Tuesday, September 01, 2020

Warmer, acidifying ocean brings extinction for reef-building corals, renewal for relatives

Changes in ocean chemistry and temperature have had a dramatic effect on the diversity of corals and sea anemones, according to a team of scientists who have traced their evolution through deep time. A new study, published Aug. 31 in the journal Nature Ecology and Evolution, finds that reef-building corals emerged only when ocean conditions supported the construction of these creatures' stony skeletons, whereas diverse softer corals and sea anemones flourished at other times. Without a significant change to anthropogenic carbon emissions, the new findings present stark implications for the present and future of hard-bodied corals while suggesting a silver lining for the diversity of some of their softer-bodied relatives.

New genetic analyses show that corals, which together with sea anemones make up a class of animals known as anthozoans, have been on the planet for 770 million years. That is 250 million years before the earliest undisputed fossil evidence of their existence—and long enough to experience massive shifts in climate, fluctuations in ocean chemistry and several mass extinctions.

In the new study, a research team led by scientists from Harvey Mudd College, the American Museum of Natural History and the Smithsonian's National Museum of Natural History examined how these past conditions affected anthozoan diversity. That was possible thanks to a new molecular approach developed by Andrea Quattrini, research zoologist and curator of corals at the National Museum of Natural History, Catherine McFadden, a biologist at Harvey Mudd College, and Estefanía Rodríguez, a curator at the American Museum of Natural History, which allowed the team to compare nearly 2,000 key regions of anthozoan genomes to discern the evolutionary relationships between species. The team analyzed hundreds of anthozoan specimens that were collected from around the world and are now stored in museum collections. When this molecular data was aligned with fossil evidence of anthozoan history, it revealed how these diverse animals evolved over geologic time.

Over the Earth's history, changes in acidity and ion concentrations have shifted the ocean's chemical composition between two states, known as aragonite and calcite seas. These changes, as well as changes in ocean water temperature, appear to have played an important role in determining what kinds of skeletons corals were able to produce and, thus, how anthozoans evolved.

Stony corals—the type that build massive reefs that support complex marine ecosystems—take up minerals from the water to construct hard skeletons from a form of calcium carbonate known as aragonite. Other corals, such as sea fans and black corals, build their softer skeletons from protein or calcite (a less soluble form of calcium carbonate), whereas sea anemones have no skeleton at all.

Working with an international team of researchers, including Gabriela Farfan, the National Museum of Natural History's Coralyn W. Whitney Curator of Gems and Minerals, Quattrini and colleagues found that stony corals did not arise until conditions favored the construction of their aragonite skeletons—periods of aragonite seas, when ocean temperatures were relatively cool. During periods of calcite seas, when carbon dioxide is more abundant in the atmosphere and oceans are more acidic, evolution favored anemones and corals that built their skeletons from protein or calcite.

Notably, it was these other anthozoans that fared best after reef crises—times when up to 90% of reef-building organisms died off as oceans warmed and became more acidic. "Our study showed that after these reef crises, we actually get an increased diversification of anthozoans in general, particularly those that can do well under these climate conditions—ones that aren't producing aragonite and aren't making big reefs," Quattrini said.

That is consistent with observations from today's reefs, which are threatened by climate change and other human activities. "Current ecological studies have shown that when stony corals die off, these other anthozoans start to colonize dead coral and prosper," Quattrini said. "We actually see that in our evolutionary tree, too."

"Unfortunately, although these softer-bodied species may adapt better to climate change than stony corals, they don't form large reefs," McFadden said. "So, in the future, reefs may be replaced by different marine communities. This already appears to be happening in the Caribbean where stony corals are being replaced by 'forests' of sea fans."

Today, about 1,300 species of stony coral inhabit the ocean, favored by aragonite sea conditions. But rising levels of carbon dioxide in the atmosphere are warming and acidifying the waters, making them less hospitable for these and other organisms whose shells and skeletons are made from aragonite. "Aragonite is expected to dissolve under ocean acidification," Quattrini said. "As our seas are becoming more acidic and warmer, it's likely that the skeletons of corals will dissolve or not be able to grow."

The new study suggests that as the climate changes, these ecosystems may also see increased diversification of anthozoans without aragonite skeletons. Nevertheless, loss of reef-building corals will have devastating consequences for communities who depend on reefs and the rich, complex ecosystems they support for fishing, shoreline protection and tourism. "Corals have suffered extinctions in the past when climate has posed challenges, and we'll likely see that in the future," Quattrini said. "The best way to protect them is to curb our carbon emissions."

"This study shows us how nature through evolution is able to adapt, survive and reinvent itself, so when hard corals are not able to survive, their soft-bodied relatives such as sea anemones will thrive instead," Rodríguez said. "The question is whether we will be able to adapt and reinvent ourselves once nature, as we currently know it, is not there anymore."

Explore further

Ocean acidification causing coral 'osteoporosis' on iconic reefs

More information: Palaeoclimate ocean conditions shaped the evolution of corals and their skeletons through deep time, Nature Ecology and Evolution (2020). DOI: 10.1038/s41559-020-01291-1 , www.nature.com/articles/s41559-020-01291-1

Journal information: Nature Ecology & Evolution

Provided by Smithsonian

How power shaped the 'success story' of genetically modified cotton in Burkina Faso

by Jessie Luna, Brian Dowd-Uribe, The Conversation FARMING

Credit: Pixabay/CC0 Public Domain

The West African nation of Burkina Faso was once the poster child for genetically modified (GM) crop advocates. Its 2008 adoption of GM cotton for smallholder farmers was hailed as an example of how these technologies could alleviate poverty and food insecurity by protecting crops from pests and increasing yields.

But this much celebrated success story came to an abrupt halt in 2016, when the Burkina Faso government and cotton companies decided to abandon GM cotton.

What happened?

Burkina Faso was the first African country where a GM crop was principally grown by smallholder farmers. The crop was an insect resistant cotton variety, developed through a partnership with the US-based agri-business company Monsanto (now Bayer Crop Science). At its height, nearly 150,000 Burkinabè households grew GM cotton.

Supporters quickly broadcast study findings demonstrating increased average yields and incomes. This developed into a prominent narrative of success.

Observers were shocked when only eight years later Burkina Faso abandoned genetically modified cotton. The reason: it had shorter-fiber lint and ginning machines extracted proportionally less lint from harvested cotton bolls. This led to US$76 million in losses for cotton companies.

Other problems also surfaced. New evidence showed that GM cotton yields were less than half of early projections. And there were significant variations among farmers. Many farmers lost money.

How could such a prominent success story turn so quickly to failure?

Our new research, which draws on over 250 interviews and in-depth research in Burkina Faso spanning over a decade, traces what happened. We found that rather than an abrupt turnaround, these problems were known by cotton sector officials as early as 2006—ten years before Burkina Faso abandoned GM cotton.

The puzzle we unravel is how a success narrative could be built when problems were readily apparent.

In short, the story has a lot to do with power.

Silences and omissions

Burkina Faso's cotton success narrative was built on a series of studies with significant methodological problems. Studies contained well-documented issues in data collection, failing to sufficiently control for differences between comparison groups. In most cases, they also failed to provide sufficient evidence to evaluate how data were collected.

These faulty evaluation studies reported yield and income results in averages, which advocates quickly circulated as evidence of success. These same studies often showed large variability in yields and profits for farmers, but didn't highlight these findings.

Significant conflicts of interest shaped the collection and reporting of findings. Monsanto provided funding for the evaluation studies in a contract with the Burkina Faso Institute for Environment and Agricultural Research. This meant that Monsanto had ultimate control over research findings—and a strong interest in projecting success.

The institute depended on Monsanto funding that accompanied the adoption of GM cotton. Highly skilled Burkinabè researchers also jockeyed for limited jobs with Monsanto.

In our interviews, which included Monsanto representatives, participants said it was difficult to challenge the success narrative. Concerns they raised were often silenced or left unexamined. At times, their expertise was dismissed.

Ignoring local dynamics

Evaluation studies had additional problems, particularly with regard to the differential impacts of GM cotton. Previous research in Burkina Faso has detailed how local dynamics can determine the extent to which a farmer profits from cotton production. These dynamics weren't included in the evaluation studies that built the success narrative.

Our research, which paid close attention to local-level dynamics, revealed that these missing pieces were critical factors shaping farmers' experiences with GM cotton.

Poorer farmers faced additional challenges: they used less fertilizer, which compounded yield issues in GM cotton, and they were often burdened by having to pay for replacement seeds in cases when their first planting didn't germinate. This additional seed cost resulted from complex relationships between farmers and cotton company employees who often belittled small-scale farmers. These dynamics and additional costs were invisible to overly narrow evaluation studies.

As a result, the success narrative gave a false impression that even farmers with few resources were achieving "average" yield gains.

Profiting from an exaggerated success narrative

The power to shape a narrative—based on faulty studies that overlooked important realities—turned out to be good for Monsanto's bottom line. The final royalty contract signed by Monsanto and Burkinabè partners ostensibly gave 28% of the "added value" of GM cotton to Monsanto, and the rest for farmers and cotton companies. But Monsanto received far more than this.

The royalty contract used an inflated yield estimate (30%) to establish the amount of added value from GM cotton. Even in the best years, actual cotton yields didn't approach this estimate.

Monsanto also received this inflated payment irrespective of the actual performance of the technology, since it was paid according to the number of hectares planted. Monsanto profited more than was agreed to in the contract, and assumed none of the risk shouldered by cotton companies and farmers.

Monsanto also benefited from a reliable GM crop success story. This narrative is still used to advance other ventures in Africa.

Looking ahead

Anthropologist Glenn Stone has argued:

"We are naïve in swallowing empirical claims without a careful consideration of how vested interests affect the creation of facts."

As this case shows, vested interests played a significant role in shaping a success narrative despite apparent problems.

Moving forward, it will be important to learn from the Burkinabè case, not just about what happened, but about how knowledge was produced. An examination of vested interests is one such take away. This is particularly important now as multiple African nations consider a wide array of GM crops for commercialisation.

Many GM crops under consideration in Africa are not the domain of a big agri-business company like Monsanto. This does not mean, however, that vested interests will not still shape how knowledge about these crops gets produced.

Evaluation studies will need to be independent, transparent, rigorous, and methodologically diverse, to accurately reflect the realities of these crops. Studies must anticipate challenges and shortcomings. This is particularly true to understand whether and how genetically modified crops aid resource-poor, women, and marginalized farmers.

For too long agricultural technologies like GM crops have been evaluated as if they exist in a social and political vacuum. Understanding how GM crops perform for farmers needs close attention to local-level dynamics and context. The role that power plays in that context must be a part of how we understand GM crops moving forward

Top African producer bans GM cotton

Provided by The Conversation

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Why Kenya's urban poor are exploited by informal water markets

by Anindita Sarkar, The Conversation

LIKE THE POOR IN FLINT, MICHIGAN

Informal urban water markets—as opposed to piped water—have long supported many of Kenya's urban areas. Those that use them are either unserved, or inadequately served, by public utilities.

A large number of people depend on them as only about 20% of the Nairobi residents who live in low income areas have piped water. The rest depend on uncovered wells, rivers, open springs and informal water markets.

There are different types of informal water markets. Some sell water legally, some illegally. There are also different ways in which people buy water. If they have water storage facilities, and live in an area accessible to water vendors, water can be bought in bulk from vendors who source it from private boreholes.

But most people won't have storage facilities and will usually buy water from water vendors and carry it home. These water vendors get their supplies from a variety of sources including; rivers, wells, households with connections, communal standpipes and water ATMs. Water ATMs, installed by NGOs, provide users with cheap, clean water on demand. They swipe a smart-card and collect.

Water vendors also sometimes get water illegally by cutting through municipal piped networks.

In a recent study I looked at how informal water markets operate and how they serve the urban poor. My research focused on Mathare, a large informal settlement in Nairobi. About 206,000 people live there.

I found that—despite high water prices (in comparison to water sold in standpipes and water ATMs), poor quality and inconvenience—the urban poor continued to buy water from private vendors because it's still their best option. The other options were either too unreliable or hard to reach.

Nairobi's county government is taking steps to formalize informal water vendors as a way of providing more people with water. Though urban informal water markets have the potential to deliver water to the unserved poor, they can also trap the poor in highly unjust water delivery arrangements. More must be done to prevent this from happening.

Last, better option

Mathare is characterized by unsafe and overcrowded housing. Most people live in shacks made of corrugated iron and lack access to essential services, such as sanitation and electricity. Around 90% of residents do not have piped water.

I conducted interviews, surveys and focus group discussions with 258 households and 20 water vendors in Mathare in 2016 and 2017. I also interviewed six key government officials.

More than half of the residents from my survey accessed water from informal water vendors. And about 36% households depended exclusively on them.

But the quality of water was inconsistent. Residents I interviewed said they sometimes found debris in the water, or that it sometimes tasted bad. This could be because when vendors illegally cut municipality pipes, the water becomes contaminated.

High prices

The water vendors' prices also fluctuated. They ranged from Ksh2 (US$0.02) to Ksh50 (US$0.50) per 20 liters depending on where the clients lived and the availability of alternative sources of water. During periods of drought, when their water supplies might run dry, vendors would recoup costs by driving up prices.

In some cases, high prices were artificially created. Water vendors sometimes cut municipal pipes to create artificial shortages or colluded with cartels who controlled community yard taps.

The vendors also had erratic schedules. People would sometimes be late for work or miss work and forgo their daily wages to buy water.

While some clients reported having strong bonds with their vendors, the majority said they were rude and inconsiderate.

Differential treatment among different clients belonging to a particular tribe or of a particular economic status was another major bone of contention. Nevertheless, the customers were fearful about questioning the vendors.

Last option

There were several reasons why, despite these issues, people opted to use water vendors.

Water ATMs, though cheapest (about US$0.50 for 20 liters of water), were very few in number and located around the main road of the slum. It's very difficult to carry heavy water over the undulating slum terrain. The ATM tanks were also often empty, making them an unpredictable and unreliable supply source. As for the standpipes, they operated only twice or three times a week but with no fixed timing or price.

And, even if in-house municipality connections are available, many poor households cannot afford the initial set-up cost. A new connection fee can vary between Ksh2500 (about US$25) and Ksh15000 (about US$150). The average household income in Mathare is less than US$3 a day.

Water vendors are a last option but residents depend on them. They're more easily accessible and give people more control over their daily costs. For instance, people may use Mathare river to wash clothes or flush toilets, and buy water just for drinking and cooking.

Policy implications

The main reason for the growth of the informal water market is government failure to deliver adequate public services. To address the deficit, private vendors are gradually being regulated. Kenyan municipalities have asked authorized private water providers to make supply arrangements in informal settlements a compulsory prerequisite for license renewals.

But more must be done to prevent corruption and the creation of cartels.Vendors must also develop their strength through association and business training to help them lobby and defend their rights. Creating a union will also create rules for water transactions and prices.

Finally, when providing licenses, the government should demarcate the areas where vendors operate to reduce conflict between vendors. This will also make it easier for utility officers to monitor their prices and modes of water transactions.

Researchers find what makes 'black market' water vendors work more reliably and fairlyProvided by The Conversation

Discovery of an ancient dog species may teach us about human vocalization

by NIH/National Human Genome Research Institute

In a study published in PNAS, researchers used conservation biology and genomics to discover that the New Guinea singing dog, thought to be extinct for 50 years, still thrives. Scientists found that the ancestral dog population still stealthily wanders in the Highlands of New Guinea. This finding opens new doors for protecting a remarkable creature that can teach biologists about human vocal learning. The New Guinea singing dog can also be utilized as a valuable and unique animal model for studying how human vocal disorders arise and finding potential treatment opportunities. The study was performed by researchers at the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, Cenderawasih University in Indonesia, and other academic centers.

The New Guinea singing dog was first studied in 1897, and became known for their unique and characteristic vocalization, able to make pleasing and harmonic sounds with tonal quality. Only 200-300 captive New Guinea singing dogs exist in conservation centers, with none seen in the wild since the 1970s.

"The New Guinea singing dog that we know of today is a breed that was basically created by people," said Elaine Ostrander, Ph.D., NIH Distinguished Investigator and senior author of the paper. "Eight were brought to the United States from the Highlands of New Guinea and bred with each other to create this group."

According to Dr. Ostrander, a large amount of inbreeding within captive New Guinea singing dogs changed their genomic makeup by reducing the variation in the group's DNA. Such inbreeding is why the captive New Guinea singing dogs have most likely lost a large number of genomic variants that existed in their wild counterparts. This lack of genomic variation threatens the survival of captive New Guinea singing dogs. Their origins, until recently, had remained a mystery.

Another New Guinea dog breed found in the wild, called the Highland Wild Dog, has a strikingly similar physical appearance to the New Guinea singing dogs. Considered to be the rarest and most ancient dog-like animal in existence, Highland Wild Dogs are even older than the New Guinea singing dogs.

Researchers previously hypothesized that the Highland Wild Dog might be the predecessor to captive New Guinea singing dogs, but the reclusive nature of the Highland Wild Dog and lack of genomic information made it difficult to test the theory.

In 2016, in collaboration with the University of Papua, the New Guinea Highland Wild Dog Foundation led an expedition to Puncak Jaya, a mountain summit in Papua, Indonesia. They reported 15 Highland Wild Dogs near the Grasberg Mine, the largest gold mine in the world.

A follow-up field study in 2018 allowed researchers to collect blood samples from three Highland Wild Dogs in their natural environment as well as demographic, physiological and behavioral data.

NHGRI staff scientist Heidi Parker, Ph.D., led the genomic analyses, comparing the DNA from captive New Guinea singing dogs and Highland Wild Dogs.

"We found that New Guinea singing dogs and the Highland Wild Dogs have very similar genome sequences, much closer to each other than to any other canid known. In the tree of life, this makes them much more related to each other than modern breeds such as German shepherd or bassett hound," Dr. Parker said.

According to the researchers, the New Guinea singing dogs and the Highland Wild Dogs do not have identical genomes because of their physical separation for several decades and due to the inbreeding among captive New Guinea singing dogs—not because they are different breeds.

In fact, the researchers suggest that the vast genomic similarities between the New Guinea singing dogs and the Highland Wild Dogs indicate that Highland Wild Dogs are the wild and original New Guinea singing dog population. Hence, despite different names, they are, in essence, the same breed, proving that the original New Guinea singing dog population are not extinct in the wild.

The researchers believe that because the Highland Wild Dogs contain genome sequences that were lost in the captive New Guinea singing dogs, breeding some of the Highland Wild Dogs with the New Guinea singing dogs in conservation centers will help generate a true New Guinea singing dogs population. In doing so, conservation biologists may be able to help preserve the original breed by expanding the numbers of New Guinea singing dogs.

"This kind of work is only possible because of NHGRI's commitment to promoting comparative genomics, which allows researchers to compare the genome sequences of the Highland Wild Dog to that of a dozen other canid species," Dr. Ostrander said.

Although New Guinea singing dogs and Highland Wild Dogs are a part of the dog species Canis lupus familiaris, researchers found that each contain genomic variants across their genomes that do not exist in other dogs that we know today.

"By getting to know these ancient, proto-dogs more, we will learn new facts about modern dog breeds and the history of dog domestication," Dr. Ostrander said. "After all, so much of what we learn about dogs reflects back on humans."

The researchers also aim to study New Guinea singing dogs in greater detail to learn more about the genomics underlying vocalization (a field that, to date, heavily relies on birdsong data). Since humans are biologically closer to dogs than birds, researchers hope to study New Guinea singing dogs to gain a more accurate insight into how vocalization and its deficits occur, and the genomic underpinnings that could lead to future treatments for human patien

They were once domestic pets, then natural selection made dingoes wild

More information: Suriani Surbakti el al., "New Guinea highland wild dogs are the original New Guinea singing dogs," PNAS (2020). www.pnas.org/cgi/doi/10.1073/pnas.2007242117

Journal information: Proceedings of the National Academy of Sciences

Provided by NIH/National Human Genome Research Institute

Newly hatched Florida sea turtles are consuming dangerous quantities of floating plastic

by David Duffy and Catherine Eastman, The Conversation

Plastic pollution has been found in practically every environment on the planet, with especially severe effects on ocean life. Plastic waste harms marine life in many ways—most notably, when animals become entangled in it or consume it.

We work as scientists and rehabilitators at The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital at the University of Florida. Our main focus is on sea turtle diseases that pose conservation threats, such as fibropapillomatosis tumor disease.

However, it's becoming increasingly hard to ignore evidence that plastic pollution poses a growing, hidden threat to the health of endangered sea turtles, particularly our youngest patients. In a newly published study, we describe how we examined 42 post-hatchling loggerhead sea turtles that stranded on beaches in Northeast Florida. We found that almost all of them had ingested plastic in large quantities.

An ocean of plastic

Ocean plastic pollution originates mostly from land-based sources, such as landfills and manufacturing plants. One recent study estimates that winds carry 200,000 tons of tiny plastic particles from degraded tires alone into the oceans every year.

Plastics are extremely durable, even in salt water. Materials that were made in the 1950s, when plastic mass production began, are still persisting and accumulating in the oceans. Eventually these objects disintegrate into smaller fragments, but they may not break down into their chemical components for centuries.

Overall, some 11 million tons of plastic enter the ocean each year. This amount is projected to grow to 29 million tons by 2040.

A microplastic diet

Many forms of plastic threaten marine life. Sea turtles commonly mistake floating bags and balloons for their jellyfish prey. Social media channels are replete with videos and images of sea turtles with plastic straws stuck in their nostrils, killed in plastic-induced mass mortality events, or dying after ingesting hundreds of plastic fragments.

So far, however, scientists don't know a lot about the prevalence and health effects of plastic ingestion in vulnerable young sea turtles. In our study, we sought to measure how much plastic was ingested by post-hatchling washback sea turtles admitted to our rehabilitation hospital.

Post-hatchling washbacks are recently hatched baby turtles that successfully travel from their nesting beaches out to the open ocean and start to feed, but are then washed back to shore due to strong winds or ill health. This is a crucial life stage: Turtles need to feed to recover from their frenzied swim to feeding grounds hundreds of miles offshore. Feeding well also helps them grow large enough to avoid most predators.

We examined 42 dead washbacks, and found that 39 of them, or 93%, had ingested plastic—often in startling quantities. A majority of it was hard fragments, most commonly colored white.

One turtle that weighed 48 grams or 1.6 ounces – roughly equivalent to 16 pennies – had ingested 287 plastic pieces. Another hatchling that weighed just 27 grams, or less than one ounce, had ingested 119 separate pieces of plastic that totaled 1.23% of its body weight. The smallest turtle in our study, with a shell just 4.6 centimeters (1.8 inches) long, had ingested a piece of plastic one-fourth the length of its shell.

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Consuming such large quantities of plastic increases the likelihood that broken-down plastic nanoparticles or chemicals that leach from them will enter turtles' bloodstreams, with unknown health effects. Ingested plastic can also block turtles' stomachs or intestines. At a minimum, it limits the amount of space that's physically available for consuming and digesting genuine prey that they need to survive and grow.

Turtles at this life stage live at the ocean's surface, sheltering in floating mats of seaweed, where they feed on invertebrate prey such as zooplankton. These floating seaweed mats gather in the Atlantic, in an area known as the Sargasso Sea,which is bounded by four major ocean currents and covers much of the central Atlantic Ocean. The area is heavily polluted with plastic, as both seaweed and plastic travel on and are concentrated by the same ocean currents. Our study suggests that these baby turtles are mistakenly feeding on plastic floating in and around the seaweed.

Post-hatchling sea turtles are young and need to feed and grow rapidly. This means they are particularly at risk from the harmful consequences of ingesting plastic. We find it especially troubling that almost all of the animals we assessed had ingested plastic in such large quantities. Plastic pollution is only one of many human-related threats that these charismatic and endangered creatures face at sea.

Stemming the plastic tsunami

Since plastic persists for hundreds of years in the environment, clearing it from the oceans will require ingenious cleanup technologies, as well as lower-tech beach and shore cleanups. But in our view, the top priority should be curbing the rampant flow of plastic that is swamping oceans and coasts.

Earth's ecosystems, especially the oceans, are interconnected, so reducing plastic waste will require global solutions. They include improving methods for recycling plastics; developing bio-based plastics; banning single-use plastic items in favor of more sustainable or reusable alternatives; and reducing shipment of plastic waste abroad to countries with lax regulatory regimes, from where it is more likely to enter the environment.

Our observations in post-hatchling turtles are part of a growing body of research showing how plastic pollution is harming wildlife. We believe it is time for humanity to face up to its addiction to plastic, before we find ourselves wading through swathes of plastic debris and wondering what went wrong.

160 turtles caught in plastic waste rescued from Bangladesh beach

Provided by The Conversation

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Researchers develop new chip design for analyzing plant-microbe interactions

by Joan Koka, Argonne National Laboratory

Plants interact with certain microbes, such as bacteria and fungi, in mutually beneficial ways that scientists are only beginning to fully understand. Researchers at the U.S. Department of Energy's (DOE) Argonne National Laboratory have discovered a way to gain new insights about these interactions using a newly designed microfluidic device, a chip etched with tiny channels. This device can help support research to uncover better ways of promoting plant growth, engineering drought-resistant crops, remediating the environment and even boosting bioenergy feedstock production.

The root of the problem

Plant root-microbe interactions (RMI) are hidden beneath the soil, posing a challenge for researchers seeking to continuously observe activities such as attachment of microbes and nutrient exchange without interruption over long periods. To get around this challenge, researchers have traditionally analyzed the root environment by growing plants in pots, in between glass sheets, or in agar plates, and then observed the roots for physical changes and microbial interactions by sacrificing the sample.

However, the ideal way to monitor the relationship between plant roots and the microorganisms surrounding them in the rhizosphere—the nutrient-rich region of the soil surrounding the plant root—is to watch these interactions as they happen over extended periods at high resolution. So researchers in Argonne's Biosciences division, together with scientists at Argonne's Center for Nanoscale Materials, a DOE Office of Science user facility, developed an RMI-chip: a tiny microfluidic device that allows minute amounts of fluid to flow across microchannels or pathways on a chip measuring just a few square centimeters across.

"The channels are created via soft lithography, an approach for fabricating 3-D structures using soft materials," said Gyorgy Babnigg, a bioinformatician and molecular biologist at Argonne, who co-developed the device.

Babnigg and his peers used this technique to create a negative mold of their device. They then poured a plastic similar to silicone over the mold and heated it up, allowing it to harden, then removed it from the mold. Next, researchers punched holes in the material to form inlets and outlets, and finally, fused it with a piece of microscope cover glass so they could observe what was happening within the channels through a microscope.

A miniaturized lab to study trees

Microfluidic devices like the one Babnigg and his team created have long been used by researchers to study root-microbe interactions, albeit solely in small, short-lived flowering plants, like Arabidopsis thaliana, known as thale cress or mouse-ear cress. The Argonne device is the first to be used on live, woody plants.

The Argonne team chose to use their device to analyze the quaking or trembling of Aspen trees (Populus tremuloides), a hardy, fast-growing deciduous tree that is the most widely distributed tree species in North America. They started by nurturing Aspen tree seeds into seedlings, then transplanted the seedlings into individual channels of their chip.

"Unlike other shorter studies, we were able to figure out all of the plumbing to grow the seedlings in the chip for several weeks," Babnigg said. "It did take a while. Not only did we need to transfer the root tips into the chip, but then we had to wait until the roots reached the inlet where the nutrients were flowing and then wait another week before we could add the plant growth-promoting microbes to that system."

The microbes added to the system were engineered by researchers to fluoresce unique colors, which would allow researchers to distinguish their behavior under a microscope.

And while researchers continually flowed a simple salt solution through the system to support seedling growth, they withheld nutrients required for the microbes to grow. This meant that, for the microbes to survive, they had to feed off the plants.

Designing their experiment in this way allowed researchers to distinguish whether symbiotic interactions—such as microbes accepting nutrients exuded at the plant root or releasing materials like phosphorus and plant hormones that guided the movement of the root—were observable.

For weeks, researchers continuously observed how different types of microbes grew and interacted with the live roots through a microscope and found that, in the absence of outside nutrients, microbes did latch onto the root surface and use the root exudates to grow.

"We observed particular behaviors of the bacteria on the roots, from alignment of the bacteria to the formation of dense biofilms," said Marie-Francoise Noirot-Gros, Argonne microbiologist and lead author.

These findings reflect what's been demonstrated in past experiments, validating the team's approach and application of their device.

"We visualized all these interactions all while the plant was still alive," Babnigg said. "Our ability to do this using our device and over the course of several weeks is what makes this work stand apart."

The research paper, titled "Functional imaging of microbial interactions with tree roots using a microfluidics setup," is published in Frontiers in Plant Science.

Explore further

How plants harness microbes to get nutrients

More information: Marie-Francoise Noirot-Gros et al. Functional Imaging of Microbial Interactions With Tree Roots Using a Microfluidics Setup, Frontiers in Plant Science (2020). DOI: 10.3389/fpls.2020.00408

Provided by Argonne National Laboratory

Researchers study how weather news impacts public transit ridership

by Paul Gabrielsen, University of Utah

Credit: Pixabay/CC0 Public Domain

If the words in a weather forecast, such as "cool," "sunny" or "windy," can influence the way you dress for the day—can they also influence whether or not you take public transit?

In new research published in Vehicles, U researchers found a correlation between words used in media coverage related to weather or air quality, and transit ridership. It's not enough yet to say that media coverage causes changes in ridership, say authors Tabitha Benney and Daniel Mendoza. But it's enough to explore what factors in to a person's decision to ride transit and whether that decision can be nudged.

"This is encouraging," Benney says. "There's a lot of potential in terms of reaching a lot of different actors that could have a big influence or encourage ridership."

Scanning the media

Mendoza, a research assistant professor in the Department of Atmospheric Sciences and visiting assistant professor in the Department of City & Metropolitan Planning, previously studied how transit ridership along the Wasatch Front, on the buses and trains of the Utah Transit Authority (UTA), impacted air quality. The impact is greater when more people are riding since low-ridership trips, particularly on older buses, can actually have a net contribution to air pollution.

Around the same time Tabitha Benney, an associate professor in the Department of Political Science, was looking at surveys of Utahns that included their reasons for using transit or not. "We were surprised at some of the responses," she says, "and that led me to pursue asking questions about what matters in terms of what could be in the media or how it could be influencing people."

So Mendoza and Benney, along with co-authors Martin Buchert and John Lin, looked at how media coverage of the weather and air quality correlated with transit ridership. For the years 2014-2016, they scanned 40 local Utah media outlets for words related to weather (such as "cloudy," "freezing," or "summer"), air quality (red, yellow or green air day, according to the state's color-coded air quality system) and air pollution (such as "ozone," "PM2.5" or "particulate matter"). Then they looked at the transit ridership the day after the media coverage and noted the actual air quality of that day.

"We wanted to ask if there are any additional factors that would encourage or discourage ridership," Mendoza says.

Comfort and safety

UTA has three main modes of transportation: buses, light rail (TRAX) and commuter rail (FrontRunner). FrontRunner riders tend to ride for farther distances, and their rider behavior, the authors found, didn't vary much with media terms. The most variation, they found, was in bus ridership.

Within that variation, a few media terms related to weather stood out. On average, more usage of the term "good weather" was correlated with more ridership the following day. Similarly, more usage of "winter" was associated with increased ridership, but that may be related to the seasonal nature of U students, the authors say, as the U is the single largest paid pass purchaser from UTA.

Few UTA bus stops have a weather shelter, Mendoza says (although UTA has added more shelters in recent years). Media reports of bad weather, he suggests, could discourage bus ridership.

When looking at color-coded air quality terms, the researchers found less ridership on the bus system on days following use of "orange air day" and "red air day." That could be due to non-commuter bus users who ride the bus for discretionary transportation choosing to stay home to avoid poor air quality and the cold temperatures that typically accompany poor air quality days.

"Ridership is associated with favorable weather conditions and air quality," the authors wrote, "suggesting that ridership volume may be influenced by an overall sense of comfort and safety."

They also found that less technical terms, such as "particulate matter" instead of "PM2.5," were correlated with greater changes in ridership. Same with the color-coded "red air day" term.

"That kind of surprised us," Benney says. Another surprise was the finding that reports of bad air quality reduced ridership, and that reports of good air quality didn't boost it.

"You would expect a strong relationship to clean air with people wanting to move in that direction," she says. "And that's obviously significant."

Moving the needle

Benney says that the study focused on web-accessible media outlets and did not take into account social media, which could have a significant influence on younger audiences, who tend to ride buses more. Upcoming work, she says, will look closer at the sources of Utahns' information about weather and air quality, including from religious services.

The study is encouraging, she adds, because it suggests that messages may be able to influence day-to-day rider behavior. "This opens up a lot of opportunities for large institutional actors to help promote better air quality through ridership," she says.

And the impact has already begun. The Utah Legislature passed a bill in 2019 that launched a three-year pilot program to provide free fares on UTA transit on poor air quality days. Preliminary findings from this research, Mendoza says, provided part of the bill's supporting scientific basis.

Additionally, he says, some of the largest employers in the Salt Lake Valley, including the University of Utah, may be able to use these findings to effectively encourage employees to make air-friendly choices through riding transit or choosing to telework. "And now we're all getting really used to telework!" he says. "Because of that we can actually start to potentially move the needle by reducing the vehicular traffic."

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More information: Daniel L. Mendoza et al, The Association of Media and Environmental Variables with Transit Ridership, Vehicles (2020). DOI: 10.3390/vehicles2030028
Provided by University of Utah

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