
Senior Research Writer/Editor
catherine.barzler@gatech.edu

A school of planktivorous fish sheltering around a coral on a reef in the Solomon Islands in the Coral Triangle. Credit: Mark Hay.

Coral reef conservation is a steppingstone to protect marine biodiversity and life in the ocean as we know it. The health of coral also has huge societal implications: reef ecosystems provide sustenance and livelihoods for millions of people around the world. Conserving biodiversity in reef areas is both a social issue and a marine biodiversity priority.

In the face of climate change, Annalisa Bracco, professor in the School of Earth and Atmospheric Sciences at Georgia Institute of Technology, and Lyuba Novi, a postdoctoral researcher, offer a new methodology that could revolutionize how conservationists monitor coral. The researchers applied machine learning tools to study how climate impacts connectivity and biodiversity in the Pacific Ocean’s Coral Triangle — the most diverse and biologically complex marine ecosystem on the planet. Their research, recently published in Communications Biology [below], overcomes time and resource barriers to contextualize the biodiversity of the Coral Triangle, while offering hope for better monitoring and protection in the future.

“We saw that the biodiversity of the Coral Triangle is incredibly dynamic,” Bracco said. “For a long time, it has been postulated that this is due to sea level change and distribution of land masses, but we are now starting to understand that there is more to the story.”

Connectivity refers to the conditions that allow different ecosystems to exchange genetic material such as eggs, larvae, or the young. Ocean currents spread genetic material and also create the dynamics that allow a body of water — and thus ecosystems — to maintain consistent chemical, biological, and physical properties. If coral larvae are spread to an ecoregion where the conditions are very similar to the original location, the larvae can start a new coral.

Bracco wanted to see how climate, and specifically the El Niño Southern Oscillation (ENSO) in its phases — El Niño, La Niña, and neutral conditions — impacts connectivity in the Coral Triangle. Climate events that move large masses of warm water in the Pacific Ocean bring enormous changes and have been known to exacerbate coral bleaching, in which corals turn white due to environmental stressors and become vulnerable to disease.

“Biologists collect data in situ, which is extremely important,” Bracco said. “But it’s not possible to monitor enormous regions in situ for many years — that would require a constant presence of scuba divers. So, figuring out how different ocean regions and large marine ecosystems are connected over time, especially in terms of foundational species like coral, becomes important.”

Machine Learning for Discovering Connectivity

Years ago, Bracco and collaborators developed a tool, Delta Maps, that uses machine learning to identify “domains,” or regions within any kind of system that share the same dynamic. Bracco initially used it to analyze domains of climate variability in models but also suspected it could be used to study ecoregions in the ocean.

For this study, they used the tool to map out domains of connectivity in the Coral Triangle using 30 years of sea surface temperature data. Sea surface temperatures change in response to ocean currents over scales of weeks and months and across distances of tens of kilometers. These changes are relevant to coral connectivity, so the researchers built their machine learning tool based on this observation, using changes in surface ocean temperature to identify regions connected by currents. They also separated the time periods that they were considering into three categories: El Niño events, La Niña events, and neutral or “normal” times, painting a picture of how connectivity was impacted during major climate events in particular ecoregions.

Novi then applied a ranking system to the different ecoregions they identified. She used rank page centrality, a machine learning tool that was invented to rank webpages on the internet, on top of Delta Maps to identify which coral ecoregions were most strongly connected and able to receive the most coral larvae from other regions. Those regions would be the ones most likely sustain and survive through a bleaching event.

Communications Biology

Fig. 1: The CT and Indian Ocean study area, with superposed coral reef and spawning locations.

In yellow the distribution of coral reefs in the study area, as obtained from the UNEP-WCMC (UNEP-World Conservation Monitoring Centre), WorldFish Centre, WRI (World Resources Institute), TNC (The Nature Conservancy) Global distribution of Coral Reefs database [66*],[67],[68],[69]; in cyan known coral spawning locations within the study area, from the Coral Spawning Database [65]. Topographic and bathymetric background: USGS Imagery Topo, courtesy of the U.S. Geological Survey.

Fig. 2: Conceptual framework and workflow.

Schematic representation of the proposed ecoregionalization, connectivity and resilience framework.

*See the science paper for cited references.

For further illustrations see the science paper.

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.

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Please help promote STEM in your local schools.

The Georgia Institute of Technology is a public research university and institute of technology located in the Midtown neighborhood of Atlanta, Georgia. It is a part of the University System of Georgia and has satellite campuses in Savannah, Georgia; Metz, France; Athlone, Ireland; Shenzhen, China; and Singapore.

The school was founded in 1885 as the Georgia School of Technology as part of Reconstruction plans to build an industrial economy in the post-Civil War Southern United States. Initially, it offered only a degree in mechanical engineering. By 1901, its curriculum had expanded to include electrical, civil, and chemical engineering. In 1948, the school changed its name to reflect its evolution from a trade school to a larger and more capable technical institute and research university.

Today, The Georgia Institute of Technology is organized into six colleges and contains 31 departments/units, with emphasis on science and technology. It is well recognized for its degree programs in engineering, computing, industrial administration, the sciences and design. Georgia Tech is ranked 8th among all public national universities in the United States, 35th among all colleges and universities in the United States by U.S. News & World Report rankings, and 34th among global universities in the world by Times Higher Education rankings. Georgia Tech has been ranked as the “smartest” public college in America (based on average standardized test scores).

Student athletics, both organized and intramural, are a part of student and alumni life. The school’s intercollegiate competitive sports teams, the four-time football national champion Yellow Jackets, and the nationally recognized fight song “Ramblin’ Wreck from Georgia Tech”, have helped keep Georgia Tech in the national spotlight. Georgia Tech fields eight men’s and seven women’s teams that compete in the NCAA Division I athletics and the Football Bowl Subdivision. Georgia Tech is a member of the Coastal Division in the Atlantic Coast Conference.

From The Rosenstiel School of Marine and Atmospheric and Earth Science At The University of Miami: “New study finds coral reefs in the eastern Pacific could survive into the 2060’s”

From The Rosenstiel School of Marine and Atmospheric and Earth Science

At

The University of Miami

2.13.23
Diana Udel

Ana Palacio-Castro, Ph.D., surveys a coral reef in the eastern Pacific near Panama dominated by Pocillopora corals. Photo: Viktor Brandtneris.

Some reefs increase their resilience to elevated temperatures by being built by corals that shuffle algal partners following ocean heatwaves.

Scientists at the University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science found that some reefs in the tropical Pacific Ocean could maintain high coral cover into the second half of this century by shuffling the symbiotic algae they host. The findings offer a ray of hope in an often-dire picture of the future of coral reefs worldwide.

While global warming is causing the loss of coral reefs globally, scientists believe that some corals are increasing their tolerance to heat by changing the symbiotic algae communities they host, which through photosynthesis provide them with the energy they need to live.

“Our results suggest that some reefs in the eastern tropical Pacific, which includes the Pacific coasts of Panama, Costa Rica, Mexico, and Colombia, might be able to maintain high coral cover through the 2060s,” said coral biologist Ana Palacio-Castro, lead author of the study, alumna of the Rosenstiel School, and a postdoctoral associate at the school’s Cooperative Institute for Marine and Atmospheric Studies. “However, while this may be seen as good news for these reefs, their survival may not continue past that date unless we reduce global greenhouse gas emissions and curtail global warming on a larger scale.”

Shallow coral reefs in the eastern tropical Pacific Ocean are predominantly built by branching corals in the genus Pocillopora, which are extremely important for the reefs in the region. The microscopic algae they host in their tissue harvest light to help the coral produce energy to grow. The loss of these symbiotic algae causes the coral to turn white, or bleach, and the coral struggles to meet their energy needs, which can often prove fatal.

To better understand how corals improved their tolerance to heat stress, the researchers examined over 40 years’ worth of coral reef-monitoring data from Panama, one of the longest datasets of its kind in the world. They analyzed temperature, coral cover, bleaching and mortality data spanning three ocean heatwaves – in 1982–1983, 1997–1998, and 2015–2016 – along with data on algal symbiont community data during the last two.

The analysis showed that the 1982-83 heatwave significantly reduced coral cover on the reef, but the effects of the 1997-98 and 2015-16 El Niño were milder, especially for corals in the genus Pocillopora — sometimes known as cauliflower coral — the predominant reef-building coral in the eastern tropical Pacific. They also confirmed that during strong ocean heatwaves, the heat-tolerant alga Durusdinium glynnii becomes increasingly common in this particular lineage of corals, allowing them to better withstand periods of elevated temperatures. When combined with climate projections of future heat stress, the reefs that were predominantly composed of Pocillopora corals and that hosted this heat-tolerant alga were found to be better equipped to survive and maintain high levels of coral cover well into the second half of the current century, indicating that some reef systems may be more resilient to warming than previously thought.

“This study shows that there are some unusual reefs that may be able to survive for several decades as a result of their ability to shuffle symbionts,” said Andrew Baker, professor of marine biology and ecology at the Rosenstiel School, and senior author of the study. “While we don’t think that most reefs will be able to survive in this way, it does suggest that vestiges of our current reefs may persist for longer than we previously thought, although potentially with many fewer species. Coral reefs are incredibly valuable natural assets, providing coastal protection and fisheries benefits, and supporting many local communities. We can still make a difference by protecting them.”

The study was published on Feb.13, 2023, in the journal PNAS [below]. The study’s authors include: Ana M. Palacio-Castro, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Cooperative Institute for Marine and Atmospheric Studies and NOAA Atlantic Oceanographic and Meteorological Laboratory; Andrew C. Baker, Grace A. Snyder and Peter W. Glynn, University of Miami Rosenstiel School; Tyler B. Smith and Viktor Brandtneris, Center for Marine and Environmental Studies, University of the Virgin Islands; Ruben van Hooidonk, Cooperative Institute for Marine and Atmospheric Studies and NOAA Atlantic Oceanographic and Meteorological Laboratory; Juan L. Maté, Smithsonian Tropical Research Institute; Derek Manzello, Coral Reef Watch, NOAA and Peggy Fong, University of California Los Angeles.

PNAS

Increased dominance of heat-tolerant symbionts creates resilient coral reefs in near-term ocean warming.

More instructive images are available in the science paper.

See the full article here.

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”

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Please help promote STEM in your local schools.

Stem Education Coalition

The Rosenstiel School of Marine and Atmospheric and Earth Science is an academic and research institution for the study of oceanography and the atmospheric sciences within the University of Miami. It is located on a 16-acre (65,000 m^²) campus on Virginia Key in Miami, Florida. It is the only subtropical applied and basic marine and atmospheric research institute in the continental United States.

Up until 2008, RSMAS was solely a graduate school within the University of Miami, while it jointly administrated an undergraduate program with UM’s College of Arts and Sciences. In 2008, the Rosenstiel School has taken over administrative responsibilities for the undergraduate program, granting Bachelor of Science in Marine and Atmospheric Science (BSMAS) and Bachelor of Arts in Marine Affairs (BAMA) baccalaureate degree. Master’s, including a Master of Professional Science degree, and doctorates are also awarded to RSMAS students by the UM Graduate School.

The Rosenstiel School’s research includes the study of marine life, particularly Aplysia and coral; climate change; air-sea interactions; coastal ecology; and admiralty law. The school operates a marine research laboratory ship, and has a research site at an inland sinkhole. Research also includes the use of data from weather satellites and the school operates its own satellite downlink facility. The school is home to the world’s largest hurricane simulation tank.

The University of Miami is a private research university in Coral Gables, Florida. As of 2020, the university enrolled approximately 18,000 students in 12 separate colleges and schools, including the Leonard M. Miller School of Medicine in Miami’s Health District, a law school on the main campus, and the Rosenstiel School of Marine and Atmospheric Science focused on the study of oceanography and atmospheric sciences on Virginia Key, with research facilities at the Richmond Facility in southern Miami-Dade County.

The university offers 132 undergraduate, 148 master’s, and 67 doctoral degree programs, of which 63 are research/scholarship and 4 are professional areas of study. Over the years, the university’s students have represented all 50 states and close to 150 foreign countries. With more than 16,000 full- and part-time faculty and staff, The University of Miami is a top 10 employer in Miami-Dade County. The University of Miami’s main campus in Coral Gables has 239 acres and over 5.7 million square feet of buildings.

The University of Miami is classified among “R1: Doctoral Universities – Very high research activity”. The University of Miami research expenditure in FY 2019 was $358.9 million. The University of Miami offers a large library system with over 3.9 million volumes and exceptional holdings in Cuban heritage and music.

The University of Miami also offers a wide range of student activities, including fraternities and sororities, and hundreds of student organizations. The Miami Hurricane, the student newspaper, and WVUM, the student-run radio station, have won multiple collegiate awards. The University of Miami’s intercollegiate athletic teams, collectively known as the Miami Hurricanes, compete in Division I of the National Collegiate Athletic Association. The University of Miami’s football team has won five national championships since 1983 and its baseball team has won four national championships since 1982.

Research

The University of Miami is classified among “R1: Doctoral Universities – Very high research activity”. In fiscal year 2016, The University of Miami received $195 million in federal research funding, including $131.3 million from the Department of Health and Human Services and $14.1 million from the National Science Foundation. Of the $8.2 billion appropriated by Congress in 2009 as a part of the stimulus bill for research priorities of The National Institutes of Health, the Miller School received $40.5 million. In addition to research conducted in the individual academic schools and departments, Miami has the following university-wide research centers:

The Center for Computational Science
The Institute for Cuban and Cuban-American Studies (ICCAS)
Leonard and Jayne Abess Center for Ecosystem Science and Policy
The Miami European Union Center: This group is a consortium with Florida International University (FIU) established in fall 2001 with a grant from the European Commission through its delegation in Washington, D.C., intended to research economic, social, and political issues of interest to the European Union.
The Sue and Leonard Miller Center for Contemporary Judaic Studies
John P. Hussman Institute for Human Genomics – studies possible causes of Parkinson’s disease, Alzheimer’s disease and macular degeneration.
Center on Research and Education for Aging and Technology Enhancement (CREATE)
Wallace H. Coulter Center for Translational Research

The Miller School of Medicine receives more than $200 million per year in external grants and contracts to fund 1,500 ongoing projects. The medical campus includes more than 500,000 sq ft (46,000 m^2) of research space and the The University of Miami Life Science Park, which has an additional 2,000,000 sq ft (190,000 m^2) of space adjacent to the medical campus. The University of Miami’s Interdisciplinary Stem Cell Institute seeks to understand the biology of stem cells and translate basic research into new regenerative therapies.

As of 2008, The Rosenstiel School of Marine and Atmospheric Science receives $50 million in annual external research funding. Their laboratories include a salt-water wave tank, a five-tank Conditioning and Spawning System, multi-tank Aplysia Culture Laboratory, Controlled Corals Climate Tanks, and DNA analysis equipment. The campus also houses an invertebrate museum with 400,000 specimens and operates the Bimini Biological Field Station, an array of oceanographic high-frequency radar along the US east coast, and the Bermuda aerosol observatory. The University of Miami also owns the Little Salt Spring, a site on the National Register of Historic Places, in North Port, Florida, where RSMAS performs archaeological and paleontological research.

The University of Miami built a brain imaging annex to the James M. Cox Jr. Science Center within the College of Arts and Sciences. The building includes a human functional magnetic resonance imaging (fMRI) laboratory, where scientists, clinicians, and engineers can study fundamental aspects of brain function. Construction of the lab was funded in part by a $14.8 million in stimulus money grant from the National Institutes of Health.

In 2016 the university received $161 million in science and engineering funding from the U.S. federal government, the largest Hispanic-serving recipient and 56th overall. $117 million of the funding was through the Department of Health and Human Services and was used largely for the medical campus.

The University of Miami maintains one of the largest centralized academic cyber infrastructures in the country with numerous assets. The Center for Computational Science High Performance Computing group has been in continuous operation since 2007. Over that time the core has grown from a zero HPC cyberinfrastructure to a regional high-performance computing environment that currently supports more than 1,200 users, 220 TFlops of computational power, and more than 3 Petabytes of disk storage.

From The University of Melbourne (AU): “The smallest marine microbes share nutrients – briefly”

From The University of Melbourne (AU)

2.10.23
Dr Douglas R. Brumley

Microorganisms-or microbes-are the engines driving large-scale ecological and biogeochemical processes in the ocean.

They process light and nutrients at a massive scale and represent the base of the marine food web.

The ocean is full of microscopic organisms that power global processes like the carbon cycle. Photo: NASA

While microbial activity in the ocean has typically been studied at large scales to understand things like global oxygen production and CO₂ sequestration, there is increasing evidence that the intricate small-scale movement of individual cells plays a major role in shaping the productivity of the ocean.

BACTERIA SWIM TOWARDS LARGE PHYTOPLANKTON

Two types of microbes dominate in the ocean, phytoplankton[WHOI (below)] and bacteria.

Phytoplankton are the tiny ‘plants’ of the open ocean, soaking up sunlight and using this energy to create food and oxygen. The exchange of nutrients between phytoplankton and bacteria regulates ocean productivity.

Under the microscope, marine bacteria (around one micrometre, or 1/1000th of a millimetre wide) are often seen clustering around large phytoplankton cells (like diatoms, which are approximately 0.5 to one millimetre in size), feeding from nutrients that seep into the environment.

Assorted diatoms as seen through a microscope. These specimens were living between crystals of annual sea ice in McMurdo Sound, Antarctica. Image digitized from original 35mm Ektachrome slide. These tiny phytoplankton are encased within a silicate cell wall. Prof. Gordon T. Taylor, Stony Brook University.

Nutrient-rich areas around phytoplankton, referred to as phycospheres [Nature Microbiology (below) The ISME Journal (below)], attract bacteria, which home in on them using a process called chemotaxis [PNAS].

However, phytoplankton come in a vast array of shapes and sizes, and the most abundant are also some of the smallest.

Picophytoplankton like Synechococcus (which are a form of photosynthetic bacteria called a cyanobacterium) can be hundreds of times smaller than diatoms.

Synechococcus are tiny solar powered nutrient production factories in the ocean. Photo: Wikimedia.

Because of their tiny size – just a few micrometres wide – the prevailing view has been that cell-to-cell interactions between picophytoplankton and other bacteria are not possible. The chances of bumping into one another to share nutrients seemed incredibly slim, like needles finding other needles in a haystack.

FOLLOW THE [CHEMICAL] MONEY

In collaboration with colleagues in the Climate Change Cluster at the University of Technology Sydney and around the world, we devised a series of experiments and mathematical models – published in Nature Microbiology [below] – to test if and how swimming and navigation can help bacteria find these picophytoplankton ‘needles in the haystack’.

To test if nutrients were being transferred between these different organisms, we grew the bacteria and picophytoplankton separately with different forms of nitrogen and carbon (called stable isotopes), and then grew them together for three hours in the lab.

Next, our team measured the nitrogen and carbon composition of individual cells and found that some of these nutrients had indeed transferred between the two types of organisms.

HOW IMPORTANT IS BACTERIAL MOVEMENT?

For the experiment, we used bacteria that were chemotactic – they could swim towards food. But is swimming important for this nutrient exchange, and in fact, for cells in the ocean that are so small, is there any point at all in swimming?

To find out, we repeated these experiments with two different types of bacteria: bacteria that could swim but not navigate towards food and bacteria that could not swim at all.

The exchange of nutrients with the picophytoplankton was much lower in each case.

Chemotactic bacteria can swim towards the nutrient-rich water around picophytoplankton, but they don’t stay long. Image: supplied.

This demonstrated that the prevailing view was wrong. Bacterial swimming behaviour is key in exchanging nutrients and using chemotaxis; bacteria can indeed home in on their nutrient-rich picophytoplankton targets.

MATHEMATICAL MODELLING SHOWS US HOW IT’S DONE

Although bacterial sensing and movement are complex, their behaviour can be very accurately captured by simplified mathematical models.

And the great thing about a good mathematical model is it does not just reproduce the experimental data but provides new insights into the system that are difficult or impossible to see in other ways.

Our mathematical model directly simulates the motion of thousands of bacteria swimming within a small droplet of seawater.

The model backed up our experimental findings that swimming enhances nutrient uptake from picophytoplankton. It also allowed us to follow individual bacterial cells and calculate how far from a food source they were – at all times.

A NEW TYPE OF SYMBIOSIS

We discovered that bacteria capable of performing chemotaxis will swim towards the picophytoplankton hotspots, but will frequently get ‘lost’ and move away.

Their targets are so small and the signal so weak that even with very precise navigation, it’s impossible for them to reside indefinitely near a picophytoplankton cell. Their swimming movement will inadvertently take them away from the cell, and they then have to find their way back, or to another cell, a quite laborious process for these tiny bacteria.

This seems a very inefficient way to get nutrients but, in the same way that the casino house always wins in the end, the chemotactic cells gain up to 160 per cent more nutrients than those that can’t navigate.

This is because these bacteria spend a little more time in the very narrow nutrient-rich environment surrounding each hotspot.

The effect of visiting nutrient pulses more often and for slightly longer results in a significantly higher growth rate over time.

Our team’s findings represent a new form of symbiosis, in which significant two-way exchanges occur between organisms, but over fleeting timescales of a few seconds. These results are in contrast to typical symbioses, which involve organisms sitting in close proximity to one another indefinitely.

MICROSCALE MOVEMENT IS KEY

The main finding of our work is that cell behaviour has a tremendous role in shaping metabolic partnerships between microorganisms.

Even though the cells are extremely small, the fine-scale movement of individual cells provides conspicuous advantages, which ultimately scale up to enhanced growth rates and help to shape overall ocean productivity.

Beyond the ocean, this work also shows that chemotaxis may play an unexpected role in the metabolic exchanges between individual cells across a whole range of other environments.

WHOI

Diatoms are one of several major types of marine phytoplankton. These microorganisms that live near the ocean surface and convert carbon dioxide into organic carbon via photosynthesis. They produce much of the oxygen we breathe and are the base of the marine food chain. They also play an important role in drawing heat-trapping carbon dioxide from the atmosphere into the ocean. (Woods Hole Oceanographic Institution)

Nature Microbiology 2017
The ISME Journal 2022

Fig. 1: Experimental designs and overview of the dynamics of Prochlorococcus-Alteromonas co-cultures from first encounter and over multiple transfers.

A Schematic illustration of the experimental design. One ml from Experiment E1 was transferred into 20 ml fresh media after 100 days, starting experiment E2. Experiment E2 was similarly transferred into fresh media after 140 days, starting experiment E3. Additional experiments replicating these transfers are described in Supplementary Fig. S1. B Overview of the growth curves of the 25 Prochlorococcus-Alteromonas co-cultures over three transfers spanning ~1.2 years (E1, E2 and E3). Results show mean + standard error from biological triplicates, colored by Prochlorococcus strain as in panel D. C Axenic Prochlorococcus grew exponentially in E1 but failed to grow when transferred into fresh media after 60, 100, or 140 days. Axenic Alteromonas cultures were counted after 60 and 100 days, as their growth cannot be monitored sensitively and non-invasively using fluorescence (optical density is low at these cell numbers). D High reproducibility and strain-specific dynamics of the initial contact between Prochlorococcus and Alteromonas strains (E1). Three biological replicates for each mono-culture and co-culture are shown. Note that the Y axis is linear in panels B, C and logarithmic in panel D. Au: arbitrary units.

Fig. 2: Growth analysis and principal component analysis (PCA) of the growth curves from all co-cultures during 140 days of E1.

A Growth rate, B Maximum fluorescence, and C duration of lag phase during experiment E1. Box-plots represent mean and 75th percentile of co-cultures, circles represent measurements of individual cultures of the axenic controls. The only significant difference between axenic and co-cultures is in the length of the lag phase for MIT9313 (Bonferroni corrected ANOVA, p < 0.001). D PCA ordination of the growth curves colored by Prochlorococcus (left) and by Alteromonas (right) strains. The growth curves cluster by Prochlorococcus strain (Adonis test, F(4,68) = 42.3, R2 = 0.71, p = 0.001) and only marginally by Alteromonas strain (Adonis test, F(4,68) = 2.29, R2 = 0.11, p = 0.017). Au arbitrary units.
See this science paper for further illustrations.

The ISME Journal 2022

Fig. 1: Comparison of the temporal dynamics of biotic and abiotic parameters between field and mesocosm samples.

A, E Chlorophyll a (Chl a) and dissolved organic carbon (DOC) concentrations, (B, F) Nitrate (NO3−) and phosphate (PO43−) concentrations, (C, G) Bacterial abundance (BA) and bacterial production (BP), and (D, H) Transcription of the 15 most active prokaryotic taxa. Arrows indicate the time points when metatranscriptome samples were taken. Error bars denote standard deviation of triplicate mesocosms, except for day 0, which were taken from pooled water used for filling the tanks (n = 1).
See this science paper for further illustrations.

The ISME Journal 2022

PNAS 2019

Nature Microbiology

See the full article here .

See especially many images from the cited science papers.

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.

five-ways-keep-your-child-safe-school-shootings
Please help promote STEM in your local schools.

Stem Education Coalition

The University of Melbourne (AU) is an Australian public research university located in Melbourne, Victoria. Founded in 1853, it is Australia’s second oldest university and the oldest in Victoria. Times Higher Education ranks Melbourne as 33rd in the world, while the Academic Ranking of World Universities places Melbourne 44th in the world (both first in Australia).

Melbourne’s main campus is located in Parkville, an inner suburb north of the Melbourne central business district, with several other campuses located across Victoria. Melbourne is a sandstone university and a member of The Group of Eight, Universitas 21 and The Association of Pacific Rim Universities. Since 1872 various residential colleges have become affiliated with the university. There are 12 colleges located on the main campus and in nearby suburbs offering academic, sporting and cultural programs alongside accommodation for Melbourne students and faculty.

Melbourne comprises 11 separate academic units and is associated with numerous institutes and research centres, including the Walter and Eliza Hall Institute of Medical Research, Florey Institute of Neuroscience and Mental Health, the Melbourne Institute of Applied Economic and Social Research and the Grattan Institute. Amongst Melbourne’s 15 graduate schools the Melbourne Business School, the Melbourne Law School and the Melbourne Medical School are particularly well regarded.

Four Australian prime ministers and five governors-general have graduated from Melbourne. Nine Nobel laureates have been students or faculty, the most of any Australian university.

From Monash University (AU): “World first study sheds light on why microbes in the deep ocean live without sunlight”

From Monash University (AU)

2.7.23
Tania Ewing, Monash University
taniaewing@taniaewing.com
M: +61 (0)408 378 422

media@monash.edu
T: +61 (0) 3 9903 4840

Dr Rachael Lappan from Monash Biomedicine Discovery Institute

A world first study challenges the idea that the bulk of life in the ocean is fueled by photosynthesis via sunshine, revealing that many ocean microbes in fact get their energy from hydrogen and carbon monoxide.

It has always been a mystery as to how microbes growing in deepest parts of the sea survive, with no sunlight. A new study, from researchers at the Monash University published in the journal Nature Microbiology [below], shows that a distinct process called chemosynthesis – growth using inorganic compounds – fuels microbes in these darkest depths.

The five-year study, led by Dr Rachael Lappan and Professor Chris Greening from the Biomedicine Discovery Institute, reveals that two common gases – hydrogen and carbon monoxide – serve as the fuel for trillions of microbes in the ocean from the tropics to the poles.

Fig. 1: Ex situ oxidation of CO and H2 by seawater communities.

a,b, Results are shown for four samples in a transect at Port Phillip Bay, Victoria, Australia (a) and eight samples in the Munida transect off the coast of Otago, New Zealand (b). Each 120 ml sealed serum vial contained 60 ml of native seawater samples incubated in a 60 ml ambient-air headspace supplemented with ~2.5 ppmv H2 or CO. At each timepoint, the mixing ratio of each gas in the headspace of each vial was measured on a gas chromatograph and converted to dissolved gas concentrations (nM). Data are presented as mean ± s.e.m. of three biologically independent samples. Source data

According to Professor Greening, until now most scientists have believed that ocean microbial life is primarily driven by photosynthesis (growth by using light energy). “But what about those regions so deep that light can’t penetrate or so nutrient-poor that algae can’t thrive? We showed in this study that instead chemosynthesis is dominant in these regions,” he said.

“Hydrogen and carbon monoxide in fact “fed” microbes in all regions we’ve looked at: from urban bays to around tropical islands to hundreds of metres below the surface. Some can even be found beneath Antarctica’s ice shelves.”

The study involved combining chemical measurements during oceanic voyages with laboratory-based characterization of microbial cultures. The research team also extensively used metagenomic sequencing, “which tells us the genetic blueprints of all of the microbes present in a given region of the ocean,” Dr Lappan said. “We found the genes that enable hydrogen consumption across eight distantly related types of microbes, known as phyla, and this survival strategy becomes more common the deeper they live.”

For this project, the researchers were inspired by their previous work on soil bacteria. Professor Greening and colleagues have previously showed most soil bacteria can live by consuming hydrogen and carbon monoxide from the atmosphere.

“The surface layers of the world’s oceans generally contain high levels of dissolved hydrogen and carbon monoxide gases due to various geological and biological processes. So it made sense that oceanic bacteria used the same gases as their terrestrial cousins,” Dr Lappan said.

These findings provide insights into how life evolved. Professor Greening concludes that “The first life probably emerged in deep-sea vents using hydrogen and not sunlight as the energy source. It’s incredible that, 3.7 billion years later so many microbes in the oceans are still using this high-energy gas and we’ve completely overlooked this until now.”

Nature Microbiology

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

Monash University (AU) is an Australian public research university based in Melbourne, Australia. Founded in 1958, it is the second oldest university in the State of Victoria. Monash is a member of Australia’s Group of Eight and the ASAIHL, and is the only Australian member of the influential M8 Alliance of Academic Health Centers, Universities and National Academies. Monash is one of two Australian universities to be ranked in the The École des Mines de Paris (Mines ParisTech) ranking on the basis of the number of alumni listed among CEOs in the 500 largest worldwide companies. Monash is in the top 20% in teaching, top 10% in international outlook, top 20% in industry income and top 10% in research in the world in 2016.

Monash enrolls approximately 47,000 undergraduate and 20,000 graduate students, It also has more applicants than any university in the state of Victoria.

Monash is home to major research facilities, including the Australian Synchrotron, the Monash Science Technology Research and Innovation Precinct (STRIP), the Australian Stem Cell Centre, 100 research centres and 17 co-operative research centres. In 2011, its total revenue was over $2.1 billion, with external research income around $282 million.

The university has a number of centres, five of which are in Victoria (Clayton, Caulfield, Berwick, Peninsula, and Parkville), one in Malaysia. Monash also has a research and teaching centre in Prato, Italy, a graduate research school in Mumbai, India and a graduate school in Jiangsu Province, China. Since December 2011, Monash has had a global alliance with The University of Warwick (UK). Monash University courses are also delivered at other locations, including South Africa.

The Clayton campus contains the Robert Blackwood Hall, named after the university’s founding Chancellor Sir Robert Blackwood and designed by Sir Roy Grounds.

In 2014, the University ceded its Gippsland campus to Federation University (AU). On 7 March 2016, Monash announced that it would be closing the Berwick campus by 2018.

From The Woods Hole Oceanographic Institution Via “phys.org” : “The ocean twilight zone could eventually store vast amounts of carbon captured from the atmosphere”

From The Woods Hole Oceanographic Institution

Via

“phys.org”

2.2.23

A large robot, loaded with sensors and cameras, designed to explore the ocean twilight zone. Credit: Marine Imaging Technologies, LLC, Woods Hole Oceanographic Institution.

Deep below the ocean surface, the light fades into a twilight zone where whales and fish migrate and dead algae and zooplankton rain down from above. This is the heart of the ocean’s carbon pump, part of the natural ocean processes that capture about a third of all human-produced carbon dioxide and sink it into the deep sea, where it remains for hundreds of years.

There may be ways to enhance these processes so the ocean pulls more carbon out of the atmosphere to help slow climate change. Yet little is known about the consequences.

Peter de Menocal, a marine paleoclimatologist and director of Woods Hole Oceanographic Institution, discussed ocean carbon dioxide removal at a recent TEDxBoston: Planetary Stewardship event. In this interview, he dives deeper into the risks and benefits of human intervention and describes an ambitious plan to build a vast monitoring network of autonomous sensors in the ocean to help humanity understand the impact.

First, what is ocean carbon dioxide removal, and how does it work in nature?

The ocean is like a big carbonated beverage. Although it doesn’t fizz, it has about 50 times more carbon than the atmosphere. So, for taking carbon out of the atmosphere and storing it someplace where it won’t continue to warm the planet, the ocean is the single biggest place it can go.

Ocean carbon dioxide removal, or ocean CDR uses the ocean’s natural ability to take up carbon on a large scale and amplifies it.

Methods of ocean carbon storage. Credit: Natalie Renier/Woods Hole Oceanographic Institution.

Carbon gets into the ocean from the atmosphere in two ways.

In the first, air dissolves into the ocean surface. Winds and crashing waves mix it into the upper half-mile or so, and because seawater is slightly alkaline, the carbon dioxide is absorbed into the ocean.

The second involves the biologic pump. The ocean is a living medium—it has algae and fish and whales, and when that organic material is eaten or dies, it gets recycled. It rains down through the ocean and makes its way to the ocean twilight zone, a level around 650 to 3,300 feet (roughly 200 to 1,000 meters) deep.

The ocean twilight zone sustains biologic activity in the oceans. It is the “soil” of the ocean where organic carbon and nutrients accumulate and are recycled by microbes. It is also home to the largest animal migration on the planet. Each day trillions of fish and other organisms migrate from the depths to the surface to feed on plankton and one another, and go back down, acting like a large carbon pump that captures carbon from the surface and shunts it down into the deep oceans where it is stored away from the atmosphere.

Credit: The Conversation.

Why is ocean CDR drawing so much attention right now?

The single most shocking sentence I have read in my career was in the Intergovernmental Panel on Climate Change’s Sixth Assessment Report, released in 2021. It said that we have delayed action on climate change for so long that removing carbon dioxide from the atmosphere is now necessary for all pathways to keep global warming under 1.5 degrees Celsius (2.7 F). Beyond that, climate change’s impacts become increasingly dangerous and unpredictable.

Because of its volume and carbon storage potential, the ocean is really the only arrow in our quiver that has the ability to take up and store carbon at the scale and urgency required.

A 2022 report by the national academies outlined a research strategy for ocean carbon dioxide removal. The three most promising methods all explore ways to enhance the ocean’s natural ability to take up more carbon.

The first is ocean alkalinity enhancement. The oceans are salty—they’re naturally alkaline, with a pH of about 8.1. Increasing alkalinity by dissolving certain powdered rocks and minerals makes the ocean a chemical sponge for atmospheric CO2.

A second method adds micronutrients to the surface ocean, particularly soluble iron. Very small amounts of soluble iron can stimulate greater productivity, or algae growth, which drives a more vigorous biologic pump. Over a dozen of these experiments have been done, so we know it works.

Third is perhaps the easiest to understand—grow kelp in the ocean, which captures carbon at the surface through photosynthesis, then bale it and sink it to the deep ocean.

But all of these methods have drawbacks for large-scale use, including cost and unanticipated consequences.

I’m not advocating for any one of these, or for ocean CDR more generally. But I do believe accelerating research to understand the impacts of these methods is essential. The ocean is essential for everything humans depend on—food, water, shelter, crops, climate stability. It’s the lungs of the planet. So we need to know if these ocean-based technologies to reduce carbon dioxide and climate risk are viable, safe and scalable.

You’ve talked about building an ‘internet of the ocean’ to monitor changes there. What would that involve?

The ocean is changing rapidly, and it is the single biggest cog in Earth’s climate engine, yet we have almost no observations of the subsurface ocean to understand how these changes are affecting the things we care about. We’re basically flying blind at a time when we most need observations. Moreover, if we were to try any of these carbon removal technologies at any scale right now, we wouldn’t be able to measure or verify their effectiveness or assess impacts on ocean health and ecosystems.

Top predators such as whales, tuna, swordfish and sharks rely on the twilight zone for food, diving down hundreds or even thousands of feet to catch their prey. Credit: Eric S. Taylor/Woods Hole Oceanographic Institution.

So, we are leading an initiative at Woods Hole Oceanographic Institution to build the world’s first internet for the ocean, called the Ocean Vital Signs Network. It’s a large network of moorings and sensors that provides 4D eyes on the oceans—the fourth dimension being time—that are always on, always connected to monitor these carbon cycling processes and ocean health.

Right now, there is about one ocean sensor in the global Argo program for every patch of ocean the size of Texas. These go up and down like pogo sticks, mostly measuring temperature and salinity.

We envision a central hub in the middle of an ocean basin where a dense network of intelligent gliders and autonomous vehicles measure ocean properties including carbon and other vital signs of ocean and planetary health. These vehicles can dock, repower, upload data they’ve collected and go out to collect more. The vehicles would be sharing information and making intelligent sampling decisions as they measure the chemistry, biology and environmental DNA for a volume of the ocean that’s really representative of how the ocean works.

Having that kind of network of autonomous vehicles, able to come back in and power up in the middle of the ocean from wave or solar or wind energy at the mooring site and send data to a satellite, could launch a new era of ocean observing and discovery.

Does the technology needed for this level of monitoring exist?

Mesobot starts its descent toward the ocean twilight zone. Credit: Marine Imaging Technologies, LLC, Woods Hole Oceanographic Institution.

We’re already doing much of this engineering and technology development. What we haven’t done yet is stitch it all together.

For example, we have a team that works with blue light lasers for communicating in the ocean. Underwater, you can’t use electromagnetic radiation as cellphones do, because seawater is conductive. Instead, you have to use sound or light to communicate underwater.

We also have an acoustics communications group that works on swarming technologies and communications between nearby vehicles. Another group works on how to dock vehicles into moorings in the middle of the ocean. Another specializes in mooring design. Another is building chemical sensors and physical sensors that measure ocean properties and environmental DNA.

This summer, 2023, an experiment in the North Atlantic called the Ocean Twilight Zone Project will image the larger functioning of the ocean over a big piece of real estate at the scale at which ocean processes actually work.

We’ll have acoustic transceivers that can create a 4D image over time of these dark, hidden regions, along with gliders, new sensors we call “minions” that will be looking at ocean carbon flow, nutrients and oxygen changes. “Minions” are basically sensors the size of a soda bottle that go down to a fixed depth, say 1,000 meters (0.6 miles), and use essentially an iPhone camera pointing up to take pictures of all the material floating down through the water column. That lets us quantify how much organic carbon is making its way into this old, cold deep water, where it can remain for centuries.

The Ocean Twilight Zone: Earth’s Final Frontier.
Premiered Mar 11, 2020
The mysteries of the ocean twilight zone are waiting to be explored. What was once thought to be desert-like isn’t a desert at all. Where the deep sea creatures lurk there are incredible biomass and biodiversity. The ocean twilight zone is a huge habitat that is very difficult to explore. Woods Hole Oceanographic Institution is poised to change this because we have the engineers that can help us overcome these challenges. Making new discoveries in ocean exploration is more important now than ever.

For the first time we’ll be able to see just how patchy productivity is in the ocean, how carbon gets into the ocean and if we can quantify those carbon flows.

That’s a game-changer. The results can help establish the effectiveness and ground rules for using CDR. It’s a Wild West out there—nobody is watching the oceans or paying attention. This network makes observation possible for making decisions that will affect future generations.

Do you believe ocean CDR is the right answer?

Humanity doesn’t have a lot of time to reduce carbon emissions and to lower carbon dioxide concentrations in the atmosphere.

The reason scientists are working so diligently on this is not because we’re big fans of CDR, but because we know the oceans may be able to help. With an ocean internet of sensors, we can really understand how the ocean works including the risks and benefits of ocean CDR.

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.

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Woods Hole Oceanographic Institution

Mission Statement

The Woods Hole Oceanographic Institution is dedicated to advancing knowledge of the ocean and its connection with the Earth system through a sustained commitment to excellence in science, engineering, and education, and to the application of this knowledge to problems facing society.

Vision & Mission

The ocean is a defining feature of our planet and crucial to life on Earth, yet it remains one of the planet’s last unexplored frontiers. For this reason, WHOI scientists and engineers are committed to understanding all facets of the ocean as well as its complex connections with Earth’s atmosphere, land, ice, seafloor, and life—including humanity. This is essential not only to advance knowledge about our planet, but also to ensure society’s long-term welfare and to help guide human stewardship of the environment. WHOI researchers are also dedicated to training future generations of ocean science leaders, to providing unbiased information that informs public policy and decision-making, and to expanding public awareness about the importance of the global ocean and its resources.

The Institution is organized into six departments, the Cooperative Institute for Climate and Ocean Research, and a marine policy center. Its shore-based facilities are located in the village of Woods Hole, Massachusetts and a mile and a half away on the Quissett Campus. The bulk of the Institution’s funding comes from grants and contracts from the National Science Foundation and other government agencies, augmented by foundations and private donations.

WHOI scientists, engineers, and students collaborate to develop theories, test ideas, build seagoing instruments, and collect data in diverse marine environments. Ships operated by WHOI carry research scientists throughout the world’s oceans. The WHOI fleet includes two large research vessels (R/V Atlantis and R/V Neil Armstrong); the coastal craft Tioga; small research craft such as the dive-operation work boat Echo; the deep-diving human-occupied submersible Alvin; the tethered, remotely operated vehicle Jason/Medea; and autonomous underwater vehicles such as the REMUS and SeaBED.
WHOI offers graduate and post-doctoral studies in marine science. There are several fellowship and training programs, and graduate degrees are awarded through a joint program with the Massachusetts Institute of Technology. WHOI is accredited by the New England Association of Schools and Colleges . WHOI also offers public outreach programs and informal education through its Exhibit Center and summer tours. The Institution has a volunteer program and a membership program, WHOI Associate.

On October 1, 2020, Peter B. de Menocal became the institution’s eleventh president and director.

History

In 1927, a National Academy of Sciences committee concluded that it was time to “consider the share of the United States of America in a worldwide program of oceanographic research.” The committee’s recommendation for establishing a permanent independent research laboratory on the East Coast to “prosecute oceanography in all its branches” led to the founding in 1930 of the Woods Hole Oceanographic Institution.

A $2.5 million grant from the Rockefeller Foundation supported the summer work of a dozen scientists, construction of a laboratory building and commissioning of a research vessel, the 142-foot (43 m) ketch R/V Atlantis, whose profile still forms the Institution’s logo.

WHOI grew substantially to support significant defense-related research during World War II, and later began a steady growth in staff, research fleet, and scientific stature. From 1950 to 1956, the director was Dr. Edward “Iceberg” Smith, an Arctic explorer, oceanographer and retired Coast Guard rear admiral.

In 1977 the institution appointed the influential oceanographer John Steele as director, and he served until his retirement in 1989.

On 1 September 1985, a joint French-American expedition led by Jean-Louis Michel of IFREMER and Robert Ballard of the Woods Hole Oceanographic Institution identified the location of the wreck of the RMS Titanic which sank off the coast of Newfoundland 15 April 1912.

On 3 April 2011, within a week of resuming of the search operation for Air France Flight 447, a team led by WHOI, operating full ocean depth autonomous underwater vehicles (AUVs) owned by the Waitt Institute discovered, by means of sidescan sonar, a large portion of debris field from flight AF447.

In March 2017 the institution effected an open-access policy to make its research publicly accessible online.

The Institution has maintained a long and controversial business collaboration with the treasure hunter company Odyssey Marine. Likewise, WHOI has participated in the location of the San José galleon in Colombia for the commercial exploitation of the shipwreck by the Government of President Santos and a private company.

In 2019, iDefense reported that China’s hackers had launched cyberattacks on dozens of academic institutions in an attempt to gain information on technology being developed for the United States Navy. Some of the targets included the Woods Hole Oceanographic Institution. The attacks have been underway since at least April 2017.

From “Eos” : “Deep-Sea Pressure Crushes Carbon Cycling”

From “Eos”

AT

AGU

1.11.23
Elise Cutts

The extreme pressure in the deep sea stifles microbes’ appetite for organic carbon. This finding could have important implications for carbon budgets and geoengineering.

Scientists used a clever device to measure deep-sea organic carbon degradation rates underwater, avoiding the need to keep samples in finicky and expensive pressure chambers. Credit: Chie Amano.

When the research submarine Alvin sank off the coast of Massachusetts in 1968, it took the crew’s lunch with it. Sandwiches wrapped in wax paper, a few thermoses of broth, and an apple or two came to rest with the legendary exploration vessel. And to the shock of the scientists who later returned to recover the wreck, there they remained—practically unspoiled despite sitting more than a kilometer below the surface for nearly a year.

A sandwich left out on your countertop or casually thrown into the sea would be lucky to last more than a day or two before going bad or getting gobbled up. So why didn’t something eat the Alvin crew’s lunch?

New evidence suggests that the extreme pressures of the deep sea slow down microbial carbon degradation, the process responsible for spoiling sandwiches and recycling organic carbon into carbon dioxide, a critical step in the carbon cycle. The research team behind the new study says that their findings could have important implications for carbon budgets, which are used in climate models, and future geoengineering strategies that propose storing excess carbon on the seafloor. The results were published in Nature Geoscience [below].

Fig. 1: In situ bulk leucine incorporation rates normalized to rates obtained at atmospheric pressure conditions.

Symbols correspond to the different research expeditions (Extended Data Fig. 1). Regression equation is a power law function: Pinsitu = 494z^−0.321 (n = 56, number of samples incubated at in situ), where Pinsitu is the percentage of in situ leucine incorporation rate normalized to mean leucine incorporation rate under atmospheric pressure (Atm.) and z is depth (m). Shaded area indicates 95% confidence interval for the regression. Note that the data points at 0 m (n = 4) correspond to instrumental tests in which epi- to bathypelagic waters were incubated with the ISMI under atmospheric pressure conditions and compared with bottle incubations used for atmospheric pressure incubations to assess the potential bias associated with the instrument. These points are excluded from calculating the regression line.

Fig. 2: Cell-specific leucine uptake by prokaryotes.

[a], Distribution of cell-specific leucine uptake expressed as the percentage of total active cell counts (upper panels) and the percentage of total uptake (lower panels). Water was collected at meso- and bathypelagic depths and incubated under in situ and atmospheric pressure (Atm.) conditions (Supplementary Tables 1 and 2). [b], A microscopic view of a bathypelagic sample (2,000 m) collected in the Atlantic and incubated under atmospheric pressure conditions. Black halos around the cells are silver grains corresponding to their activities. The highly active cells (>0.5 amol Leu cell−1 d−1, indicated by arrows) were barely found in in situ pressure incubations. Typical low-activity cells in the bathypelagic depths are indicated by circles. Green fluorescence, EUB338 probe mix; light blue, DAPI-stained cells. Scale bar, 5 µm. [c], Leucine uptake by taxonomical groups: S11, SAR11 clade; S202, SAR202 clade; S406, SAR406 clade; Alt, Alteromonas; Cf, Bacteroidetes; Cren, Thaumarchaeota; Eury, Euryarchaeota. The grey line connects the same location and depth between in situ and Atm. samples representing the change in leucine uptake beween the two incubation conditions.

Fig. 3: Depth-related changes in the metaproteome of three abundant deep-sea bacterial taxa.

[a], Venn diagrams indicating the number of shared and unique up- and down-regulated proteins among Alteromonas, Bacteroidetes and SAR202 of meso- versus epipelagic layers, bathy- versus mesopelagic layers and bathy- versus epipelagic layers. Numbers indicate the protein abundance. Epi, epipelagic; Meso, mesopelagic; Bathy, bathypelagic waters. [b], Comparison of expressed proteins produced by Alteromonas, Bacteroidetes and SAR202. Significance of the change between depth layers is indicated by different colours: not significant (NS), P ≥ 0.05; up-regulated proteins (Up), P < 0.05 and log2 fold change ≥1; down-regulated proteins (Down), P < 0.05 and log2 fold change ≤ −1. The P values are shown in Supplementary Data 1.

Challenging Deeps

For decades, scientists have wondered whether microbial carbon degradation is suppressed in the deep sea. But answering this seemingly simple question has proven challenging.

Shallow-water microbes continually fall into the deep ocean from the sunlit surface. These unwilling interlopers would presumably break down carbon more slowly at depth because they have not adapted to the pressure.

“These microbes survive, barely, in the deep sea. But they are not feeling really comfortable there,” said marine microbiologist Gerhard Herndl of the University of Vienna.

But other microbes don’t mind pressure much at all. Some will even die if they’re decompressed. Some of these pressure-loving piezophiles seem to have hearty appetites for organic carbon, leading some scientists to think that microbial activity in the deep sea could actually be rather high—though it’s possible that when scientists sample these communities, “we’re just isolating the ‘weeds’ that grow quickly,” said marine microbiologist Douglas Bartlett of the Scripps Institution of Oceanography, who was not involved in the new study.

Complicating everything further is the enormous technical challenge of working in the deep. Keeping a deep-sea sample under pressure after bringing it to the surface requires a tough titanium chamber that can tolerate pressure differences hundreds of times greater than that between the inside and outside of the International Space Station.

“That’s really hard engineering to do,” Bartlett said. So scientists have mostly measured deep-sea carbon degradation rates in depressurized samples brought up to the surface.

But without a way to make measurements under natural deep-sea conditions—pressure and all—it’s impossible to know whether the observations researchers have made in decompressed samples reflect what’s going on in the depths.

Getting to the Bottom of It

After years of trying to get pressure chambers to work, Herndl and his colleagues took a different approach; instead of bringing deep-sea samples to the surface for experiments, they’d bring their experiments to the deep sea.

Previously, researchers in Japan worked with Herndl’s group to develop a device that can be lowered from a ship to make measurements under water. The device takes a water sample, performs an experiment, and then adds a special fluid into the sample to “fix” it, preserving microbes exactly as they were in the deep sea. Then the sample is brought to the surface for measurements.

In the Pacific, Atlantic, and Southern Oceans, experiments with this device revealed that as a whole, microbial communities consumed carbon about one third as quickly at 4000 meters deep as at the surface.

Roughly 85% of microbes consumed carbon at about the same rate regardless of depth, and only about 5% of the microbes in seawater samples were pressure-loving piezophiles. The remaining 10% of microbes were pressure hating. These communities “respond tremendously when you release them from pressure,” gobbling up carbon much faster than they do in the deep sea, Herndl said. Because these organisms are much more active at sea surface pressure, previous estimates of the carbon degradation rates of deep-sea microbial communities were “really grossly overestimated,” he added.

Carbon Budgeting

The discovery could have important implications for geoengineering and for the carbon budgets that scientists use to build climate models.

“One of the issues of our time now is what to do about climate impacts,” Bartlett said. Pumping carbon dioxide into the atmosphere drives climate change, prompting some to devise creative carbon storage solutions. “People consider ways to bring more particulate organic carbon into the deep ocean to bury it and to sequester that carbon,” so knowing the rate that microbes break down organic carbon in the deep sea “is really important,” he said.

With respect to carbon budgeting, Herndl added, the discovery resolves a long-standing problem. Previous estimates of deep-ocean carbon degradation rates found a troubling mismatch: The supply of organic material sinking down from the surface seemed far smaller than deep-sea microbes’ appetite for that carbon. If the budgets really are misbalanced, “then apparently we don’t understand how the deep ocean works,” Herndl said.

But the new, lower carbon demand measured in this study lines up neatly with supply. The mismatch looks like it was simply a matter of overestimating carbon degradation rates in depressurized samples, Herndl and Bartlett said.

“It seems like that was the magic bullet—the solution that had eluded microbial oceanographers all these years,” Bartlett said, “not [measuring] microbial activity under the actual deep-sea conditions.”

“Microbes are by far the main contributors to carbon processing in the deep ocean,” Herndl said. “So it makes a difference when you [calculate] a global carbon budget…it makes a difference whether you estimate microbial activity in the deep correctly or not.”

Science paper:
Nature Geoscience

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.

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“Eos” is the leading source for trustworthy news and perspectives about the Earth and space sciences and their impact. Its namesake is Eos, the Greek goddess of the dawn, who represents the light shed on understanding our planet and its environment in space by the Earth and space sciences.