Ecology

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RESEARCH HIGHLIGHT
06 June 2023

After gulls switched their focus from southern right whale mothers to calves, scientists recorded a drop in calf survival. More

The Tara during its 100,000-kilometre voyage around the Pacific Ocean.Credit: François Aurat/Tara Ocean Foundation

Scientists have known for decades that the biodiversity we know is a fraction of the biodiversity that exists. Even when it comes to perhaps the simplest measure, the number of species, researchers estimate that there could be anywhere between 3 million and 100 million species, of which some 1.7 million have been described. Every year, the names of some 10,000 new ones get added to the list.Gathering good biodiversity data can be a mission in itself, especially on marine biodiversity. One dependable source is a schooner called Tara, which celebrates 20 years at sea as a research ship this year. Tara has been to the Arctic Ocean and the Mediterranean Sea. Last week, researchers reported the results of its latest voyage, Tara Pacific, a two-year expedition across the Pacific Ocean, published in a collection of articles in Springer Nature journals (go.nature.com/45puzhk).
Epic voyage finds astonishing microbial diversity among coral reefs
Coral reefs are among Earth’s most diverse ecosystems, supporting 25% of marine life and providing services such as food, jobs and coastal protection to nearly one billion people worldwide. One region of the Pacific, the Coral Triangle — which includes the waters of Indonesia, Malaysia and the Philippines — has around 75% of the world’s coral species. But these nurseries for marine life are under threat: globally, around 50% of living corals have been lost since the 1950s (T. D. Eddy et al. One Earth 4, 1278–1285; 2021). Moreover, climate change poses a large risk to their continued survival.One of Tara Pacific’s research groups has been focusing on genetic diversity — in particular, that of microbial communities (bacteria and archaea) living in Pacific Ocean corals. The scientists, led by marine microbiologist Pierre Galand at the Banyuls Oceanological Observatory in Banyuls-sur-Mer, France, collected more than 5,000 samples, and focused on analysing the 16S ribosomal DNA marker gene, which is used to identify and classify microorganisms. They found around half a million distinct DNA sequences known as amplicon sequence variants (ASVs), which can be used as a measure of the genetic diversity in a sample (Nature https://doi.org/kddz; 2023). From these data, the researchers estimated that the microbial diversity of coral reefs globally is probably around 2.8 million ASVs (P. E. Galand et al. Nature Commun. 14, 3039; 2023). For comparison, this is close to the lower end of one genetic-diversity estimate of all of Earth’s bacterial and archaeal communities — a proposed range of 2.72 million and 5.44 million ASVs (S. Louca et al. PLoS Biol. 17, e3000106; 2019). Galand and his colleagues’ work, which builds on smaller-scale studies of coral reefs (M. Chiarello et al. Proc. R. Soc. B 287, 20200642; 2020), confirms that Earth’s microbial genetic diversity is much higher and richer than previously thought.
Collection: Tara Pacific
The research ship has a stirring and unusual back story. Its original captain was Peter Blake, a much-decorated professional yachtsman from New Zealand. After retirement, Blake became an environmental envoy to the United Nations but was killed by pirates at the mouth of the Amazon River while on an expedition in 2001. Agnès Troublé, a French fashion designer known as Agnès B, and her son Etienne Bourgois acquired the boat, determined to continue Blake’s original vision. They established the Tara Ocean Foundation and invited scientists and research funders to join them on various missions.The logistics of converting a schooner into a floating laboratory and taking it on a 100,000-kilometre journey cannot be underestimated, especially considering the present complicated relations between Pacific nations. And then there’s the logistics of the research itself: organizing 3,000 dives; sending samples for PCR analysis en route; keeping the voyage on track.Researchers must continue to build on the work being reported and refine our understanding of the importance of diversity for safeguarding ecosystem stability and function. The project is a great example of visionary thinkers such as Troublé and Bourgois working closely with funders and scientists to help us to understand the breathtaking diversity of the world around us before it is too late. When it comes to preserving the natural systems we all depend on, more such collaborations are needed. More

Farming today is unsustainable, with its greenhouse-gas emissions and its destruction of wildlife habitats. Agriculture now takes up half of Earth’s hospitable land surface, at the expense of these habitats.Developing sustainable food production will require multiple approaches. My PhD research at Wageningen University in the Netherlands is inspired by alternative, indoor methods of food production, such as farming leafy green vegetables vertically and growing meat in a laboratory. I wondered — if you can grow meat without an animal, can you grow fruit without a plant?This could be done inside, which might help us to return some agricultural land to nature.During my master’s programme in agricultural engineering, I discussed indoor fruit production with my professor. He invited me to write a master’s thesis on the subject of growing fruits without the plant. Now, we’re testing this idea.The main task of my PhD is to collect immature fruit or flowers from tomato plants, and try to grow the stems into healthy, high-quality tomatoes in the lab. Ultimately, we want to produce fruit from tomato meristem cells — undifferentiated cells from which new plant organs can grow — and skip using a plant entirely.The jars in this photo contain some of the early results of my research, when I was testing different growing conditions at different stages of tomato development. The lighting is an energy-efficiency measure; we use blue and red LEDs, the best colours for photosynthesis.Some people get excited about the possibilities of my work, but most are hesitant, which I understand. In the past, people have rushed into using food technologies, such as cage-grown chickens and the extensive use of synthetic fertilizer, without considering the potential downsides. An important part of my PhD programme will be to assess the sustainability of my method. More

An air-quality monitoring station in London is located near a deer park, so it picks up DNA from species such as Dama dama (fallow deer) in its filters.Credit: Robert Knell

Scientists might be able to keep tabs on the world’s flora and fauna by analysing DNA floating through the air. That’s the conclusion of a study published on 5 June in Current Biology1, in which a team identified more than 180 types of organism, including plants, fungi, insects and animals, using DNA captured by filters from air-pollution monitoring stations. The researchers say that, because of the ubiquity of such stations, the method could transform the monitoring of biodiversity on Earth, and might even be able to detect rare species.Global biodiversity is plummeting — some estimates suggest a 69% drop in wildlife populations since 1970. Scientists struggle to keep track of changes in ecosystems and rates of species decline because they lack infrastructure to measure biodiversity on large scales. Typically, researchers or conservation volunteers monitor a few terrestrial species in small regions using labour-intensive methods such as camera surveillance, in-person observations and examining traces including footprints and faeces. Over large scales, only very general measurements are possible, such as assessments of forest cover.

Source: Ref. 1

But environmental DNA (eDNA) — small amounts of genetic material shed by living things — that is collected automatically using air-pollution tracking networks could help solve this problem, says Elizabeth Clare, a molecular ecologist at York University in Toronto, Canada, and lead author of the study.Scientists have been collecting and sequencing eDNA from soil and water samples for about 20 years to track rare or endangered species, such as the great crested newt (Triturus cristatus) in the United Kingdom and Gouldian finches (Erythrura gouldiae) in Australia. Regulatory agencies have used eDNA to detect invasive species; for example, the US Fish and Wildlife Service uses it to monitor silver carp (Hypophthalmichthys molitrix) in the Great Lakes system. But it wasn’t until last year that scientists, including Clare, reported that eDNA can be captured from air samples and used to explore terrestrial biodiversity2. The DNA probably comes from cells shed by organisms, researchers say.Biodiversity-monitoring stations?In the latest research, Clare and her colleagues ran a pilot study in which they got access to existing UK air-quality monitoring stations in London and near Edinburgh, to see whether they could trap airborne eDNA from the local flora and fauna. Both are designed to monitor atmospheric pollutants such as lead in particulate matter that becomes trapped in the devices’ filters. The Edinburgh station is part of a UK-wide network that is run in part by the National Physical Laboratory (NPL) in Teddington.

The US Fish and Wildlife Service uses eDNA to monitor silver carp (Hypophthalmichthys molitrix), an invasive species.Credit: Jason Lindsey/Alamy

The researchers set up the London station, which is next to a deer park, to take samples over various time intervals, from one hour to one week, allowing them to test whether sampling time is important. They also explored how long samples could be preserved by analysing the Edinburgh stations’ filters, which had collected DNA for a week before being stored for eight months.The research team, which included scientists from the NPL, extracted and sequenced eDNA from one-quarter of each filter. The scientists then compared the sequences with those available in DNA databases such as GenBank, run by the US National Institutes of Health.The researchers were surprised to find DNA from so many groups of organism on the filters. These included 34 species of bird, such as wrens (Troglodytes troglodytes) and great tits (Parus major), as well as ash trees (of the genus Fraximus), nettles (of the genus Soleirolia) and pathogenic Septoriella fungi (see ‘Keeping tabs on taxa’).Working out the detailsThe advantage of using existing air-monitoring stations is that this infrastructure is already set up in many countries around the world, including across North and Central America, Europe, Asia and the Southern Hemisphere, the researchers say. They urge monitoring-station operators to preserve filters after air-quality analysis so ecologists can use them.“Until we truly understand their ecological value, we’ve got to stop throwing them away,” Clare says.

Researchers retrieved wildlife DNA from the Auchencorth Moss air-quality monitoring station near Edinburgh.Credit: National Physical Laboratory/Local Site Operator

Eily Allan, a molecular biologist and chief scientist of the eDNA Collaborative, a research programme at the University of Washington in Seattle, says the automated collection of airborne eDNA using existing networks of air-monitoring stations could “push environmental monitoring into the twenty-first century”. It moves the research community from disjointed sampling to regular, repeated, long-term data collection, she adds.But before the monitoring method can be rolled out widely, researchers need to work out some details, including the optimal sampling time to ensure broad eDNA collection. The team says its data suggest that a day is too short for sampling, but a week is too long — there is a sweet spot between collecting enough DNA and keeping it for so long that the material degrades.Other unknowns include how far eDNA travels in air, which will determine how large an area this method can monitor. Study co-author Joanne Littlefair, a molecular ecologist at Queen Mary University of London, says the team is also still working out what ecological information eDNA can provide beyond identifying species. For example, she suggests it is unlikely that the method will be able to measure species abundance. But it could monitor bird migrations and how they are changing in response to climate change.“We don’t know really what you can reliably look at yet,” she says. More

Wild descendants of the hippo population introduced in Colombia by Pablo Escobar.Credit: Raul Arboleda/AFP via Getty

Colombia’s invasive hippo population is even larger than researchers had thought, according to the most thorough census of the animals conducted yet. Scientists were already concerned about the hippos — considered the largest invasive animal in the world — threatening native plants and animals in the country, and had been calling for drastic measures to reduce the population. The census results have only heightened that fear.
Pablo Escobar’s ‘cocaine hippos’ spark conservation row
A few years ago, researchers estimated how fast the animals were reproducing, to project that about 98 hippos were living along the country’s Magdalena River and its tributaries in 20201. But the new study, for which a research team counted the animals in person, by drone and using other tracking methods, estimates that there are 181–215 of them residing in Colombia.“Before, one argument against dealing with the hippos was that our information was limited and our arguments theoretical,” says ecologist Rafael Moreno, who participated in the study while at the Alexander von Humboldt Biological Resources Research Institute in Bogotá. “But we have put that argument to bed now. This study shows that this is a real issue, and that the state must act urgently.”By drone and on footColombia’s ‘cocaine hippos’ are all descendants of three females and one male illegally imported by drug-cartel leader Pablo Escobar. After he died in the 1993, the hippos (Hippopotamus amphibius) escaped from his estate and established themselves in the Magdalena River. Without the natural predators or droughts of their native Africa to keep them in check, the giant herbivores have bred rapidly to form the largest population of the animals outside that continent.Colombian officials have struggled to manage the hippos. After they ordered an aggressive male to be killed in 2009, a photo of soldiers posing with the corpse sparked outrage and halted efforts to rein them in. Some communities now depend on the tourism the hippos bring, whereas others — particularly fishing communities — live in fear of the highly territorial animals, which can weigh 3 tonnes and can tear off a person’s limbs or trample them.
Landmark Colombian bird study repeated to right colonial-era wrongs
Colombia’s environment ministry commissioned the census to get a better picture of the problem and how to manage it. Completing it was challenging: despite the hippos’ large size, it is difficult to find and count them accurately. They are nocturnal, immerse themselves in water for 16 hours a day and roam large distances.Comprising researchers at the National University of Colombia in Bogotá, the Humboldt Institute and Cornare, an environmental body managing an area where the hippos live, the team made various trips in 2021 and 2022 by car, boat and on foot to count the hippos. In locations where the animals could not be reached safely, they used drones to count them or footprints to estimate the population.

One way of managing the hippo population is by contraception, administered using a dart.Credit: Cornare via Reuters

The researchers found that 37% are juveniles, indicating that the animals are breeding rapidly. One hypothesis for this is that the hippos are reaching sexual maturity earlier than they do in Africa owing to the lush conditions in Colombia. Another is that the animals are having greater reproductive success because there are fewer fights among them for territory and resources, Moreno says. But evidence is needed to confirm the actual cause.While counting the hippos, the team documented the myriad ways in which the animals are damaging Colombia’s ecosystems. As they waddle their huge bodies to and from rivers, the hippos are eroding riverbanks and carving out muddy paths that divide forests. Moreover, they are outcompeting other animals for habitat and resources, with the West Indian manatee (Trichechus manatus), neotropical otter (Lontra longicaudis) and capybara (Hydrochoerus hydrochaeris) most under threat.Exploring solutionsWith serious attacks on humans in 2020 and 2021, and a car crash leaving a hippo dead on the highway in April, solutions are needed, scientists say.One strategy currently being tried is to administer contraceptives to the animals by dart. That might eventually get rid of the hippos by preventing their reproduction, but it is slow, costly and hasn’t been tested on hippos on such a scale before. A modelling study published in April2 estimated that this method could eradicate the hippos in 45 years at a cost of at least US$850,000.
The world’s species are playing musical chairs: how will it end?
Another strategy — capturing, anaesthetizing and transporting the hippos by helicopter to a facility to be castrated — would cost at least $530,000 and take up to 52 years for eradication, the study found. Both calculations are underestimates, given that the models were fed earlier, lower estimates of the hippo population, before the census results had been released.Meanwhile, the regional agency responsible for dealing with the hippos is strapped for funding and relying on donations of contraceptives from the United States. Agency officials are negotiating with countries, including India and Mexico, to export some of the animals to sanctuaries abroad. But this would cost $3.5 million, according to those working on the strategy.There is no single best solution, says Olga Montenegro, a biologist at the National University who worked on the census. The hippos live in various groups, some of which might be easily relocated, but others are well established and are breeding quickly.Many researchers advocate culling the animals. They say it is the swiftest, most humane thing to do and that it would solve the problem before it becomes impossible to fix. The cost of killing the hippos must be weighed against that of losing native flora and fauna in Colombia — the second-most biodiverse country in the world — they add.Nature asked the environment ministry how it would manage the growing hippo population, given the new findings, but it did not comment.“There is a moral weight to the decision to cull a hippo. But the weight of the other decision — inaction — is far greater,” Moreno says. “I hope this is something the politicians will understand.” More

Extreme weather, such as has occurred in Bangladesh, is having a disproportionate impact on vulnerable communities.Credit: Tanbir Miraj/AFP/Getty

How many biophysical boundaries does our planet have? What are the limits of, say, carbon dioxide emissions, ocean acidification, chemicals and air pollution beyond which existence becomes unsafe for Earth and its inhabitants?
A safe operating space for humanity
Back in 2009, a team of researchers led by environmental scientist Johan Rockström grappled with these questions in an article published in Nature (J. Rockström et al. Nature 461, 472–475; 2009). In the researchers’ view, planet-altering human activities could be assembled into nine groups. Thresholds were calculated for most of them, beyond which the result could spell danger for the planet and its people. The scientists concluded that humanity has crossed three of these nine ‘planetary boundaries’, and that the remaining six would also be crossed unless remedial action was taken.That article, called ‘A safe operating space for humanity’, has been extraordinarily influential in a relatively short time. Cities around the world have been experimenting with how to apply the findings, and researchers (including many in the original 2009 team) have continued to refine the planetary boundaries in response to feedback and new data.A gap in the original concept was that it lacked environmental justice and equity — it needed to take into account the fact that everyone, especially the most vulnerable, has an absolute right to water, food, energy and health, alongside the right to a clean environment.This week, Rockström, together with sustainability scientist Steven Lade and a team of researchers, have modified their original concept to incorporate justice alongside the biophysical boundaries. The resulting findings, which build on a study published in March in Nature Sustainability (J. Gupta et al. Nature Sustain. https://doi.org/grwfbk; 2023), show that seven out of eight thresholds have been crossed (see ‘Planetary boundaries reboot’): the eight are climate, natural ecosystem area, ecosystem functional integrity, surface water, groundwater, nitrogen, phosphorus and aerosols.

Planetary boundaries reboot. The concept of ‘planetary boundaries’ has been updated to take into account the fact that everyone, particularly the most vulnerable, has an absolute right to water, food, energy and health, alongside the right to a clean environment. The red lines indicate a limit to what is ‘safe’ for the planet. The green space represents the threshold that is both safe for the planet and protects the world’s most vulnerable populations (‘safe and just’). The Earth-shaped icons show how, in seven of eight cases, thresholds for a safe and just world have already been crossed.Source: J. Rockström et al.

Stark warningThe findings are an even starker warning than were those reported in 2009. Arguably, the most striking change since 2009 is that the authors advocate that global warming should be limited to 1 °C above pre-industrial levels. This is lower than the 1.5 °C target agreed at the 2015 Paris climate conference. It is also a stricter constraint than the recommendation in the 2009 study to keep carbon emissions to 350 parts per million by volume (the pre-industrial value was 280 parts per million by volume).
Read the paper: Safe and just Earth system boundaries
The authors reason that keeping to 1.5 °C might well enable the world’s more-affluent people to protect themselves, but it would create significant harm for the most vulnerable. The researchers estimate that some 200 million people would be exposed to unprecedented temperature increases and that 500 million people would be exposed to long-term sea-level rise.In incorporating ideas of justice into their research, Rockström and colleagues build on a body of recent work. Not long after the 2009 paper was published, justice and equity were included in discussions that led to the United Nations Sustainable Development Goals (SDGs), announced in 2015. Environmental justice is also at the core of an innovative idea called doughnut economics. In 2012, economist Kate Raworth, then working for the aid agency Oxfam, and colleagues adapted the 2009 study’s findings to include what Raworth called a “safe and just space”. This space was represented by an area enclosed by a double circle, the ‘doughnut’, whose boundaries could not be crossed. Such a threshold would be measured using the indicators and methodology underpinning the SDGs.
How to identify unjust planetary change
The latest study shows how members of the 2009 team, working with a new generation of scientists and a more multinational team, have risen to the challenge of triangulating their original work with doughnut economics and the SDGs. This has not been easy, and the new work is very much an initial step. In an accompanying News & Views article, Stephen Humphreys, who studies law and social justice at the London School of Economics, acknowledges the difficulty of setting numerical values when integrating ideas from the natural and social sciences. Readers can see how this process worked: alongside the paper, we are publishing the full discussion between authors and reviewers (J. Rockström et al. Nature https://doi.org/10.1038/s41586-023-06083-8; 2023). It underscores where there is agreement and disagreement, and where more data and further refinement will be needed.This is a wonderful example of how well science functions when different teams study and refine each others’ work. But there is a troubling aspect to the new findings, too. If seven of the eight thresholds have been crossed, what does that mean for our still-feeble efforts to move to a more sustainable path?Researchers vary widely in their views on how this question should be addressed — from those who advocate working within the current economic system (known as green growth) to those arguing that the present economic system was itself a factor (if not the defining factor) in bringing about the present situation and requires transformation (known as post-growth or degrowth). Some months ago, we urged scientists representing these different approaches to forge more channels of communication between them.The paper we are publishing represents one such opportunity. If the findings are anything to go by, there is no time to lose. More

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