Netherlands Institute of Ecology

Heteren, Netherlands

Netherlands Institute of Ecology

Heteren, Netherlands
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News Article | April 17, 2017
Site: phys.org

Having a good conversation: Soil fungus Fusarium and the unrelated soil bacteria. Credit: 21 Lux photography/Heike Engel If you're small, smells are a good way to stand out. A team of researchers led by the Netherlands Institute of Ecology (NIOO-KNAW) has demonstrated for the first time that two different types of micro-organisms—bacteria and fungi—use fragrances, known as terpenes, to hold conversations. And that's not all: "We actually believe that terpenes are the most popular chemical medium on our planet to communicate through," they report. Research by microbial ecologists from NIOO and their colleagues has demonstrated that two very different groups of micro-organisms use fragrances to communicate with each other, the most common type being terpenes. In only one gram of soil, billions of micro-organisms thrive, all communicating chemically. This chemical communication is likely prevalent in other life forms, as well, as the research team reports in Scientific Reports. The researchers have demonstrated that bacteria and fungi do, in fact, respond to each other—in other words, they can hold conversations. Group leader Paolina Garbeva explains: "Serratia, a soil bacterium, can smell the fragrant terpenes produced by Fusarium, a plant pathogenic fungus. It responds by becoming motile and producing a terpene of its own." The researchers established this by studying which genes were activated by the bacterium, which proteins it began to produce, and which fragrance by using transcriptomic, proteomic and metabolomic techniques. "Such fragrances—or volatile organic compounds—are not just some waste product, they are instruments targeted specifically at long-distance communication between these minute fungi and bacteria." But how widespread is this language of smells? Pathogenic soil fungi such as Fusarium also have an effect aboveground, where they make plants sick. Can they communicate with those plants? Garbeva says, "We have known for some time that plants and insects use terpenes to communicate with each other. But we've only just begun to realise that it's actually much wider. There is a much larger group of 'terpene-speakers': micro-organisms." For fungi, protists, bacteria, and even higher animals, terpenes act as pheromones—chemical signals used by animals—which makes them a regular ingredient of perfumes. So it's likely that the language of terpenes forms a vast chemical communications network, indeed. Terpenes are by no means the only volatile organic compounds that are in for a good chat. The researchers found others, as well. Garbeva's Ph.D. student, Ruth Schmidt, the first author of the article, adds: "Organisms are multilingual, but 'terpene' is the language that's used most often." Who knows? Maybe without realising it, humans are native speakers too. Explore further: Sniffing out your dinner in the dark: How miniature predators get their favourite soil bacteria More information: Ruth Schmidt et al, Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C, Scientific Reports (2017). DOI: 10.1038/s41598-017-00893-3


News Article | April 18, 2017
Site: www.eurekalert.org

IMAGE:  Are barnacle geese capable of predicting climate change? They need to arrive at their breeding grounds just as the snow has melted. But the climate in the Arctic is changing... view more The breeding grounds of Arctic migratory birds such as the barnacle goose are changing rapidly due to accelerated warming in the polar regions. They won't be able to keep up with this climate change unless they can somehow anticipate it. A research team from the Netherlands Institute of Ecology (NIOO-KNAW) employed computer models to assess the future of the geese and their young. Results are being published online by the scientific journal Global Change Biology. It's the time of year when barnacle geese and many other migratory birds prepare to depart for their breeding grounds above the Arctic Circle. From their wintering grounds in the Netherlands, the geese fly all the way up to the Barentsz Sea in northern Russia, where they should arrive just as the snow has melted. But in the polar regions, the climate is warming much more rapidly than in more temperate areas like the Netherlands - a phenomenon known as 'Arctic amplification'. It's hard enough for humans to get to grips with the accelerated warming, let alone for barnacle geese, as an earlier NIOO-led study showed. After all, how can they tell from their wintering grounds if the snow has begun to melt thousands of kilometres away? So is it possible for the barnacle geese to advance their spring migration nonetheless, to predict climate change? Ecologist Thomas Lameris and his fellow researchers from NIOO, and also the Swiss Ornithological Institute among other institutions, have tried to find the answer. "This is the first study that tests if migratory birds are in any way able to adjust their timing to the accelerated warming in the polar regions. We used a model to show that the availability of enough edible grass to build up reserves for their journey is not a problem for the barnacle geese. It's the unpredictability of the climatic changes in their breeding grounds that spells trouble for them." If the geese continue to mistime their arrival, their reproductive success will be reduced. Lameris: "They miss their optimal breeding window and the peak in local food abundance, so fewer goslings will survive." Some compensation for this comes from the fact that as well as starting earlier, the breeding season is becoming longer. This gives the goslings more time to grow. But that's not enough. To establish the barnacle geese's potential for anticipating climate change, the researchers built a model that tracks individual geese as they fly to their breeding grounds in northern Russia and make stopovers along the route. "In the model, the geese have to make a choice each day: stay in their present location and continue to feed, or fly to the next stopover." The researchers tested the model for various gradations of climatic warming. The barnacle goose is an ideal 'model species' for studying the effects of climate changes, because researchers have been able to study this animal for decades. But it's not just about a single species. Lameris: "Our results are probably valid for many more species of Arctic-breeding migratory birds, and certainly for other geese such as the white-fronted and the brent goose." On the whole, geese are clever birds. Goslings learn the migration route from their parents, including the best places to stop over and build up fat reserves. "So if they do change the timing of their arrival, it would be easy to pass that on to the next generation", Lameris argues hopefully. "The main question is whether geese and other migratory birds can adapt as fast as the climate changes, to keep up." With more than 300 staff members and students, NIOO is one of the largest research institutes of the Royal Netherlands Academy of Arts and Sciences (KNAW). The institute specialises in water and land ecology. As of 2011, the institute is located in an innovative and sustainable research building in Wageningen, the Netherlands. NIOO has an impressive research history that stretches back 60 years and spans the entire country, and beyond.


News Article | April 19, 2017
Site: phys.org

Each spring, barnacle geese have to fly a long way to their breeding grounds. It's a couple of thousand kilometres to Arctic Russia, where they have to arrive just as the snow has melted. Are they able to predict the vastly changing climate there from their wintering grounds? Credit: Jasper Koster The breeding grounds of Arctic migratory birds such as the barnacle goose are changing rapidly due to accelerated warming in the polar regions. They won't be able to keep up with this climate change unless they can somehow anticipate it. A research team from the Netherlands Institute of Ecology (NIOO-KNAW) employed computer models to assess the future of the geese and their young. Results are being published online by the scientific journal Global Change Biology. It's the time of year when barnacle geese and many other migratory birds prepare to depart for their breeding grounds above the Arctic Circle. From their wintering grounds in the Netherlands, the geese fly all the way up to the Barentsz Sea in northern Russia, where they should arrive just as the snow has melted. But in the polar regions, the climate is warming much more rapidly than in more temperate areas like the Netherlands - a phenomenon known as 'Arctic amplification'. It's hard enough for humans to get to grips with the accelerated warming, let alone for barnacle geese, as an earlier NIOO-led study showed. After all, how can they tell from their wintering grounds if the snow has begun to melt thousands of kilometres away? So is it possible for the barnacle geese to advance their spring migration nonetheless, to predict climate change? Ecologist Thomas Lameris and his fellow researchers from NIOO, and also the Swiss Ornithological Institute among other institutions, have tried to find the answer. "This is the first study that tests if migratory birds are in any way able to adjust their timing to the accelerated warming in the polar regions. We used a model to show that the availability of enough edible grass to build up reserves for their journey is not a problem for the barnacle geese. It's the unpredictability of the climatic changes in their breeding grounds that spells trouble for them." If the geese continue to mistime their arrival, their reproductive success will be reduced. Lameris: "They miss their optimal breeding window and the peak in local food abundance, so fewer goslings will survive." Some compensation for this comes from the fact that as well as starting earlier, the breeding season is becoming longer. This gives the goslings more time to grow. But that's not enough. To establish the barnacle geese's potential for anticipating climate change, the researchers built a model that tracks individual geese as they fly to their breeding grounds in northern Russia and make stopovers along the route. "In the model, the geese have to make a choice each day: stay in their present location and continue to feed, or fly to the next stopover." The researchers tested the model for various gradations of climatic warming. The barnacle goose is an ideal 'model species' for studying the effects of climate changes, because researchers have been able to study this animal for decades. But it's not just about a single species. Lameris: "Our results are probably valid for many more species of Arctic-breeding migratory birds, and certainly for other geese such as the white-fronted and the brent goose." On the whole, geese are clever birds. Goslings learn the migration route from their parents, including the best places to stop over and build up fat reserves. "So if they do change the timing of their arrival, it would be easy to pass that on to the next generation", Lameris argues hopefully. "The main question is whether geese and other migratory birds can adapt as fast as the climate changes, to keep up." Explore further: Climate change has mixed effects on migratory geese More information: Thomas K. Lameris et al, Potential for an Arctic-breeding migratory bird to adjust spring migration phenology to Arctic amplification, Global Change Biology (2017). DOI: 10.1111/gcb.13684


News Article | May 11, 2017
Site: www.scientificamerican.com

The record piles of snow across California’s Sierra Nevada are melting away, exposing once again its breathtaking alpine meadows. As temperatures warm the moist soil, the meadows quicken, cycling carbon from the ground into the atmosphere and back again in a pattern essential to the planet's health. Scientists and land managers are heading into the mountains to measure the greenhouse gas activity at 16 hand-picked meadows—some recently restored, others degraded from a century of grazing and logging. The four-year study is part of California's pioneering effort to reduce carbon emissions. The project is designed to determine whether restored meadows hold more carbon than those that have been degraded. The outcome could prove pivotal for California and the planet. Worldwide, soils store three times more carbon than vegetation and the atmosphere combined. If the research shows restored meadows improve carbon storage, it could stimulate meadow restoration around the world. The $4.8-million project has an unusual twist, too. It is funded by the California Air Resources Board, which wants to know if restored meadows can hold enough tonnage of carbon dioxide equivalents, per acre per year, to qualify as carbon credits in California’s cap-and-trade market. “It’s kind of geeky but we’re poised to do something that’s never been done with alpine meadows,” says Mark Drew, Sierra Headwaters director at California Trout, who is coordinating the work. Meadows are new to soil carbon research. Carbon enters the soil as plants use solar energy to draw carbon dioxide from the atmosphere and make their own food. More enters the ground when plants die and are decomposed by microbes. And yet living plant roots expel carbon dioxide, and so do microbes as they decompose the dead plant matter, creating a cycle of carbon uptake and emission by soil. It is common for agricultural land to lose a fair portion of its original carbon stock as it is relentlessly farmed—as much as 50 to 70 percent, according to several estimates. Scientists suspect meadows may lose carbon as well, especially when they are degraded by logging and grazing activities that compact soils, erode streams and deplete native plants and animals. Some scientists also think global warming itself is changing soil carbon stocks. A December study published in Nature, led by Thomas Crowther at Netherlands Institute of Ecology, found rising temperatures are stimulating a net loss of soil carbon to the atmosphere. Warmer soils accelerate the flux, sending more carbon into the ground and more carbon dioxide back out into the atmosphere. As warmth increases microbial activity, decomposition and respiration outpace photosynthesis, particularly in the world’s colder places. “That’s when the losses start to happen,” Crowther says. The changes could drive a carbon–climate feedback loop that could accelerate climate change. Drew was already starting to collaborate with several meadow restoration groups in 2014, when the Air Resources Board announced funding to study carbon flux in Sierra meadows. Rather than compete for small pots of money, the various stakeholders decided to work together—PhD scientists side by side with ranchers and landowners. Together they could build a database far larger than any one project could, Drew says. The group already knew meadow restoration—usually done with heavy equipment to fill braided channels and re-create functioning floodplains—has well-documented ecosystem benefits. Returning streams to their natural meanders and raising the water table rejuvenates habitat for golden trout, willow flycatchers and other endangered species. Restoring meadows also improves their capacity to store and release water, a boon to a state that depends on the Sierra region for more than 60 percent of its water supply. Spurred by Air Board funding, the meadow partners set out to see what restoration could do for carbon storage as well. The research covers meadows from the base of Lassen Peak in the north to areas nearer to Los Angeles. The meadows range in elevation from 3,045 to nearly 8,700 feet; they include granitic, volcanic and metamorphic soils. A critical facet of the partnership is developing precise procedures for when and how to measure and analyze meadow greenhouse gases. Although scientists have established protocols for monitoring carbon flux in forests and wetlands, none exist for alpine meadows. “We’re the guinea pigs,” Drew says. Work has just begun and will continue until winter closes access. The data collection begins with pushing an eight-inch segment of PVC pipe into the ground vertically to seal off a small segment of meadow, then capping the cylindrical chamber. A monitor pokes a syringe into a tiny hole in the cap, drawing a sample of whatever meadow gases are captured inside. By taking three samples 15 minutes apart repeatedly over several months scientists can compare the ambient air with gases coming directly out of the meadow. The rate of change in the concentration of gases determines the soil’s CO emission rate. The researchers are also monitoring soil carbon by extracting core samples. Comparing the data from restored meadows with geographically similar degraded sites will show the effects of restoration. The researchers have a hint of what they might find from a limited study conducted by the University of Nevada, Reno (U.N.R.). Scientists collected soil samples at seven meadows in the northern Sierra restored between 2001 and 2016, pairing restored sites with similar, adjacent unrestored sites. The preliminary results found an average of 20 percent more soil carbon in restored meadows, with one site recording an increase of over 80 percent. Meadows immediately begin storing carbon following restoration, with significant increases over 15 years, says Cody Reed, a research assistant working with Ben Sullivan, a U.N.R. soil scientist and assistant professor. The investigation seems to show restored meadows add soil carbon and also slow losses to the atmosphere. Another limited study looked at the effects of water in meadow soils. Steve Hart, an ecology professor at University of California, Merced, and Joseph Blankinship, assistant professor of microbial biogeochemistry at the University of Arizona, researched a Sierra meadow to understand how water affects the fluxes of carbon dioxide, methane and nitrous oxide. What they found surprised them: Carbon dioxide emissions were unaffected by soil moisture content, and methane sequestration was prevalent, particularly on the dry side of wet meadow. The 2014 study also found plant species richness and soil carbon concentration appeared more important than soil moisture in explaining carbon fluxes. It is too soon to know if these results will be replicated on the larger Sierra-wide scale. With a full year of research already logged, Drew and his partners are digging in to a new season of fieldwork. A finding of dramatically increased soil carbon in restored meadows would have a limited effect globally because such large forces are at work. But the gain could be an important, added payoff for restoring these landscapes. The Sierra Meadows Partnership could also serve as a model to others working in very different landscapes that hold the potential to have a much greater effect on the carbon equation, Hart says. And if restored meadows do indeed hold significantly more carbon, then they could play a role in California's carbon market. The Sierra partners have until 2019 to present their results. “We’re poised to do something really unique,” Drew says. “Let's see where it takes us.”


Mendes R.,Laboratory of Environmental Microbiology | Garbeva P.,Netherlands Institute of Ecology | Raaijmakers J.M.,Wageningen University
FEMS Microbiology Reviews | Year: 2013

Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health. In this review, we focus on the frequency, diversity and activities of beneficial ('the good'), plant pathogenic ('the bad') and human pathogenic ('the ugly') microorganisms in the rhizosphere and how they impact on health and disease. Specific attention is given to mechanisms involved in multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we discuss strategies to re-direct or re-shape the rhizosphere microbiome in favour of those microbes that are beneficial to plant growth and health. © 2013 Federation of European Microbiological Societies.


Bodelier P.L.E.,Netherlands Institute of Ecology
Current Opinion in Environmental Sustainability | Year: 2011

Recent dynamics and uncertainties in global methane budgets necessitate research of controls of sources and sinks of atmospheric methane. Production of methane by methanogenic archaea in wetlands is a major source while consumption by methane oxidizing bacteria in upland soils is a major sink. Methane formation as well as consumption is affected by nitrogenous fertilizers as has been studied intensively. This review synthesizes the results of these studies which are contradictory and await mechanistic explanations. These can be found in the community composition and the traits of the microbes involved in methane cycling. Molecular microbial investigations, use of stable isotope labeling techniques, discoveries and isolation of new species and pathways offer new insight into interactions between nitrogen and methane cycling. © 2011 Elsevier B.V.


Schaper S.V.,Netherlands Institute of Ecology
The American naturalist | Year: 2012

Timing of reproduction in temperate-zone birds is strongly correlated with spring temperature, with an earlier onset of breeding in warmer years. Females adjust their timing of egg laying between years to be synchronized with local food sources and thereby optimize reproductive output. However, climate change currently disrupts the link between predictive environmental cues and spring phenology. To investigate direct effects of temperature on the decision to lay and its genetic basis, we used pairs of great tits (Parus major) with known ancestry and exposed them to simulated spring scenarios in climate-controlled aviaries. In each of three years, we exposed birds to different patterns of changing temperature. We varied the timing of a temperature change, the daily temperature amplitude, and the onset and speed of a seasonal temperature rise. We show that females fine-tune their laying in response to a seasonal increase in temperature, whereas mean temperature and daily temperature variation alone do not affect laying dates. Luteinizing hormone concentrations and gonadal growth in early spring were not influenced by temperature or temperature rise, possibly posing a constraint to an advancement of breeding. Similarities between sisters in their laying dates indicate genetic variation in cue sensitivity. These results refine our understanding of how changes in spring climate might affect the mismatch in avian timing and thereby population viability.


Bardgett R.D.,University of Manchester | Van Der Putten W.H.,Netherlands Institute of Ecology | Van Der Putten W.H.,Wageningen University
Nature | Year: 2014

Evidence is mounting that the immense diversity of microorganisms and animals that live belowground contributes significantly to shaping aboveground biodiversity and the functioning of terrestrial ecosystems. Our understanding of how this belowground biodiversity is distributed, and how it regulates the structure and functioning of terrestrial ecosystems, is rapidly growing. Evidence also points to soil biodiversity as having a key role in determining the ecological and evolutionary responses of terrestrial ecosystems to current and future environmental change. Here we review recent progress and propose avenues for further research in this field. © 2014 Macmillan Publishers Limited. All rights reserved.


Gienapp P.,Netherlands Institute of Ecology
Philosophical transactions of the Royal Society of London. Series B, Biological sciences | Year: 2013

Populations need to adapt to sustained climate change, which requires micro-evolutionary change in the long term. A key question is how the rate of this micro-evolutionary change compares with the rate of environmental change, given that theoretically there is a 'critical rate of environmental change' beyond which increased maladaptation leads to population extinction. Here, we parametrize two closely related models to predict this critical rate using data from a long-term study of great tits (Parus major). We used stochastic dynamic programming to predict changes in optimal breeding time under three different climate scenarios. Using these results we parametrized two theoretical models to predict critical rates. Results from both models agreed qualitatively in that even 'mild' rates of climate change would be close to these critical rates with respect to great tit breeding time, while for scenarios close to the upper limit of IPCC climate projections the calculated critical rates would be clearly exceeded with possible consequences for population persistence. We therefore tentatively conclude that micro-evolution, together with plasticity, would rescue only the population from mild rates of climate change, although the models make many simplifying assumptions that remain to be tested.


Van Der Putten W.H.,Netherlands Institute of Ecology
Annual Review of Ecology, Evolution, and Systematics | Year: 2012

Changes in climate, land use, fire incidence, and ecological connections all may contribute to current species' range shifts. Species shift range individually, and not all species shift range at the same time and rate. This variation causes community reorganization in both the old and new ranges. In terrestrial ecosystems, range shifts alter aboveground-belowground interactions, Influencing species abundance, community composition, ecosystem processes and services, and feedbacks within communities and ecosystems. Thus, range shifts may result in no-analog communities where foundation species and community genetics play unprecedented roles, possibly leading to novel ecosystems. Long-distance dispersal can enhance the disruption of aboveground-belowground interactions of plants, herbivores, pathogens, symbiotic mutualists, and decomposer organisms. These effects are most likely stronger for latitudinal than for altitudinal range shifts. Disrupted aboveground-belowground interactions may have Influenced historical postglacial range shifts as well. Assisted migration without considering aboveground-belowground interactions could enhance risks of such range shift-induced invasions. © 2012 by Annual Reviews. All rights reserved.

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