Felling pine trees to study their wind resistance

Forestry experts of the French Institute for Agricultural Research INRA together with technicians from NEIKER-Tecnalia and the Chartered Provincial Council of Bizkaia felled radiata pine specimens of different ages in order to find out their resistance to gales and observe the force the wind needs to exert to blow down these trees in the particular conditions of the Basque Country.

This experience is of great interest for the managers of forests and will help them to manage their woodlands better and incorporate the wind variable into decisions like the distribution of plantations, or the most propitious moment for felling the trees.

Professionals like timber growers in the forestry sector, foresters, forestry technicians and researchers gathered to witness the simulation from close quarters. The trees were felled with steel cables that act as the wind force and which were fitted with sensors to measure the force need to bring the trees down. Each radiata pine had been fitted with three tilt meters that recorded the degree of tilt according to the force exerted on the tree. That way it was possible to determine the resistance of the roots and the strength of the trunk, two essential parameters to find out the capacity of the tree to withstand the thrust of the wind.

The experience carried out this morning is part of the seminar ‘FORRISK: Wind damage risk in forests’, which took place in the Bizkaia Aretoa in Bilbao, and was organised by NEIKER-Tecnalia in collaboration with the Chartered Provincial Council of Bizkaia, HAZI and the Atlantic Regional Office of EFI (European Forest Institute). The seminar is part of the European project “FORRISK- Network for innovation in silviculture and integrated systems for forest risk management”. This initiative has been co-funded by the ERDF and by the Sub-Ministry for Agriculture, Fisheries and Food Policy of the Government of the Basque Autonomous Community (region). The seminar took place in Bilbao because of its status as European Forest City 2014.

The seminar was used to present the detailed map of the characteristics of the wind in the Basque Country, which timber growers and forestry managers can now avail themselves of.The map has been produced by researchers at INRA, the French Institute for Agricultural Research, who have used information from the 57 meteorological stations equipped with anemometers in the network of the Basque Meteorological Authority, Euskalmet.

A tool for estimating wind damage

Those attending the seminar also had the chance to get to know the ForestGALES computing tool that allows managers to estimate the probability of wind damage in forests. ForestGALES was originally created for Britain and has been adapted to the characteristics of the Basque geography by INRA, NEIKER-Tecnalia and HAZI technicians. This innovative application is of great use in specifying concrete actions (for example: spacing, silvicultural interventions like clearing or thinning) bearing in mind the probability of wind damage on each plot.

To get the most out of this tool, it is necessary to know the resistance of the roots and strength of the trunks of the relevant species, as well as the characteristics of the wind where the trees are growing.So today’s simulation and the Basque wind map are two fundamental components for developing the ForestGALES model.

Increase in extreme winds owing to climate change

Cyclones like Klaus (2009) and Xynthia (2010) brought down over 200,000 cubic metres of timber as they passed through the Basque Country, owing to gusts of winds in excess of 228 kilometres per hour. Predictions indicate that the frequency of extreme phenomena like these is set to increase owing to climate change. So the forestry sector needs to have information and tools that will enable it to tackle the risks resulting from the wind.

2015 DOE JGI’s science portfolio delves deeper into the Earth’s data mine

The U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, has announced that 32 new projects have been selected for the 2015 Community Science Program (CSP). From sampling Antarctic lakes to Caribbean waters, and from plant root micro-ecosystems, to the subsurface underneath the water table in forested watersheds, the CSP 2015 projects portfolio highlights diverse environments where DOE mission-relevant science can be extracted.

“These projects catalyze JGI’s strategic shift in emphasis from solving an organism’s genome sequence to enabling an understanding of what this information enables organisms to do,” said Jim Bristow, DOE JGI Science Deputy who oversees the CSP. “To accomplish this, the projects selected combine DNA sequencing with large-scale experimental and computational capabilities, and in some cases include JGI’s new capability to write DNA in addition to reading it. These projects will expand research communities, and help to meet the DOE JGI imperative to translate sequence to function and ultimately into solutions for major energy and environmental problems.”

The CSP 2015 projects were selected by an external review panel from 76 full proposals received that resulted from 85 letters of intent submitted. The total allocation for the CSP 2015 portfolio is expected to exceed 60 trillion bases (terabases or Tb)-or the equivalent of 20,000 human genomes of plant, fungal and microbial genome sequences. The full list of projects may be found at http://jgi.doe.gov/our-projects/csp-plans/fy-2015-csp-plans/. The DOE JGI Community Science Program also accepts proposals for smaller-scale microbial, resequencing and DNA synthesis projects and reviews them twice a year. The CSP advances projects that harness DOE JGI’s capability in massive-scale DNA sequencing, analysis and synthesis in support of the DOE missions in alternative energy, global carbon cycling, and biogeochemistry.

Among the CSP 2015 projects selected is one from Regina Lamendella of Juniata College, who will investigate how microbial communities in Marcellus shale, the country’s largest shale gas field, respond to hydraulic fracturing and natural gas extraction. For example, as fracking uses chemicals, researchers are interested in how the microbial communities can break down environmental contaminants, and how they respond to the release of methane during oil extraction operations.

Some 1,500 miles south from those gas extraction sites, Monica Medina-Munoz of Penn State University will study the effect of thermal stress on the Caribbean coral Orbicella faveolata and the metabolic contribution of its coral host Symbiodinium. The calcium carbonate in coral reefs acts as carbon sinks, but reef health depends on microbial communities. If the photosynthetic symbionts are removed from the coral host, for example, the corals can die and calcification rates decrease. Understanding how to maintain stability in the coral-microbiome community can provide information on the coral’s contribution to the global ocean carbon cycle.

Longtime DOE JGI collaborator Jill Banfield of the University of California (UC), Berkeley is profiling the diversity of microbial communities found in the subsurface from the Rifle aquifer adjacent to the Colorado River. The subsurface is a massive, yet poorly understood, repository of organic carbon as well as greenhouse gases. Another research question, based on having the microbial populations close to both the water table and the river, is how they impact carbon, nitrogen and sulfur cycles. Her project is part of the first coordinated attempt to quantify the metabolic potential of an entire subsurface ecosystem under the aegis of the Lawrence Berkeley National Laboratory’s Subsurface Biogeochemistry Scientific Focus Area.

Banfield also successfully competed for a second CSP project to characterize the tree-root microbial interactions that occur below the soil mantle in the unsaturated zone or vadose zone, which extends into unweathered bedrock. The project’s goal is to understand how microbial communities this deep underground influence tree-based carbon fixation in forested watersheds by the Eel River in northwestern California.

Several fungal projects were selected for the 2015 CSP portfolio, including one led by Kabir Peay of Stanford University. He and his colleagues will study how fungal communities in animal feces decompose organic matter. His project has a stated end goal of developing a model system that emulates the ecosystem at Point Reyes National Seashore, where Tule elk are the largest native herbivores.

Another selected fungal project comes from Timothy James of University of Michigan, who will explore the so-called “dark matter fungi” – those not represented in culture collections. By sequencing several dozen species of unculturable zoosporic fungi from freshwater, soils and animal feces, he and his colleagues hope to develop a kingdom-wide fungal phylogenetic framework.

Christian Wurzbacher of Germany’s the Leibniz Institute of Freshwater Ecology and Inland Fisheries, IGB, will characterize fungi from the deep sea to peatlands to freshwater streams to understand the potentially novel adaptations that are necessary to thrive in their aquatic environments. The genomic information would provide information on their metabolic capabilities for breaking down cellulose, lignin and other plant cell wall components, and animal polymers such as keratin and chitin.

Many of the selected projects focus on DOE JGI Flagship Plant Genomes, with most centered on the poplar (Populus trichocarpa.) For example, longtime DOE JGI collaborator Steve DiFazio of West Virginia University is interested in poplar but will study its reproductive development with the help of a close relative, the willow (Salix purpurea). With its shorter generation time, the plant is a good model system and comparator for understanding sex determination, which can help bioenergy crop breeders by, for example, either accelerating or preventing flowering.

Another project comes from Posy Busby of the University of Washington, who will study the interactions between the poplar tree and its fungal, non-pathogenic symbionts or endophytes. As disease-causing pathogens interact with endophytes in leaves, he noted in his proposal, understanding the roles and functions of endophytes could prove useful to meeting future fuel and food requirements.

Along the lines of poplar endophytes, Carolin Frank at UC Merced will investigate the nitrogen-fixing endophytes in poplar, willow, and pine, with the aim of improving growth in grasses and agricultural crops under nutrient-poor conditions.

Rotem Sorek from the Weizmann Institute of Science in Israel takes a different approach starting from the hypothesis that poplar trees have an adaptive immunity system rooted in genome-encoded immune memory. Through deep sequencing of tissues from single poplar trees (some over a century old, others younger) his team hopes to gain insights into the tree genome’s short-term evolution and how its gene expression profiles change over time, as well as to predict how trees might respond under various climate change scenarios.

Tackling a different DOE JGI Flagship Plant Genome, Debbie Laudencia-Chingcuangco of the USDA-ARS will develop a genome-wide collection of several thousand mutants of the model grass Brachypodium distachyon to help domesticate the grasses that are being considered as candidate bioenergy feedstocks. This work is being done in collaboration with researchers at the Great Lakes Bioenergy Research Center, as the team there considers Brachypodium “critical to achieving its mission of developing productive energy crops that can be easily processed into fuels.”

Continuing the theme of candidate bioenergy grasses, Kankshita Swaminathan from the University of Illinois will study gene expression in polyploidy grasses Miscanthus and sugarcane, comparing them against the closely related diploid grass sorghum to understand how these plants recycle nutrients.

Baohong Zhang of East Carolina University also focused on a bioenergy grass, and his project will look at the microRNAs in switchgrass. These regulatory molecules are each just a couple dozen nucleotides in length and can downregulate (decrease the quantity of) a cellular component. With a library of these small transcripts, he and his team hope to identify the gene expression variation associated with desirable biofuel traits in switchgrass such as increased biomass and responses to drought and salinity stressors.

Nitin Baliga of the Institute of Systems Biology will use DOE JGI genome sequences to build a working model of the networks that regulate lipid accumulation in Chlamydomonas reinhardtii, still another DOE JGI Plant Flagship Genome and a model for characterizing biofuel production by algae.

Other accepted projects include:

The study of the genomes of 32 fungi of the Agaricales order, including 16 fungi to be sequenced for the first time, will be carried out by Jose Maria Barrasa of Spain’s University of Alcala. While many of the basidiomycete fungi involved in wood degradation that have been sequenced are from the Polyporales, he noted in his proposal, many of the fungi involved in breaking down leaf litter and buried wood are from the order Agaricales.

Now at the University of Connecticut, Jonathan Klassen conducted postdoctoral studies at GLBRC researcher Cameron Currie’s lab at University of Wisconsin-Madison. His project will study interactions in ant-microbial community fungus gardens in three states to learn more about how the associated bacterial metagenomes contribute to carbon and nitrogen cycling.

Hinsby Cadillo-Quiroz, at Arizona State University, will conduct a study of the microbial communities in the Amazon peatlands to understand their roles in both emitting greenhouse gases and in storing and cycling carbon. The peatlands are hotspots of soil organic carbon accumulation, and in the tropical regions, they are estimated to hold between 11 percent and 14 percent, or nearly 90 gigatons, of the global carbon stored in soils.

Barbara Campbell, Clemson University will study carbon cycling mechanisms of active bacteria and associated viruses in the freshwater to marine transition zone of the Delaware Bay. Understanding the microbes’ metabolism would help researchers understand they capabilities with regard to dealing with contaminants, and their roles in the nitrogen, sulfur and carbon cycles.

Jim Fredrickson of Pacific Northwest National Laboratory will characterize functional profiles of microbial mats in California, Washington and Yellowstone National Park to understand various functions such as how they produce hydrogen and methane, and break down cellulose.

Joyce Loper of USDA-ARS will carry out a comparative analysis of all Pseudomonas bacteria getting from DOE JGI the sequences of just over 100 type strains to infer a evolutionary history of the this genus — a phylogeny — to characterize the genomic diversity, and determine the distribution of genes linked to key observable traits in this non-uniform group of bacteria.

Holly Simon of Oregon Health & Science University is studying microbial populations in the Columbia River estuary, in part to learn how they enhance greenhouse gas CO2 methane and nitrous oxide production.

Michael Thon from Spain’s University of Salamanca will explore sequences of strains of the Colletotrichum species complex, which include fungal pathogens that infect many crops. One of the questions he and his team will ask is how these fungal strains have adapted to break down the range of plant cell wall compositions.

Kathleen Treseder of UC Irvine will study genes involved in sensitivity to higher temperatures in fungi from a warming experiment in an Alaskan boreal forest. The team’s plan is to fold the genomic information gained into a trait-based ecosystem model called DEMENT to predict carbon dioxide emissions under global warming.

Mary Wildermuth of UC Berkeley will study nearly a dozen genomes of powdery mildew fungi, including three that infect designated bioenergy crops. The project will identify the mechanisms by which the fungi successfully infect plants, information that could lead to the development of crops with improved resistance to fungal infection and limiting fungicide use to allow more sustainable agricultural practices.

Several researchers who have previously collaborated with the DOE JGI have new projects:

Ludmila Chistoserdova from the University of Washington had a pioneering collaboration with the DOE JGI to study microbial communities in Lake Washington. In her new project, she and her team will look at the microbes in the Lake Washington sediment to understand their role in metabolizing the potent greenhouse gas methane.

Rick Cavicchioli of Australia’s University of New South Wales will track how microbial communities change throughout a complete annual cycle in three millennia-old Antarctic lakes and a near-shore marine site. By establishing what the microbes do in different seasons, he noted in his proposal, he and his colleagues hope to learn which microbial processes change and about the factors that control the evolution and speciation of marine-derived communities in cold environments.

With samples collected from surface waters down to the deep ocean, Steve Hallam from Canada’s University of British Columbia will explore metabolic pathways and compounds involved in marine carbon cycling processes to understand how carbon is regulated in the oceans.

The project of Hans-Peter Klenk, of DSMZ in Germany, will generate sequences of 1,000 strains of Actinobacteria, which represent the third most populated bacterial phylum and look for genes that encode cellulose-degrading enzymes or enzymes involved in synthesizing novel, natural products.

Han Wosten of the Netherlands’ Utrecht University will carry out a functional genomics approach to wood degradation by looking at Agaricomycetes, in particular the model white rot fungus Schizophyllum commune and the more potent wood-degrading white rots Phanaerochaete chrysosporium and Pleurotus ostreatus that the DOE JGI has previously sequenced.

Wen-Tso Liu of the University of Illinois and his colleagues want to understand the microbial ecology in anaerobic digesters, key components of the wastewater treatment process. They will study microbial communities in anaerobic digesters from the United States, East Asia and Europe to understand the composition and function of the microbes as they are harnessed for this low-cost municipal wastewater strategy efficiently removes waster and produces methane as a sustainable energy source.

Another project that involves wastewater, albeit indirectly, comes from Erica Young of the University of Wisconsin. She has been studying algae grown in wastewater to track how they use nitrogen and phosphorus, and how cellulose and lipids are produced. Her CSP project will characterize the relationship between the algae and the bacteria that help stabilize these algal communities, particularly the diversity of the bacterial community and the pathways and interactions involved in nutrient uptake and carbon sequestration.

Previous CSP projects and other DOE JGI collaborations are highlighted in some of the DOE JGI Annual User Meeting talks that can be seen here: http://usermeeting.jgi.doe.gov/past-speakers/. The 10th Annual Genomics of Energy and Environment Meeting will be held March 24-26, 2015 in Walnut Creek, Calif. A preliminary speakers list is posted here (http://usermeeting.jgi.doe.gov/) and registration will be opened in the first week of November.

The Atlantic Ocean dances with the sun and volcanoes

Imagine a ballroom in which two dancers apparently keep in time to their own individual rhythm. The two partners suddenly find themselves moving to the same rhythm and, after a closer look, it is clear to see which one is leading.

It was an image like this that researchers at Aarhus University were able to see when they compared studies of solar energy release and volcanic activity during the last 450 years, with reconstructions of ocean temperature fluctuations during the same period.

The results actually showed that during the last approximately 250 years – since the period known as the Little Ice Age – a clear correlation can be seen where the external forces, i.e. the Sun’s energy cycle and the impact of volcanic eruptions, are accompanied by a corresponding temperature fluctuation with a time lag of about five years.

In the previous two centuries, i.e. during the Little Ice Age, the link was not as strong, and the temperature of the Atlantic Ocean appears to have followed its own rhythm to a greater extent.

The results were recently published in the scientific journal Nature Communications.

In addition to filling in yet another piece of the puzzle associated with understanding the complex interaction of the natural forces that control the climate, the Danish researchers paved the way for linking the two competing interpretations of the origin of the oscillation phenomenon.

Temperature fluctuations discovered around the turn of the millennium

The climate is defined on the basis of data including mean temperature values recorded over a period of thirty years. Northern Europe thus has a warm and humid climate compared with other regions on the same latitudes. This is due to the North Atlantic Drift (often referred to as the Gulf Stream), an ocean current that transports relatively warm water from the south-west part of the North Atlantic to the sea off the coast of Northern Europe.

Around the turn of the millennium, however, climate researchers became aware that the average temperature of the Atlantic Ocean was not entirely stable, but actually fluctuated at the same rate throughout the North Atlantic. This phenomenon is called the Atlantic Multidecadal Oscillation (AMO), which consists of relatively warm periods lasting thirty to forty years being replaced by cool periods of the same duration.

The researchers were able to read small systematic variations in the water temperature in the North Atlantic in measurements taken by ships during the last 140 years.

Although the temperature fluctuations are small – less than 1°C – there is a general consensus among climate researchers that the AMO phenomenon has had a major impact on the climate in the area around the North Atlantic for thousands of years, but until now there has been doubt about what could cause this slow rhythm in the temperature of the Atlantic Ocean. One model explains the phenomenon as internal variability in the ocean circulation – somewhat like a bathtub sloshing water around in its own rhythm. Another model explains the AMO as being driven by fluctuations in the amount of solar energy received by the Earth, and as being affected by small changes in the energy radiated by the Sun itself and the after-effects of volcanic eruptions. Both these factors are also known as ‘external forces’ that have an impact on the Earth’s radiation balance.

However, there has been considerable scepticism towards the idea that a phenomenon such as an AMO could be driven by external forces at all – a scepticism that the Aarhus researchers now demonstrate as unfounded.

“Our new investigations clearly show that, since the Little Ice Age, there has been a correlation between the known external forces and the temperature fluctuations in the ocean that help control our climate. At the same time, however, the results also show that this can’t be the only driving force behind the AMO, and the explanation must therefore be found in a complex interaction between a number of mechanisms. It should also be pointed out that these fluctuations occur on the basis of evenly increasing ocean temperatures during the last approximately fifty years – an increase connected with global warming,” says Associate Professor Mads Faurschou Knudsen, Department of Geoscience, Aarhus University, who is the main author of the article.

Convincing data from the Earth’s own archives

Researchers have attempted to make computer simulations of the phenomenon ever since the discovery of the AMO, partly to enable a better understanding of the underlying mechanism. However, it is difficult for the computer models to reproduce the actual AMO signal that can be read in the temperature data from the last 140 years.

Associate Professor Knudsen and his colleagues instead combined all available data from the Earth’s own archives, i.e. previous studies of items such as radioactive isotopes and volcanic ash in ice cores. This provides information about solar energy release and volcanic activity during the last 450 years, and the researchers compared the data with reconstructions of the AMO’s temperature rhythm during the same period.

“We’ve only got direct measurements of the Atlantic Ocean temperature for the last 140 years, where it was measured by ships. But how do you measure the water temperature further back in time? Studies of growth rings in trees from the entire North Atlantic region come into the picture here, where ‘good’ and ‘bad’ growth conditions are calibrated to the actual measurements, and the growth rings from trees along the coasts further back in time can therefore act as reserve thermometers,” explains Associate Professor Knudsen.

The results provide a new and very important perspective on the AMO phenomenon because they are based on data and not computer models, which are inherently incomplete. The problem is that the models do not completely describe all the physical correlations and feedbacks in the system, partly because these are not fully understood. And when the models are thus unable to reproduce the actual AMO signal, it is hard to know whether they have captured the essence of the AMO phenomenon.

Impact of the sun and volcanoes

An attempt to simply explain how external forces such as the Sun and volcanoes can control the climate could sound like this: a stronger Sun heats up the ocean, while the ash from volcanic eruptions shields the Sun and cools down the ocean. However, it is hardly as simple as that.

“Fluctuations in ocean temperature have a time lag of about five years in relation to the peaks we can read in the external forces. However, the direct effect of major volcanic eruptions is clearly seen as early as the same year in the mean global atmospheric temperature, i.e. a much shorter delay. The effect we studied is more complex, and it takes time for this effect to spread to the ocean currents,” explains Associate Professor Knudsen.

“An interesting new theory among solar researchers and meteorologists is that the Sun can control climate variations via the very large variations in UV radiation, which are partly seen in connection with changes in sunspot activity during the Sun’s eleven-year cycle. UV radiation heats the stratosphere in particular via increased production of ozone, which can have an impact on wind systems and thereby indirectly on the global ocean currents as well,” says Associate Professor Knudsen. However, he emphasises that researchers have not yet completely understood how a development in the stratosphere can affect the ocean currents on Earth.

Towards a better understanding of the climate

“In our previous study of the climate in the North Atlantic region during the last 8,000 years, we were able to show that the temperature of the Atlantic Ocean was presumably not controlled by the Sun’s activity. Here the temperature fluctuated in its own rhythm for long intervals, with warm and cold periods lasting 25 years. The prevailing pattern was that this climate fluctuation in the ocean was approximately 30󈞔% faster than the fluctuation we’d previously observed in solar activity, which lasted about ninety years. What we can now see is that the Atlantic Ocean would like to – or possibly even prefer to – dance alone. However, under certain circumstances, the external forces interrupt the ocean’s own rhythm and take over the lead, which has been the case during the last 250 years,” says Associate Professor Bo Holm Jacobsen, Department of Geoscience, Aarhus University, who is the co-author of the article.

“It’ll be interesting to see how long the Atlantic Ocean allows itself to be led in this dance. The scientific challenge partly lies in understanding the overall conditions under which the AMO phenomenon is sensitive to fluctuations in solar activity and volcanic eruptions,” he continues.

“During the last century, the AMO has had a strong bearing on significant weather phenomena such as hurricane frequency and droughts – with considerable economic and human consequences. A better understanding of this phenomenon is therefore an important step for efforts to deal with and mitigate the impact of climate variations,” Associate Professor Knudsen concludes.

Rainforests in Far East shaped by humans for the last 11,000 years

New research from Queen’s University Belfast shows that the tropical forests of South East Asia have been shaped by humans for the last 11,000 years.

The rain forests of Borneo, Sumatra, Java, Thailand and Vietnam were previously thought to have been largely unaffected by humans, but the latest research from Queen’s Palaeoecologist Dr Chris Hunt suggests otherwise.

A major analysis of vegetation histories across the three islands and the SE Asian mainland has revealed a pattern of repeated disturbance of vegetation since the end of the last ice age approximately 11,000 years ago.

The research, which was funded by the Arts and Humanities Research Council and the British Academy, is being published in the Journal of Archaeological Science. It is the culmination of almost 15 years of field work by Dr Hunt, involving the collection of pollen samples across the region, and a major review of existing palaeoecology research, which was completed in partnership with Dr Ryan Rabett from Cambridge University.

Evidence of human activity in rainforests is extremely difficult to find and traditional archaeological methods of locating and excavating sites are extremely difficult in the dense forests. Pollen samples, however, are now unlocking some of the region’s historical secrets.

Dr Hunt, who is Director of Research on Environmental Change at Queen’s School of Geography, Archaeology and Palaeoecology, said: “It has long been believed that the rainforests of the Far East were virgin wildernesses, where human impact has been minimal. Our findings, however, indicate a history of disturbances to vegetation. While it could be tempting to blame these disturbances on climate change, that is not the case as they do not coincide with any known periods of climate change. Rather, these vegetation changes have been brought about by the actions of people.

“There is evidence that humans in the Kelabit Highlands of Borneo burned fires to clear the land for planting food-bearing plants. Pollen samples from around 6,500 years ago contain abundant charcoal, indicating the occurrence of fire. However, while naturally occurring or accidental fires would usually be followed by specific weeds and trees that flourish in charred ground, we found evidence that this particular fire was followed by the growth of fruit trees. This indicates that the people who inhabited the land intentionally cleared it of forest vegetation and planted sources of food in its place.

“One of the major indicators of human action in the rainforest is the sheer prevalence of fast-growing ‘weed’ trees such as Macaranga, Celtis and Trema. Modern ecological studies show that they quickly follow burning and disturbance of forests in the region.

“Nearer to the Borneo coastline, the New Guinea Sago Palm first appeared over 10,000 years ago. This would have involved a voyage of more than 2,200km from its native New Guinea, and its arrival on the island is consistent with other known maritime voyages in the region at that time – evidence that people imported the Sago seeds and planted them.”

The findings have huge importance for ecological studies or rainforests as the historical role of people in managing the forest vegetation has rarely been considered. It could also have an impact on rainforest peoples fighting the advance of logging companies.

Dr Hunt continued: “Laws in several countries in South East Asia do not recognise the rights of indigenous forest dwellers on the grounds that they are nomads who leave no permanent mark on the landscape. Given that we can now demonstrate their active management of the forests for more than 11,000 years, these people have a new argument in their case against eviction.”

Gold mining ravages Peru

The Carnegie Airborne Observatory flies over the Madre De Dios region of Peru, where vast deforested and polluted areas result from gold mining. -  Image courtesy Carnegie Airborne Observatory
The Carnegie Airborne Observatory flies over the Madre De Dios region of Peru, where vast deforested and polluted areas result from gold mining. – Image courtesy Carnegie Airborne Observatory

For the first time, researchers have been able to map the true extent of gold mining in the biologically diverse region of Madre De Dios in the Peruvian Amazon. The team combined field surveys with airborne mapping and high-resolution satellite monitoring to show that the geographic extent of mining has increased 400% from 1999 to 2012 and that the average annual rate of forest loss has tripled since the Great Recession of 2008. Until this study, thousands of small, clandestine mines that have boomed since the economic crisis have gone unmonitored. The research is published in the online early edition of the Proceedings of the National Academy of Sciences the week of October 28, 2013.

The team, led by Carnegie’s Greg Asner in close collaboration with officials from the Peruvian Ministry of Environment, used the Carnegie Landsat Analysis System-lite (CLASlite) to detect and map both large and small mining operations. CLASlite differs from other satellite mapping methods. It uses algorithms to detect changes to the forest in areas as small as 10 square meters, about 100 square feet, allowing scientists to find small-scale disturbances that cannot be detected by traditional satellite methods.

The team corroborated the satellite results with on-ground field surveys and Carnegie Airborne Observatory (CAO) data. The CAO uses Light Detection and Ranging (LiDAR), a technology that sweeps laser light across the vegetation canopy to image it in 3-D. It can determine the location of single standing trees at 3.5 feet (1.1 meter) resolution. This level of detail was used to assess how well CLASlite determined forest conditions in the mining areas. The CAO data were also used to evaluate the accuracy of the CLASlite maps along the edges of large mines, as well as the inaccessible small mines that are set back from roads and rivers to avoid detection. The field and CAO data confirmed up to 94% of the CLASlite mine detections.

Lead author Asner commented: “Our results reveal far more rainforest damage than previously reported by the government, NGOs, or other researchers. In all, we found that the rate of forest loss from gold mining accelerated from 5,350 acres (2,166 hectares) per year before 2008 to15,180 acres (6,145 hectares) each year after the 2008 global financial crisis that rocketed gold prices.”

In addition to wreaking direct havoc on tropical forests, gold mining releases sediment into rivers, with severe effects on aquatic life. Other recent work has shown that Perú’s gold mining has contributed to widespread mercury pollution affecting the entire food chain, including the food ingested by people throughout the region. Miners also hunt wild game, depleting the rainforest fauna around mining areas, and disrupting the ecological balance for centuries to come.

Co-author Ernesto Raez Luna, Senior Advisor to the Minister, Peruvian Ministry of the Environment, remarked: “Obtaining good information on illegal gold mining, to guide sound policy and enforcement decisions, has been particularly difficult so far. Finally, we have very detailed and accurate data that we can turn into government action. We are using this study to warn Peruvians on the terrible impact of illegal mining in one of the most important enclaves of biodiversity in the world, a place that we have vowed, as a nation, to protect for all humanity. Nobody should buy one gram of this jungle gold. The mining must be stopped.”

As of 2012, small illicit mines accounted for more than half of all mining operations in the region. Large mines of previous focus are heavy polluters but are taking on a subordinate role to thousands of small mines in degrading the tropical forest throughout the region. This trend highlights the importance of using this newer, high-resolution monitoring system for keeping tabs on this growing cause of forest loss.

Asner emphasized: “The gold rush in Madre de Dios, Perú, exceeds the combined effects of all other causes of forest loss in the region, including from logging, ranching and agriculture. This is really important because we’re talking about a global biodiversity hotspot. The region’s incredible flora and fauna is being lost to gold fever. “

There’s gold in them thar trees

This is a eucalyptus leaf showing traces of gold. -  CSIRO
This is a eucalyptus leaf showing traces of gold. – CSIRO

Eucalyptus trees – or gum trees as they are know – are drawing up gold particles from the earth via their root system and depositing it their leaves and branches.

Scientists from CSIRO made the discovery and have published their findings in the journal Nature Communications.

“The eucalypt acts as a hydraulic pump – its roots extend tens of metres into the ground and draw up water containing the gold. As the gold is likely to be toxic to the plant, it’s moved to the leaves and branches where it can be released or shed to the ground,” CSIRO geochemist Dr Mel Lintern said.

The discovery is unlikely to start an old-time gold rush – the “nuggets” are about one-fifth the diameter of a human hair. However, it could provide a golden opportunity for mineral exploration, as the leaves or soil underneath the trees could indicate gold ore deposits buried up to tens of metres underground and under sediments that are up to 60 million years old.

“The leaves could be used in combination with other tools as a more cost effective and environmentally friendly exploration technique,” Dr Lintern said.

“By sampling and analysing vegetation for traces of minerals, we may get an idea of what’s happening below the surface without the need to drill. It’s a more targeted way of searching for minerals that reduces costs and impact on the environment.

“Eucalyptus trees are so common that this technique could be widely applied across Australia. It could also be used to find other metals such as zinc and copper.”

Using CSIRO’s Maia detector for x-ray elemental imaging at the Australian Synchrotron, the research team was able to locate and see the gold in the leaves. The Synchrotron produced images depicting the gold, which would otherwise have been untraceable.

“Our advanced x-ray imaging enabled the researchers to examine the leaves and produce clear images of the traces of gold and other metals, nestled within their structure,” principal scientist at the Australian Synchrotron Dr David Paterson said.

“Before enthusiasts rush to prospect this gold from the trees or even the leaf litter, you need to know that these are tiny nuggets, which are about one-fifth the diameter of a human hair and generally invisible by other techniques and equipment.”

CSIRO research using natural materials, such as calcrete and laterite in soils, for mineral exploration has led to many successful ore deposit discoveries in regional Australia. The outcomes of the research provide a direct boost to the national economy.

Study finds tungsten in aquifer groundwater controlled by pH, oxygen

Two Kansas geologists are helping shed new light on how tungsten metal is leached from the sediment surrounding aquifers into the groundwater. The findings may have implications for human health.

Tungsten is a naturally occurring metal that is primarily used for incandescent light bulb filaments, drill bits and an alternative to lead in bullets. Though it is thought to be nonhazardous to the environment and nontoxic to humans, it can be poisonous if ingested in large amounts. In recent years, tungsten has been tentatively linked to cases of childhood leukemia in the Western U.S.

“Very little is known about the biogeochemistry of tungsten in the environment,” said Saugata Datta, professor of geology at Kansas State University. “We need to understand how this metal is leached from the soils into groundwater because humans can be exposed to tungsten through multiple pathways.”

Datta, along with Chad Hobson, master’s student in geology, Lavonia, Ga., and colleagues at Tulane University and the University of Texas, Arlington, found that the likelihood that tungsten will seep into an aquifer’s groundwater depends on the groundwater’s pH level, the amount of oxygen in the aquifer and the number of oxidized particles in the water and sediment. Analysis also showed that tungsten-IV is the most common form of tungsten in natural sediments.

These latest findings appear in the study “Controls on tungsten concentrations in groundwater flow systems: The role of adsorption, aquifer sediment Fe(III) oxide/oxyhydroxide content, and thiotungstate formation,” published in the journal Chemical Geology.

In addition to the publication, Datta and Hobson presented the findings at the International Conference on Biogeochemistry of Trace Elements.

For the study, researchers looked at Fallon, Nev.; Sierra Vista, Ariz.; and at the Cheyenne Bottoms Refuge near Hoisington, Kan. The sites were chosen based on previous studies analyzing plants and dust collected on trees in the locations. Additionally, these areas have natural tungsten mineral deposits, nearby military bases, and mining and smelting operations in the area, Datta said.

In 2002, the Centers for Disease Control investigated several clusters of acute lymphatic leukemia in both Nevada and Arizona. The investigation found that residents’ urine had tungsten levels above the 95th percentile.

“This was important for us to know because the goal is to clarify valuable information about tungsten’s geochemistry,” Datta said. “So, we needed sites that had tungsten — and enough tungsten to measure easily. The benefit of this study is that tungsten’s geochemistry has been overlooked and until recently, largely unknown. This work will help fill the gaps in the knowledge of tungsten, which is possibly carcinogenic, and help determine its future use.”

Datta and Hobson analyzed sediment samples lining the aquifers while researchers at Tulane University and the University of Texas, Arlington analyzed the groundwater samples. The National Synchrotron Light Source was used for spectroscopic analysis of the individual particles. This helped researchers understand the speciation of tungsten in natural sediments in the environment and helped them detect why tungsten forms organosulphur complexes that can be soluble in groundwater, Datta said. Analysis also showed that tungsten-VI is the most common form of tungsten in natural sediments.

Analysis of the sediment and groundwater showed that iron oxide and oxyhydroxide particles in both substances play a key role in regulating how much tungsten is in the groundwater. The fewer iron oxides or oxyhydroxide particles, the higher the amount of tungsten, Datta said.

Similarly, the team found that the number of tungsten-regulating iron oxide particles is controlled by the pH in the groundwater. A higher pH results in more tungsten entering the water.

“Tungsten is specifically bound to these iron oxides and oxyhydroxides,” Datta said. “One of the major factors controlling tungsten’s mobility and bioavailability is pH. Ranging values of pH can affect how tungsten behaves or transforms between different tungsten species, which have different properties and factors controlling mobility.”

When tungsten is in the water it is surrounded by oxygen atoms and forms an anion, Datta said. When in the presence of phosphates, this anion tends to bind with other transition metals, commonly iron, to form poloyoxometalates. In this form, tungsten can become more soluble in water.

Researchers also found that aquifers with less dissolved oxygen had greater traces of tungsten in the groundwater than aquifers with high dissolved oxygen levels.

The process of tungsten being leached from the surrounding sediment into the groundwater can be reduced if the ironoxides are in the water and the water has a neutral pH level, according to Datta.

The study is part of a three-year, $515,000 National Science Foundation-funded project between Kansas State University and Karen Johannesson at Tulane University that is titled “Collaborative Research: Chemical Hydrogeologic Investigations of Tungsten: Field, Laboratory, and Modeling Studies of an Emerging Environmental Contaminant.” It focuses on biogeochemistry of tungsten’s reaction to the environment and how it is transported from sediments into groundwaters once it becomes geochemically mobilized.

Rising mountains, cooling oceans prompted spread of invasive species 450 million years ago

This slab of rock contains fossils of invasive species that populated the continent of Laurentia 450 million years ago after a major ecological shift occurred. Ohio University geologists found that rising mountains and cooling oceans prompted the spread of these invasive species. -  Alycia Stigall
This slab of rock contains fossils of invasive species that populated the continent of Laurentia 450 million years ago after a major ecological shift occurred. Ohio University geologists found that rising mountains and cooling oceans prompted the spread of these invasive species. – Alycia Stigall

New Ohio University research suggests that the rise of an early phase of the Appalachian Mountains and cooling oceans allowed invasive species to upset the North American ecosystem 450 million years ago.

The study, published recently in the journal PLOS ONE, took a closer look at a dramatic ecological shift captured in the fossil record during the Ordovician period. Ohio University scientists argue that major geological developments triggered evolutionary changes in the ancient seas, which were dominated by organisms such as brachiopods, corals, trilobites and crinoids.

During this period, North America was part of an ancient continent called Laurentia that sat near the equator and had a tropical climate. Shifting of the Earth’s tectonic plates gave rise to the Taconic Mountains, which were forerunners of the Appalachian Mountains. The geological shift left a depression behind the mountain range, flooding the area with cool water from the surrounding deep ocean.

Scientists knew that there was a massive influx of invasive species into this ocean basin during this time period, but didn’t know where the invaders came from or how they got a foothold in the ecosystem, said Alycia Stigall, an Ohio University associate professor of geological sciences who co-authored the paper with former Ohio University graduate student David Wright, now a doctoral student at Ohio State University.

“The rocks of this time record a major oceanographic shift, pulse of mountain building and a change in evolutionary dynamics coincident with each other,” Stigall said. “We are interested in examining the interactions between these factors.”

Using the fossils of 53 species of brachiopods that dominated the Laurentian ecosystem, Stigall and Wright created several phylogenies, or trees of reconstructed evolutionary relationships, to examine how individual speciation events occurred.

The invaders that proliferated during this time period were species within the groups of animals that inhabited Laurentia, Stigall explained. Within the brachiopods, corals and cephalopods, for example, some species are invasive and some are not.

As the geological changes slowly played out over the course of a million years, two patterns of survival emerged, the scientists report.

During the early stage of mountain building and ocean cooling, the native organisms became geographically divided, slowly evolving into different species suited for these niche habitats. This process, called vicariance, is the typical method by which new species originate on Earth, Stigall said.

As the geological changes progressed, however, species from other regions of the continent began to directly invade habitats, a process called dispersal. Although biodiversity may initially increase, this process decreases biodiversity in the long term, Stigall explained, because it allows a few aggressive species to populate many sites quickly, dominating those ecosystems.

This is the second time that Stigall and her team have found this pattern of speciation in the geological record. A study published in 2010 on the invasive species that prompted a mass extinction during the Devonian period about 375 million years ago also discovered a shift from vicariance to dispersal that contributed to a decline in biodiversity, Stigall noted.

It’s a pattern that’s happening during our modern biodiversity crisis as well, she said.

“Only one out of 10 invaders truly become invasive species. Understanding the process can help determine where to put conservation resources,” she said.

Ice-free Arctic winters could explain amplified warming during Pliocene

Year-round ice-free conditions across the surface of the Arctic Ocean could explain why the Earth was substantially warmer during the Pliocene Epoch than it is today, despite similar concentrations of carbon dioxide in the atmosphere, according to new research carried out at the University of Colorado Boulder.

In early May, instruments at the Mauna Loa Observatory in Hawaii marked a new record: The concentration of carbon dioxide climbed to 400 parts per million for the first time in modern history.

The last time researchers believe the carbon dioxide concentration in the atmosphere reached 400 ppm-between 3 and 5 million years ago during the Pliocene-the Earth was about 3.5 to 9 degrees Fahrenheit warmer (2 to 5 degrees Celsius) than it is today. During that time period, trees overtook the tundra, sprouting right to the edges of the Arctic Ocean, and the seas swelled, pushing ocean levels 65 to 80 feet higher.

Scientists’ understanding of the climate during the Pliocene has largely been pieced together from fossil records preserved in sediments deposited beneath lakes and on the ocean floor.

“When we put 400 ppm carbon dioxide into a model, we don’t get as warm a planet as we see when we look at paleorecords from the Pliocene,” said Jim White, director of CU-Boulder’s Institute of Arctic and Alpine Research and co-author of the new study published online in the journal Palaeogeography, Paleoclimatology, Palaeoecology. “That tells us that there may be something missing in the climate models.”

Scientists have proposed several hypotheses in the past to explain the warmer Pliocene climate. One idea, for example, was that the formation of the Isthmus of Panama, the narrow strip of land linking North and South America, could have altered ocean circulations during the Pliocene, forcing warmer waters toward the Arctic. But many of those hypotheses, including the Panama possibility, have not proved viable.

For the new study, led by Ashley Ballantyne, a former CU-Boulder doctoral student who is now an assistant professor of bioclimatology at the University of Montana, the research team decided to see what would happen if they forced the model to assume that the Arctic was free of ice in the winter as well as the summer during the Pliocene. Without these additional parameters, climate models set to emulate atmospheric conditions during the Pliocene show ice-free summers followed by a layer of ice reforming during the sunless winters.

“We tried a simple experiment in which we said, ‘We don’t know why sea ice might be gone all year round, but let’s just make it go away,’ ” said White, who also is a professor of geological sciences. “And what we found was that we got the right kind of temperature change and we got a dampened seasonal cycle, both of which are things we think we see in the Pliocene.”

In the model simulation, year-round ice-free conditions caused warmer conditions in the Arctic because the open water surface allowed for evaporation. Evaporation requires energy, and the water vapor then stored that energy as heat in the atmosphere. The water vapor also created clouds, which trapped heat near the planet’s surface.

“Basically, when you take away the sea ice, the Arctic Ocean responds by creating a blanket of water vapor and clouds that keeps the Arctic warmer,” White said.

White and his colleagues are now trying to understand what types of conditions could bridge the standard model simulations with the simulations in which ice-free conditions in the Arctic are imposed. If they’re successful, computer models would be able to model the transition between a time when ice reformed in the winter to a time when the ocean remained devoid of ice throughout the year.

Such a model also would offer insight into what could happen in our future. Currently, about 70 percent of sea ice disappears during the summertime before reforming in the winter.

“We’re trying to understand what happened in the past but with a very keen eye to the future and the present,” White said. “The piece that we’re looking at in the future is what is going to happen as the Arctic Ocean warms up and becomes more ice-free in the summertime.

“Will we continue to return to an ice-covered Arctic in the wintertime? Or will we start to see some of the feedbacks that now aren’t very well represented in our climate models? If we do, that’s a big game changer.”

Cracking the ice code

UWM geosciences professor John Isbell (left) and postdoctoral researcher Erik Gulbranson, University of Wisconsin, Milwaukee, look over some of the many samples they have brought back from Antarctica. The two are part of an international team of scientists investigating the last extreme climate shift on Earth, which occurred in the late Paleozoic Era. -  Troye Fox
UWM geosciences professor John Isbell (left) and postdoctoral researcher Erik Gulbranson, University of Wisconsin, Milwaukee, look over some of the many samples they have brought back from Antarctica. The two are part of an international team of scientists investigating the last extreme climate shift on Earth, which occurred in the late Paleozoic Era. – Troye Fox

What happened the last time a vegetated Earth shifted from an extremely cold climate to desert-like conditions? And what does it tell us about climate change today?

John Isbell is on a quest to coax that information from the geology of the southernmost portions of the Earth. It won’t be easy, because the last transition from “icehouse to greenhouse” occurred between 335 and 290 million years ago.

An expert in glaciation from the late Paleozoic Era, Isbell is challenging many assumptions about the way drastic climate change naturally unfolds. The research helps form the all-important baseline needed to predict what the added effects of human activity will bring.

Starting from ‘deep freeze’

In the late Paleozoic, the modern continents were fused together into two huge land masses, with what is now the Southern Hemisphere, including Antarctica, called Gondwana.

During the span of more than 60 million years, Gondwana shifted from a state of deep freeze into one so hot and dry it supported the appearance of reptiles. The change, however, didn’t happen uniformly, Isbell says.

In fact, his research has shaken the common belief that Gondwana was covered by one massive sheet of ice which gradually and steadily melted away as conditions warmed.

Isbell has found that at least 22 individual ice sheets were located in various places over the region. And the state of glaciation during the long warming period was marked by dramatic swings in temperature and atmospheric carbon dioxide (CO2) levels.

“There appears to be a direct association between low CO2 levels and glaciation,” he says. “A lot of the changes in greenhouse gases and in a shrinking ice volume then are similar to what we’re seeing today.”

When the ice finally started disappearing, he says, it did so in the polar regions first and lingered in other parts of Gondwana with higher elevations. He attributes that to different conditions across Gondwana, such as mountain-building events, which would have preserved glaciers longer.

All about the carbon

To get an accurate picture of the range of conditions in the late Paleozoic, Isbell has traveled to Antarctica 16 times and has joined colleagues from around the world as part of an interdisciplinary team funded by the National Science Foundation. They have regularly gone to places where no one has ever walked on the rocks before.

One of his colleagues is paleoecologist Erik Gulbranson, who studies plant communities from the tail end of the Paleozoic and how they evolved in concert with the climatic changes. The information contained in fossil soil and plants, he says, can reveal a lot about carbon cycling, which is so central for applying the work to climate change today.

Documenting the particulars of how the carbon cycle behaved so long ago will allow them to answer questions like, ‘What was the main force behind glaciation during the late Paleozoic? Was it mountain-building or climate change?’

Another characteristic of the late Paleozoic shift is that once the climate warmed significantly and atmospheric CO2 levels soared, the Earth’s climate remained hot and dry for another 200 million years.

“These natural cycles are very long, and that’s an important difference with what we’re seeing with the contemporary global climate change,” says Gulbranson. “Today, we’re seeing change in greenhouse gas concentrations of CO2 on the order of centuries and decades.”

Ancient trees and soil

In order to explain today’s accelerated warming, Gulbranson’s research illustrates that glaciers alone don’t tell the whole story.

Many environmental factors leave an imprint on the carbon contained in tree trunks from this period. One of the things Gulbranson hypothesizes from his research in Antarctica is that an increase in deciduous trees occurred in higher latitudes during the late Paleozoic, driven by higher temperatures.

What he doesn’t yet know is what the net effect was on the carbon cycle.

While trees soak in CO2 and give off oxygen, there are other environmental processes to consider, says Gulbranson. For example, CO2 emissions also come from soil as microbes speed up their consumption of organic matter with rising temperatures.

“The high latitudes today contain the largest amount of carbon locked up as organic material and permafrost soils on Earth today,” he says. “It actually exceeds the amount of carbon you can measure in the rain forests. So what happens to that stockpile of carbon when you warm it and grow a forest over it is completely unknown.”

Another unknown is whether the Northern Hemisphere during this time was also glaciated and warming. The pair are about to find out. With UWM backing, they will do field work in northeastern Russia this summer to study glacial deposits from the late Paleozoic.

The two scientists’ work is complementary. Dating the rock is essential to pinpointing the rate of change in the carbon cycle, which would be the warning signal we could use today to indicate that nature is becoming dangerously unbalanced.

“If we figure out what happened with the glaciers,” says Isbell, “and add it to what we know about other conditions – we will be able to unlock the answers to climate change.”