Category: Plants and Animals

Thirty Years Of Unique Data Reveal What’s Really Killing Coral Reefs

Coral reefs are considered one of the most threatened ecosystems on the planet and are dying at alarming rates around the world. Scientists attribute coral bleaching and ultimately massive coral death to a number of environmental stressors, in particular, warming water temperatures due to climate change.

A study published in the international journal Marine Biology, reveals what’s really killing coral reefs. With 30 years of unique data from Looe Key Reef in the lower Florida Keys, researchers from Florida Atlantic University’s Harbor Branch Oceanographic Institute and collaborators have discovered that the problem of coral bleaching is not just due to a warming planet, but also a planet that is simultaneously being enriched with reactive nitrogen from multiple sources.

Improperly treated sewage, fertilizers and top soil are elevating nitrogen levels, which are causing phosphorus starvation in the corals, reducing their temperature threshold for “bleaching.” These coral reefs were dying off long before they were impacted by rising water temperatures.

Nitrogen Loading

This study represents the longest record of reactive nutrients and algae concentrations for coral reefs anywhere in the world.

“Our results provide compelling evidence that nitrogen loading from the Florida Keys and greater Everglades ecosystem caused by humans, rather than warming temperatures, is the primary driver of coral reef degradation at Looe Key Sanctuary Preservation Area during our long-term study,”

said Brian Lapointe, Ph.D., senior author and a research professor at FAU’s Harbor Branch.

A key finding from the study is that land-based nutrient runoff has increased the nitrogen:phosphorus ratio (N:P) in reef algae, which indicates an increasing degree of phosphorus limitation known to cause metabolic stress and eventually starvation in corals. Concentrations of reactive nitrogen are above critical ecosystem threshold levels previously established for the Florida Keys as are phytoplankton levels for offshore reefs as evidenced by the presence of macroalgae and other harmful algal blooms due to excessive levels of nutrients.

Seawater Monitoring

Researchers gathered data from 1984 to 2014 and collected seawater samples during wet and dry seasons. Lapointe and collaborators from the University of Georgia and the University of South Florida also monitored the living coral and collected abundant species of seaweed (macroalgae) for tissue nutrient analysis.

They monitored seawater salinity, temperature and nutrient gradients between the Everglades and Looe Key. They wanted to better understand how nitrogen traveled from the Everglades downstream to the coral reefs of the Florida Keys National Marine Sanctuary, which now has the lowest amount of coral cover of any reefs in the wider Caribbean region.

bleached coral in Looe Key
As can be seen by this bleached coral in Looe Key in the lower Florida Keys in 1987, these coral reefs were dying off long before they were impacted by rising water temperatures.
Credit: Brian Lapointe, Ph.D., Florida Atlantic University’s Harbor Branch Oceanographic Institute

Data revealed that living coral cover at Looe Key Sanctuary Preservation Area declined from nearly 33 percent in 1984 to less than 6 percent in 2008. The annual rate of coral loss varied during the study, but increased from 1985 to 1987 and 1996 to 1999 following periods of heavy rainfall and increased water deliveries from the Everglades.

Between 1991 to 1995, significant increases in Everglades runoff and heavy rainfall resulted in increases of reactive nitrogen and phytoplankton levels at Looe Key above levels known to stress and cause die-off of coral reefs. Despite reduced Everglades flows, the water quality has not yet recovered to the levels of the 1980s.

Future Success Keys

Nitrogen loading to the coast is predicted to increase by 19 percent globally simply as a result of changes in rainfall due to climate change, which suggests the need for urgent management actions to prevent further degradation.

“The future success of the Comprehensive Everglades Restoration Plan will rely on recognizing the hydrological and nitrogen linkages between the Everglades, Florida Bay and the Florida Keys,” said Lapointe. “The good news is that we can do something about the nitrogen problem such as better sewage treatment, reducing fertilizer inputs, and increasing storage and treatment of stormwater on the Florida mainland.”

The impact of local land-based nitrogen contributions from sewage treatment plants that service 76,000 year-round residents and an estimated 3.8 million tourists annually is currently being mitigated by completion of centralized wastewater collection and advanced wastewater treatment plants and nutrient removal facilities throughout the Florida Keys.

According to the Florida Keys National Marine Sanctuary, ocean-related activities associated with coral reefs add more than $8.5 billion each year and 70,400 jobs to the local economy in southeast Florida.

“The Bonaire coral reefs in the Caribbean Netherlands is a great example of effective nitrogen pollution mitigation. These coral reefs are beginning to recover following the construction of a new sewage treatment plant in 2011, which has significantly reduced nitrogen loading from septic tanks,”

said Lapointe.

“Citing climate change as the exclusive cause of coral reef demise worldwide misses the critical point that water quality plays a role, too. While there is little that communities living near coral reefs can do to stop global warming, there is a lot they can do to reduce nitrogen runoff. Our study shows that the fight to preserve coral reefs requires local, not just global, action,”

said Porter.

Original Study: Nitrogen enrichment, altered stoichiometry, and coral reef decline at Looe Key, Florida Keys, USA: a 3-decade study

Cover Image: Larry Lipsky

Why Are So Many Farmed Salmon Partially Deaf?

Researchers have found out the reason that so many farm-raised salmon are partially deaf, pointing to a deformity in their ears caused by accelerated growth in aquaculture. The findings raise significant welfare issues and may also explain the poor survival of farmed hatchlings in conservation programs.

University of Melbourne scientists looked at salmon farmed in Norway, Chile, Scotland, Canada, and Australia and found the deformity was widespread.

The study’s lead author, Tormey Reimer, a master’s graduate from the School of BioSciences at the University of Melbourne, says when they went looking for the cause of the deformity they found that the fastest-growing fish were three times more likely to be afflicted than the slowest, even at the same age.

“We also found that we could reduce the incidence of the deformity by reducing how fast a fish grew. Such a clear result was unprecedented,”

says Reimer.

Deformed Otoliths

The deformity occurs in the otoliths, explains Reimer, which are tiny crystals in a fish’s inner ear that detect sound, much like the ear bones do in humans. So even a small change can cause massive hearing problems.

She says normal otoliths are made of the mineral aragonite but deformed otoliths are partly made of vaterite, which is lighter, larger, and less stable. The team showed that fish afflicted with vaterite could lose up to 50 percent of their hearing.

Otoliths have been used for decades to determine a wild fish’s age and life history, but since the age and life history of farmed fish is always known, there has never been a reason to examine them.

The deformation was first recorded in the 1960s, but in 2016 this team was the first to show it affects more than 95 percent of fully-grown hatchery-produced fish globally.

Study coauthor Tim Dempster says that the deformity is irreversible, and its effects only get worse with age.

“These results raise serious questions about the welfare of farmed fish. In many countries, farming practices must allow for the ‘Five Freedoms,’ which are freedom from hunger or thirst; freedom from discomfort; freedom from pain, injury, or disease; freedom to express (most) normal behavior; and freedom from fear and distress,”

says Dempster, an associate professor at the University of Melbourne.

The issue is that farmed salmon lead very different lives to wild salmon.

Genetics, Diet And Sunlight

Generations of selective breeding have created fish that are genetically distinct from their wild ancestors. The food pellets given to farmed fish are not the same as a wild diet, and since fish only eat and grow during the day, many farms expose their stock to bright lights 24 hours a day.

The team found that vaterite was seemingly caused by a combination of genetics, diet, and exposure to extended daylight. But there was one factor that linked them all: growth rate.

Dempster says that producing animals with deformities violates two of the freedoms: the freedom from disease and the freedom to express normal behavior.

“However, fish farms are noisy environments, so some hearing loss may reduce stress in hatcheries and sea cages. We simply don’t yet know what hearing loss means to production,” he says.

The deformity could also explain why some conservation methods aren’t very effective.

Between habitat destruction and overfishing, wild salmon are actually in decline in many areas. One strategy used to boost stocks is to release millions of farmed juveniles into spawning rivers.

Farmed juveniles are often larger than their wild peers at the same age, and would theoretically stand a better chance of surviving.

Vaterite Impacts

However, the actual survival rate of farmed juveniles is between ten and 20 times lower than that of wild salmon. In the wild, fish may use their hearing for finding prey and avoiding predators, and for a migrating species like salmon, hearing could help them navigate back to their home stream to breed.

Study coauthor Steve Swearer explains that the next step will be to determine if vaterite affects the survival rate of hatchery fish released into the wild.

“Stocking rivers with hearing-impaired fish may be throwing money and resources into the sea,” Swearer says.

Reimer says that since vaterite is irreversible once it’s begun, the key to control is prevention.

“Future research may find ways to prevent the deformity without compromising growth rate,”

she says.

Original Study: Rapid growth causes abnormal vaterite formation in farmed fish otoliths

Image: Zureks CC BY-SA 3.0

Ability To Rewrite Their Own RNA May Be Behind Octopus Intelligence

Octopuses are alien life among us. They are able to use tools, have three hearts, their arms contain 2/3 of the neurons in an octopuses body and almost have minds of their own, their blood is based on copper rather than iron, and is blue, and are thought to be the most intelligent invertebrates and an important example of advanced cognitive evolution in animals.

They also have a special way of using their genes.

Octopuses, along with other cephalopods such as squid and cuttlefish, often do not follow the genetic instructions in their DNA exactly. They use enzymes to pick out specific adenosine RNA bases (some of As, out of the As, Ts, Gs, and Us of RNA) that code for proteins and replace them with a different base, called Inosine.

This process — called “RNA editing” — is rarely used to recode proteins in most animals, but octopuses and their relatives edit RNA base pairs in over half of their transcribed genes.

When researchers did experiments to quantify and characterize the extent of this RNA editing across cephalopod species, they found evidence that this genetic strategy has profoundly constrained evolution of the cephalopod genome.

Previous research has found that octopuses use RNA editing to rapidly adapt to temperature changes and that the majority of RNA transcripts in squid neurons contain these edits. In this new study, researchers wanted to find out how commonplace these edits are, how they evolved along the cephalopod lineage, and how such extraordinary editing capabilities affect the evolution of the cephalopod genome.

RNA Editing The Rule

Vertebrate cells are capable of RNA editing. But evidence of amino acid re-coding has only been found to a very limited extent in the few species investigated so far.

Humans have 20,000 genes but only a few dozen conserved RNA editing sites that are likely encoding functional proteins.

Squids also have about 20,000 genes but have at least 11,000 active RNA editing sites affecting the proteome, many of which are conserved, according to this study’s estimates. Co-author Eli Eisenberg, a biophysicist at Tel Aviv University, said:

“Basically, this is a mechanism to make proteins that are not encoded in the DNA. They are not present in the genomic sequence. With these cephalopods, this is not the exception. This is the rule. The rule is that most of the proteins are being edited.”

In fact, RNA editing is so rare that it’s not considered part of genetics’ “Central Dogma.” Co-author Joshua Rosenthal, a cephalopod neurobiologist at the Marine Biological Laboratory in Woods Hole, explains:

“Ever since Watson and Crick figured out that genetic information is stored in DNA, we’ve had this view that all the information is stored in DNA, and it’s faithfully copied to another molecule when it’s used—that’s RNA, and from there, it’s translated into the proteins that do all the work. “And it’s generally assumed that that’s a pretty faithful process. What the squid RNA is showing is that that’s not always the case—that, in fact, organisms have developed a potent means to manipulate information in RNA.”

Slower Evolution

Most organisms extensively use splicing, the process of cutting or adding whole sections of RNA transcripts before they leave the nucleus, to diversify their proteomes, but prioritize DNA flexibility over RNA editing.

“We usually think of evolution using whatever it can to answer some challenges—so why was RNA recoding not used?” says Eisenberg. “Now, we have an example of what happens when we do use RNA editing abundantly. We know there’s a price. The price is slowing down genome evolution…Cephalopods probably chose to take this RNA bargain over genome evolution, and maybe vertebrates made the other choice—they preferred genome evolution over editing.”

Since many of the most heavily edited RNAs coded for key neural proteins, the researchers wonder whether RNA editing might contribute to the remarkable intelligence of octopuses and their kin.

Octopus bimaculoides
Octopus bimaculoides (California two-spot octopus) showing its namesake blue spot. This is the only cepalopod species that has been sequenced (in 2015). Credit: Tom Kleindinst

Not only are they smart enough to hunt, octopuses are clever enough to escape from jars, use coconut husks to hide themselves, signal to others by changing their skin color, and learn through observation.

“They’re the only taxon out there that approaches vertebrates in terms of behavioral complexity,” says Rosenthal. “These behaviorally complex coeloids all have this tremendous RNA editing, particularly in their nervous system, where they’re recoding the messenger RNAs that encode for the very things that are important for electrical excitability.”

Researchers are working on an octopus animal model to find out whether RNA editing plays a pivotal role in cephalopod behavior. Experiments that deal with the role of RNA editing in behavior will require an octopus that grows well in laboratories and can be genetically manipulated.

Study: Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods

Top Image: Matthias Kabel, CC BY 2.5

Temperate Broadleaf Forests More Susceptible To Heat Stress

Temperate broadleaf forests, such as the stands of red oak common in New England, absorb more carbon than expected along their edges, but are more susceptible to heat stress.

Over centuries, as humans have cleared fields for farms, built roads and highways, and expanded cities, we’ve been cutting down trees. Since 1850, we’ve reduced global forest cover by one-third.

We’ve also changed the way forests look.

Much of the world’s woodlands now exist in choppy fragments, with 20 percent of the remaining forest within 100 meters of an edge, like a road, backyard, cornfield, or parking lot.

Good News

Scientists have studied fragmented forests for decades, mostly to gauge their effects on wildlife and biodiversity. But recently, two Boston University scientists, Andrew Reinmann, a postdoctoral research associate, and Lucy Hutyra, an associate professor of earth and environment, have turned their attention to another issue: the effects of forest fragments on carbon storage and climate change.

Lucy Hutyra and Andrew Reinmann
Lucy Hutyra and Andrew Reinmann. Photo by Cydney Scott

The research offers some good news and bad news about forest fragmentation. It suggests that while these forests may be more valuable carbon sinks than previously thought, they are also more sensitive to climate change.

“Having accurate estimates of what those trees on the edge are doing—how much carbon they’re taking out of the atmosphere—is really important when we think about our future climate,”

says Reinmann, lead author of the paper.

The annual atmospheric concentration of carbon dioxide, a potent greenhouse gas and agent of global warming, has increased by more than 40 percent since the start of the Industrial Revolution and continues to rise. Forests play a critical role as a carbon sink, absorbing about 25 percent of the CO2 emissions we humans put into the sky.

Forest Fragments

Most of our understanding of forest carbon dynamics comes from studying intact rural forests like Hubbard Brook in New Hampshire’s White Mountains and Harvard Forest in Petersham, Massachusetts, not from studying forest fragments.

“When you fragment a forest, you change a lot of the growing conditions of the forest that’s left behind,” says Reinmann, “but we don’t have a very good understanding of how that change affects carbon sequestration and storage.”

To find out, Reinmann and Hutyra gathered data from 21 fragmented forest plots around Boston, measuring about 500 trees. In eight of those plots, they went a step further, taking sample cores from trees above 10 centimeters in diameter, a total of 420 cores from 210 trees.

tree core
Photo by Cydney Scott

They used the cores, and other data, to calculate how fast the trees grew. A tree’s size and growth rate indicate how much carbon it can absorb and also how much stress it’s experiencing.

“If this carbon sink all of a sudden shuts off, our projections for future climate will change,” says Reinmann. “So our current understanding and ecological models, which don’t account for this, are missing something important.”

Reinmann and Hutyra found that forest fragments grow faster along the edges than intact forests, absorbing more carbon than expected.

“When you create that edge, you essentially are reducing competition and freeing up resources like light, water, and nutrients for trees,”

says Reinmann, who notes that the effect extends in about 20 meters from the forest edge.

Temperate Broadleaf Forests

Curiously, the finding may hold only for temperate broadleaf forests common in New England, the Appalachians, Canada, and Europe. Amazon rainforest has the opposite effect when fragmented, with lower biomass and less carbon storage along the edges.

“Foresters and loggers have known this intuitively for a long time: if you go in and you reduce the competition for resources, the remaining individuals will grow faster,” adds Hutyra. “The novel piece of this work was to quantify it across these edges, see how far into the forest it goes, and put it into context with how much this fragmentation matters in a portion of the world—southern New England—that we know is a large net carbon sink.”

Though this seems like a win for patchy New England forests, deforestation is still bad for carbon sequestration overall.

“When you fragment a forest, the remaining forest can offset a little bit of what was lost, but not completely,” says Reinmann. “So it may not be as terrible from a carbon perspective as we thought, but it’s still bad.”

Bad News

Offsetting this somewhat good news is the paper’s other finding.

These forest edges, more exposed to wind and sun, grow more slowly when stressed by heat.

“You lose a lot of carbon benefit in hot years. But once you get much past that threshold, the trees grow much slower,”

says Reinmann, who found that the “magic number” for local trees is about 27° C (80.6° F), which corresponds to the average high temperature in July, our hottest month.

And the really bad news: if regional temperatures continue to increase at a steady pace, the current carbon benefit offered by forest edges may decline significantly.

“If this carbon sink all of a sudden shuts off, our projections for future climate will change,” says Reinmann. “So our current understanding and ecological models, which don’t account for this, are missing something important.”

Reinmann and Hutyra are currently expanding the work to study rural forests and are so far finding even larger effects there. They are also hoping to use high-resolution imaging and more precise chemical analyses to look closer at core samples to see how growth and photosynthesis change over days, seasons, heat waves, and other environmental stressors.

More data may lead to better models, says Hutyra.

The work was funded by the National Oceanic and Atmospheric Administration, the National Aeronautics and Space Administration, and the National Science Foundation.

Original Study: Edge effects enhance carbon uptake and its vulnerability to climate change in temperate broadleaf forests


90% Of Illegal Ivory Comes From Recently Killed Elephants

Over 90 percent of ivory in large, seized shipments is from elephants that died less than three years before, research shows.

Scientists arrived at the conclusion by mixing a new approach to radiocarbon dating for ivory samples with genetic analysis tools that gave conservationists a picture of when and where poachers are killing elephants.

Lesley Chesson, coauthor of the new study and CEO of Isoforensics, said:

“This work provides for the first time actionable intelligence on how long it’s taking illegal ivory to reach the marketplace. The answer is not long at all, which suggests there are very well-developed and large networks for moving ivory across Africa and out of the continent.”

Lead author Thure Cerling, professor of geology and geophysics at the University of Utah, added:

“Apart from the actual killing, there’s the trade on the ground before it gets to ports, the actual shipments through shipping containers, and then the problem of the demand side. This additional information can be helpful to people trying to address those issues.”

International Ban

In June 2016, the United States banned nearly all commerce in elephant ivory, which came 26 years after a ban on international trade in ivory. Both measures aimed to curtail the widespread poaching of elephants, whose numbers have plummeted since the 1980s.

Poaching still kills an estimated 8 percent of African elephants each year, or around 96 elephants per day. Demand for elephant ivory and other illegal products derived from endangered animals has grown in Asia in recent years, opening a fresh battleground in the struggle against illegal ivory, even as US markets shut down.

ivory seizure
An ivory seizure, 6.5 metric tons, in Singapore in 2002.Benezeth Mutayoba/Sokoine University of Agriculture

Bans typically allow the sale of ivory that was legally acquired prior to 1976, including heirloom or antique pieces. Confirming the age of those pieces, however, relies on proper documentation.

Traders in illegal ivory sometimes use this clause as a cover, claiming that their wares are older than they really are.

Researchers applied radiocarbon dating, a technique from forensic science, to estimate the age of samples in seized ivory shipments, with some adjustments for a Cold War legacy.

Above-ground nuclear weapons testing through the 1960s doubled the concentration of radioactive carbon-14 in the atmosphere. This heightened carbon-14 signature was preserved in plants, which take up atmospheric carbon, and transferred to herbivores like elephants.

Carbon-14 levels have been declining since the 1960s, and scientists can use the carbon-14 signature in a bone, tusk, or tooth to determine, within about a year, when the material was formed. And since elephants grow new material at the base of their tusks, the ivory there contains the carbon-14 signature of the plants the elephant has recently eaten.

Forensic scientists have used this “bomb carbon” signature to estimate the ages of human remains in cold cases and track the transit time of cocaine shipments. Now researchers have applied the method to seized ivory.

Lag Times

Coauthor Sam Wasser, professor of biology at the University of Washington, led efforts to gather ivory samples from large stockpiles seized by law enforcement officials between 2002 and 2014.

Of 231 samples collected, only one returned was greater than six years between the time of the elephant’s death and the seizure of the ivory — known as the lag time.

Nearly all of the analyzed ivory had a lag time of around two to three years, suggesting that the shipments did not come from stockpiles or from old sources. Instead, large shipments of ivory are likely composed of recently poached pieces.

Combining Cerling’s radiocarbon data with Wasser’s genetic analysis to determine the geographic origin of the ivory, the researchers constructed a picture of which regions have established rapid pipelines to get poached ivory to market.

In the study, seized ivory is classified as either originating in East Africa, the Tridom region of west-central Africa, West Africa, or Zambia. Additionally, samples were classified as having a rapid lag time of less than 12 months, intermediate lag time of 12 to 24 months or a slow lag time of greater than 24 months.

Ivory attributed to East Africa had a higher proportion of rapid-transit samples than the other regions, suggesting a strong distribution pipeline from the region. Ivory from Tridom was more likely to contain slow-transit ivory, and both West African and Zambian ivory exhibited intermediate lag times. The information can help law enforcement focus on the worst poaching regions and also provide information on the health of elephant populations.

“If all of the seizures are really recent, within the past two to three years, we can use that to determine the overall killing rate of elephants in Africa,” Cerling says.

Coauthors are from Save the Elephants, Oxford University, Columbia University, and the University of California, Irvine. The work received funding from the Paul G. Allen Family Foundation and Save the Elephants.

Original Study

Image: An ivory seizure made in Malaysia in 2012, weighing 6 metric tons. Syarifah Khadiejah Syed Mohd Kamil/Malaysia Department of Wildlife and National Parks