Revealing the plant genes that shaped our world

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The creation of new library of mutants of the single-celled photosynthetic green alga Chlamydomonas reinhardtii enabled a Carnegie– and Princeton University-led team of plant scientists to identify more than 300 genes that are potentially required for photosynthesis. Photosynthesis is the process by which plants, algae, and some bacteria convert energy from sunlight into carbohydrates—filling our planet’s atmosphere with oxygen as a byproduct.

Their findings are published in Nature Genetics.

Chlamydomonas represents a group of algae that are found around the globe in fresh and saltwater, moist soil, and even snow. They are photosynthetic and readily grow in the lab, even in darkness if given the right nutrients. This makes Chlamydomonas an excellent research tool for plant biologists, especially for those interested in the genetics of the photosynthetic apparatus, as well as many other aspects of plant biochemistry, such as responses to light and stress.

In this study, the research team created a library of about 80,000 Chlamydomonas mutants which they used to identify 303 genes thought to participate in photosynthesis. Of these, 65 encode proteins that were already known to play a role in photosynthesis. The remaining 238 genes had no previously known role in photosynthesis, making them targets for further research. Twenty-one of them are considered high-priorities for additional investigations.

“This work opens the door to a new understanding of the various processes associated with photosynthetic function, which are of fundamental importance to our planet’s food supply, as well as, of course, to replenishing the atmospheric oxygen that we breathe,” said Carnegie co-author Arthur Grossman.

The research team’s findings indicate that nearly half of the genes that are necessary for plants to create carbohydrates by photosynthesis have not yet been characterized.

“This is remarkable, considering that genetic research on this fundamental process began in the 1950s,” said Princeton co-author Martin Jonikas, who was formerly at Carnegie. “Our library demonstrates how much work remains to be done in revealing mechanisms underlying the biochemical process that shaped our planet’s history and created the conditions that allowed life to thrive here.”

Zhiyong Wang, Acting Director of Carnegie’s Department of Plant Biology, added: “This work really illustrates the power of using high-throughput genetic techniques to address major issues in biology.”

Read the paper: Nature Genetics

Article source: Carnegie Science

Image credit: Louisa Howard, Dartmouth College. Courtesy: National Science Foundation

Genetic diversity maps to help forests survive climate change

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Forests have a special magic for many of us. Steeped in folklore and fantasy, they are places for enchantments, mythical creatures and outlaws. But if they are to survive into the future, they may also need a helping hand from science.

Globally, forests are having a tough time. Industrial logging, wildfires and deforestation for agriculture has seen swathes of trees, and their associated habitat, destroyed.

Europe, however, is one of the few parts of the world where forested and wooded areas are actually increasing, thanks to careful forest management. The EU has around 182 million hectares of forest and other wooded land – accounting for 43% of its total land area and 5% of the world’s forests.

But the dramatic environmental changes brought by global warming are now threatening these flourishing forests. Scientists hope that by mapping the genetic diversity hidden within forests, they can identify traits to allow wooded areas to thrive under changing conditions.

‘There are concerns that climate change is happening too fast for forests to adapt to what is happening around them,’ explained Dr Barbara Vinceti, a scientist at agricultural research organisation Bioversity International, in Rome, Italy.

Pests and diseases are also a growing threat as global trade and climate change makes it easier for them to spread. The Chalara fungus, for example, has devastated up to 90% of ash trees populations in some countries in just a few years after seemingly arriving in Europe from Asia. Dutch Elm Disease, a fungus spread by elm bark beetles, caused similar destruction of elm trees across Europe in the 20th century.

‘The key is to identify and preserve the diversity we have in our forests so they can deal with future threats and risks,’ said Dr Vinceti. ‘It’s about maximising the options to meet future challenges.’

She is part of the GenTree project that is attempting to build up a record of forest genetic resources in commercially and ecologically important tree species in Europe. The idea is to use this to help inform breeding projects and forest management schemes.

Wood samples

The team have been travelling around Europe collecting wood samples from 12 different tree species at more than 120 different sites. Alongside this they are logging data about the size, shape and nutrient levels in the leaves, the quality of the wood, along with soil and water samples.

This information is being compared to the genetic information in an attempt to identify genetic adaptations or physical traits that could help tree populations deal with more extreme conditions such as drought, changing soil acidity, rising temperatures or extreme frosts. They are also looking for trees that may carry unusual levels of resistance to disease or fire resilience.

‘We are looking for genes that might be responsible for the timing of bud bursting, for example,’ said Dr Vinceti. ‘We want to look at the diversity that exists (in populations of the same species) and understand the scale. These are very complex studies and a lot of data is being gathered.’

Cuttings from trees with the right special qualities that adapt them to future conditions could then be moved to environments where these challenges are already or expected to take hold and allow them to help native forests adapt, or they could be used in breeding programmes that aim to replant entire swathes of woodland.

Among the tree species the project is looking at are the European black poplar (Populus nigra) and the Aleppo pine (Pinus halepensis) that are important for helping to maintain soil conditions and support wildlife. They are also examining commercially important varieties like the Scots Pine (Pinus sylvestris), the maritime pine (Pinus pinaster), European beech (Fagus sylvatica), and the Norway spruce (Picea abies).


The forest industry generates billions of euros of income every year. In Germany alone, forestry and logging contributed nearly €9 billion to the economy in 2015, while in France and Poland the industry contributed more than €6.5 billion and €5 billion respectively. Around half a million people are employed in the forestry and logging sector across Europe.

But it’s not all about money. As well as assisting forests to adapt to climate change, maintaining healthy forests will also help to maximise trees’ ability to pull greenhouse gases out of the air and lock it away in their tissues as they grow – a process known as carbon sequestration.

‘If we are going to start doing something in earnest about climate change, forests are expected to have a very important role in terms of carbon sequestration,’ said Professor Ljusk Ola Eriksson, an economist with the Swedish University of Agricultural Sciences (SLU).

He coordinates the ALTERFOR project, which is using computer modelling to examine how current forest management techniques in nine different European countries can be optimised to help forests not only survive the changes expected from climate change but also help to reduce its impact.

The idea is to see what might happen to a variety of different landscapes should other species of tree be planted or different forest management approaches applied under varying climate change scenarios. Solutions are likely to vary from country to country.

‘The methods in Ireland, for example, might not be applicable in somewhere like Portugal where there is a growing risk of forest fires,’ said Prof. Eriksson. He says that Portugal tends to grow a lot of eucalyptus trees, which are highly susceptible to fire and are least desirable species in terms of biodiversity, and suggests that they might need to think about using more oak, for instance, instead.

But Dr Villis Brukas, an associate professor of forest policy at SLU and ALTERFOR’s scientific coordinator, said that we shouldn’t limit forest management to the smaller groups of trees – known as stands – within woodland itself.

‘We need to scale how forests can be managed at a landscape level all the way up to whole continents,’ he said. ‘Our countries are not isolated and by working together we can make sure our forests have the best chance possible.’

Article source: Horizon Magazine

Image credit: Mehdi Pringarbe/INRA Avignon

Floodplain forests under threat: Researchers warn of the effects of summer drought and competition for ground water

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A team from the Institute of Forest Sciences at the University of Freiburg shows that the extraction of ground water for industry and households is increasingly damaging floodplain forests in Europe given the increasing intensity and length of drought periods in the summer. The scientists have published their results in the journal Frontiers in Forests and Global Change.

Floodplain forests dominated by oaks are among the most at risk in Europe. Through conversion to arable land and pastures, as well as settlements, they have lost most of their original distribution. River regulation and drainage have also changed the natural hydrologic balance. The introduction of pests and diseases decimates native tree species such as elm and ash. At the same time, these forests play an important part in the control of flooding and protection of biodiversity.

The root of the study by the Freiburg team was the observation that the vitality of old trees in the oak forests of the Rhine valley had significantly declined, and their mortality appeared to have markedly increased. Forest ecologist Prof. Dr. Jürgen Bauhus’ work group then investigated whether these trends could also be discerned from the growth patterns of trees and whether they were connected with the widespread extraction of ground water for industry and households. Pumping water can reduce the groundwater level so far that even deep-rooted oaks cannot reach it.

So the forestry scientists studied the annual growth rings of young and old trees at locations with and without noticeable extraction of ground water, in three forests of English oak in the Rhine valley, between the Freiburg Mooswald and the Hessisches Ried near Lampertheim. Their analysis of the statistical connections between the width of growth rings and climate data shows that the annual stem growth of oaks is negatively affected by summer drought. At locations with lowering of the groundwater, the sensitivity of oak growth to the summer droughts increased markedly since the start of groundwater extraction, which started 49 years ago or earlier at the different study sites. In contrast, the sensitivity of the annual ring growth remained relatively stable over time in oaks at sites without groundwater extraction. Another difference between locations with and without extraction of ground water, according to Georgios Skiadaresis, PhD student and lead author of the study, is: “Oaks with contact to groundwater can recover better in phases of favorable weather conditions, as can be seen from greater annual ring growth. But this is far less the case for oaks without contact to groundwater.” The researchers’ hypothesis that young oaks are less affected by the lowering of the groundwater, because their root system could be more adaptable than that of old oaks, was not confirmed.

The results of the study clearly show that the extraction of ground water below oak floodplain forests will worsen the negative effects of climate change. The authors indicate that adaptive strategies in other sectors, such as irrigation by agriculture, should not take place at the expense of the health of these forests. They recommend reducing rather than increasing the extraction of ground water from floodplain forests, to maintain the vitality of the trees in these ecosystems in the long term.

Read the paper: Frontiers In Forests And Global Change

Article source: University Freiburg

Image credit: Albert Reif

Algal library lends insights into genes for photosynthesis

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It isn’t easy being green. It takes thousands of genes to build the photosynthetic machinery that plants need to harness sunlight for growth. And yet, researchers don’t know exactly how these genes work.

Now a team led by Princeton University researchers has constructed a public “library” to help researchers to find out what each gene does. Using the library, the team identified 303 genes associated with photosynthesis including 21 newly discovered genes with high potential to provide new insights into this life-sustaining biological process. The study was published in Nature Genetics.

“The part of the plant responsible for photosynthesis is like a complex machine made up of many parts, and we want to understand what each part does,” said Martin Jonikas, assistant professor of molecular biology at Princeton. “This library, we hope, will be one of the foundations that people will build on to make the next generation of discoveries.”

Unlocking the role of each gene could allow researchers to engineer plants to grow more quickly, potentially meeting future world food needs. Plants could also potentially be altered to absorb more carbon dioxide, helping to address climate challenges.

The library, funded in large part through a grant from the National Science Foundation, consists of thousands of single-celled, pond-dwelling algae known as Chlamydomonas reinhardtii, or Chlamy for short. Each “book” in the library is a strain of Chlamy with a single mutation. The 62,000-plus mutant strains, housed at the University of Minnesota’s Chlamydomonas Resource Center, cover more than 80 percent of Chlamy’s genes.

Similar libraries have been made in other single-celled organisms, such as yeast, but this is the first such endeavor for any single-celled photosynthetic organism. The rapid growth of single-celled organisms make them valuable research tools.

“Because this algal species is often used as a model to understand a wider range of biological processes, this library will be an important resource,” said Karen Cone, a program director at the National Science Foundation, which was the primary funder for this research. “The partnership between the Jonikas group and the Chlamydomonas Resource Center enhances community accessibility to this valuable resource, which in turn will enable new discoveries, especially in one of NSF’s research priority areas, ‘Understanding the Rules of Life.’”

Due to various challenges inherent in Chlamy’s genome, the project took nine years to complete. Throughout the project, researchers used robots to keep generations of cells alive by changing the nutrient-rich liquid media in which the cells live.

The project started in 2010 while Jonikas and his team were at the Carnegie Institution for Science on the Stanford University campus, and was completed at Princeton where the Jonikas laboratory moved in 2016. The project was a collaboration with Arthur Grossman, a senior staff scientist at Carnegie and with the Chlamydomonas Resource Center run by Paul Lefebvre, a professor of plant and microbial biology at the University of Minnesota.

The ability to observe a Chlamy cell with just one defective gene among all the other functioning genes allows researchers to figure out what that gene does. For example, if the cell has trouble moving, then the defective gene’s function mostly likely involves governing movement.

Jonikas compared the Chlamy mutant library to a library containing thousands of copies of a manual for constructing a car, with each copy of the book missing a different section. No matter which manual was used, the resulting car would be missing a part, making it unable to operate as expected.

“The horn might not work, or the steering wheel might not turn,” Jonikas said. “Then you would know that the missing section contained the instructions for that part of the car.”

The library enables researchers to test multiple mutant Chlamy strains at once because each mutation is labeled with a unique “DNA barcode.” For the current study, investigators placed thousands of Chlamy strains in a single flask and exposed them to light. Strains that failed to grow were more likely to contain a gene involved in photosynthesis.

One of the newly identified genes is CPL3, which is thought to play a role in accumulating the protein “parts” of the photosynthetic machinery. The team is now exploring whether the gene helps the algae adjust their photosynthetic activity to changes in sunlight levels.

The mutant library can enable studies in other areas of plant biology, such as intracellular communication and Chlamy’s ability to paddle around its environment using a tail-like cilium.

Xiaobo Li, the study’s first author, was a postdoctoral researcher at Princeton when the team completed the library. “It is our hope that the Chlamydomonas mutant library and the genes identified will lead to numerous fundamental discoveries in photosynthesis, cell motility and many other processes,” Li said.

Weronika Patena, a senior bioinformatics analyst in the Jonikas laboratory, wrote computer programs to analyze large amounts of data to identify genes most likely to be involved in photosynthesis. “I believe the success of this project will greatly accelerate research into photosynthesis and other processes for which Chlamy is a good model, and provide a lot of value to the scientific community,” she said.

Read the paper: Nature Genetics

Article source: Princeton University

Image credit: Princeton University

Nitrogen Pollution’s Path to Streams Weaves through More Forests (and Faster Pace) than Suspected

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Nitrogen in rain and snow falls to the ground where, in theory, it is used by forest plants and microbes. New research by a scientific collaboration led by the USDA Forest Service shows that more nitrogen from rain and snow is making it to more streams than previously believed and flowing downstream in forests of the United States and Canada. The study, “Unprocessed atmospheric nitrate in waters of the Northern Forest Region in the USA and Canada” was published in the journal Environmental Science & Technolog.

Scientists found that some nitrate, which is a form of nitrogen that plants and microbes can use, occasionally moves too fast for biological uptake, resulting in “unprocessed” nitrate bypassing the otherwise effective filter of forest biology. The study links pollutant emissions from various and sometimes distant sources including industry, energy production, the transportation sector and agriculture to forest health and stream water quality.

“Nitrogen is critical to the biological productivity of the planet, but it becomes an ecological and aquatic pollutant when too much is present,” said Stephen Sebestyen, a research hydrologist with the USDA Forest Service’s Northern Research Station based in Grand Rapids, Minn., and the study’s lead author.

“From public land managers to woodlot owners, there is a great deal of interest in forest health and water quality. Our research identifies widespread pollutant effects, which undermines efforts to manage nitrogen pollution.”

Sebestyen and 29 co-authors completed one of the largest and longest examinations to trace unprocessed nitrate movement in forests. Scientists from several federal agencies and 12 academic institutions in the United States, Canada, and Japan collected water samples in 13 states and the province of Ontario, ultimately compiling more than 1,800 individual nitrate isotope analyses over the course of 21 years.

“We generally assumed that nitrate pollution would not travel a great distance through a forest because the landscape would serve as an effective filter,” Sebestyen said. “This study demonstrates that while we have not been wrong about that, we needed more information to be better informed.” Forests overall use most nitrate, unless rainfall and snowmelt runoff during higher flow events lead to brief, but important windows when unprocessed nitrate flows to streams; sometimes at levels that are unexpectedly high.

Too much nitrogen contributes to forest decline and growth of nuisance vegetation in lakes and ponds. Tree species have varying levels of tolerance for nitrogen. Too much nitrogen can change forest composition and provide a foothold for non-native plants. “I’m concerned with how air pollution affects forests and watersheds,” said Trent Wickman, an Air Resource Specialist with the USDA Forest Service’s Eastern Region and a co-author of the study. “There are a number of federal and state programs that aim to reduce nitrogen air pollution from vehicles and industrial sources. Understanding the fate of nitrogen that originates in the air, but ends up on land, is important to gauge the effectiveness of those pollution reduction programs.”

Sebestyen and the study’s co-authors suggest that because unprocessed nitrogen is not being filtered by natural vegetation to the extent previously believed, monitoring coupled with this baseline information is needed to give land managers a more nuanced view of forest health issues.

Read the paper: Environmental Science & Technology

Article source: USDA Forest Service – Northern Research Station)

Image credit: Stephen Sebestyen, USDA Forest Service

Pests and the plant defenses against them drive diversity in tropical rainforests

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Researchers have been baffled by tropical rainforest diversity for over a century; 650 different tree species can exist in an area covering two football fields, yet similar species never grow next to each other. It seems like it’s good to be different than your neighbors, but why?

To grow in a tropical rainforest is to engage in constant warfare. Plants battle for resources, such as sunlight, water and minerals. Similar tree species compete for resources in the same ways, so they may inhibit each other’s growth. Plants also battle against herbivore pests. Related trees share the same pests and diseases—if one gets it, the infestation can spread. Scientists have asked, “What is the primary driver in tropical forest diversity–competition for resources, or herbivore pests?”

For the first time, University of Utah biologists compared the two mechanisms in a single study.

The team analyzed how neighboring trees influence the growth and survival of nine coexisting species of the tree genus Inga in the Panama rainforest. They compared tree traits for resource acquisition, anti-herbivore defenses and the herbivores that live on the plants. They found that neighboring trees were basically the same in terms of acquiring resources, but had very different defenses and herbivores. Indeed, the defensive traits and shared pests impacted growth and survival, while resource acquisition traits had no effect on the plants’ success. These findings indicate that anything impacting pest populations, such as climate change or habitat fragmentation, will have an impact on the health of the rainforest.

“Working in these hyper-diverse tropical rainforests makes it abundantly clear just how complex the web of interacting species really is. No species or individual lives in isolation. At all levels within the food chain species are competing with one another for precious resources and contributing a huge amount of their energy to defending themselves from the barrage of enemies they face,” said Dale Forrister, doctoral candidate in the School of Biological Sciences at the University of Utah and lead author of the study. “We are excited about this study because it highlights some of the important ways these antagonistic interactions might influence tropical diversity.”

This study published in the journal Science.

It’s a jungle out there

The team conducted their analysis over five years within a 50-hectare forest plot in Barro Colorado Island, Panama. The site has growth and survival data for over 423,000 trees from a previous long-term study. The researchers analyzed every individual tree sapling from the focal Inga species and calculated the similarity of their Inga neighbors’ traits within a 10-meter “neighborhood.” They measured four resource acquisition traits, five anti-herbivore defenses and recorded which herbivores were eating which plants.

Forrister developed a complicated model to determine how neighboring trees influence sapling growth and survival. They found that resource acquisition traits had no effect on survival, while defensive traits and herbivores had a big impact.

There are only so many ways to acquire resources. Defensive traits, however, are nearly endless. Plants and herbivores are in a constant arms race to outsmart each other. Plants develop traits to deter hungry mandibles, and herbivores adapt to deal with the leaf’s defenses. The Inga genus has a quiver of anti-herbivore traits, including tiny hairs, nectar cups that attract pugnacious ant protectors, and most notably, leaves filled with poisonous compounds. Each Inga species can make hundreds or sometimes thousands of different toxins.

“People may think of a jungle like it’s a giant salad bowl. It should be paradise for pests because they’re surrounded by leaves. But plants have an infinite number of defense combinations—half the weight of a young leaf is poison,” said Phyllis Coley, Distinguished Professor of Biology at the University of Utah, research affiliate at the Smithsonian Tropical Research Institute and co-author of the study. “As a consequence of the diversity of defenses, each species of herbivore can only eat a few species of plants that they have adaptations for.”

Closely related plants have similar defensive traits, and therefore similar pests. If a plant differs from its neighbor in terms of defenses, their herbivores aren’t a threat, Coley continued. “You’ll have your own herbivores, but at least you won’t have all the critters in the neighborhood eating you.”

Confounding chemical compounds

Plant toxins are the most important weapons for tropical plants, but testing the similarity of each species’ chemicals proved problematic. Over five years, the researchers collected leaf samples in the field, dried them in a makeshift desiccator suitcase (no easy feat in 100 percent humidity) and then brought them to the University of Utah for analysis. Using high performance liquid chromatography, they separated all of the distinct compounds inside the leaves. However, only 4 percent of the Inga compounds were known to science. So, the team got creative and came up with a new metric. They used a mass spectrometer to determine the chemical structure of each compound, and established that compounds with similar structures were likely affecting herbivores in a similar way.

“Metabolomics, a relatively new field of science, offers scientists a powerful new toolbox for examining the vast amount of chemical diversity that exists out there. Chemicals play a huge role in nature, from defenses to communication they are the medium by which species interact. Being able to quantify this in a meaningful way provides a truly unique perspective,” said Forrister.

But do the herbivores “care” about the traits the team was measuring and do Inga species with similar traits share herbivores? To test this, they collected caterpillars that were eating Inga leaves and sequenced their DNA to classify each as species A, species B, etc. They were unable to name the species because most of the caterpillars were new to science. They cataloged which herbivores were eating which plants, correlated the suite of compounds in the plants and inferred which plant species shared herbivore communities.

Both old-school field research and modern techniques were indispensable to this project’s success.

“Despite state-of-the-art laboratory facilities, there’s no substitute for spending months and months in the rainforest,” said Coley. “It took us several years to collect data, and samples of leaves and herbivores. It’s hot, humid and buggy, but attempting to understand the diversity of species is a biologist’s dream.”

The study reveals the significant role of herbivores in driving diversity in tropical ecosystems, with stark implications—the loss of those populations could have catastrophic consequence on these important habitats.

“If climate change continues to increase the length of the dry season in the Americas, then the dynamics of the herbivore populations will change as well,” said Coley. “That could have implications down the road.”

María-José Endara of the University of Utah and Universidad Tecnológica Indoamérica in Quito, Ecuador, Gordon C. Younkin of the University of Utah and Thomas A. Kursar of the University of Utah and the Smithsonian Tropical Research Institute coauthored the study.

Read the paper: Science

Article source: University of Utah

Image credit: Thomas Kursar

‘Specialized’ Microbes Within Plant Species Promote Diversity, Study Finds

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It’s widely accepted within agriculture that maintaining genetic diversity is important. In areas where crop plants are more diverse, pathogens might kill some plants but are less likely to wipe out an entire crop.

Few studies, however, have focused on such highly specialized pathogens in natural plant communities. In diverse plant communities, pathogens are thought to maintain diversity by killing common species, making room for rare ones. But what happens to diversity if, like in agriculture, pathogens harm some plants within a species, but not all?

A Yale)-led research team has found that tree seedlings grew less effectively in soil located below their mother tree than in soil found under a different individual of the same species. After ruling out other potential drivers, they concluded that the differences in growth were most likely due to microbial pathogens that specialize at the genotype level. Theoretical models revealed that such highly specialized pathogens could help maintain diversity in tree communities and promote increased seed dispersal over evolutionary timescales.

“We often think of pathogens as pests,” said Jenalle Eck, a postdoctoral researcher at the University of Zurich and a former visiting doctoral student at the Yale School of Forestry & Environmental Studies (F&ES), “but we’re finding that they play a key role in a highly diverse ecosystem.”

The study was published in the Proceedings of the National Academy of Sciences. The senior author of the paper was Liza Comita, an assistant professor of tropical forest ecology at F&ES.

For the study, Eck conducted a shadehouse experiment, potting more than 200 seedlings of the tropical tree Virola surinamensis grown from seeds collected in a diverse tropical forest in Panama. The soil for the pots was sourced from either the seedlings’ maternal tree or other trees of the same species.

The researchers showed that the difference in performance between seedlings growing in “maternal” soil and “non-maternal” soil was not the result of variations in soil nutrients or beneficial symbiotic relationships with fungi, thanks to lab work conducted at Yale by Camille Delavaux ’16 M.E.Sc., currently a doctoral student at the University of Kansas.

Using computer simulation models designed by Simon Stump, a postdoctoral associate at F&ES, the team then found that these pathogens can promote species coexistence and can lead to increased seed dispersal, which creates landscapes that allow pathogens to more effectively promote diversity.

“These results suggest that highly specialized pathogens are potentially an important, but largely overlooked driver of plant population and community dynamics,” said Comita. “Our findings underscore the importance of conserving both species and genetic diversity in tropical forests.”

Read the paper: Proceedings of the National Academy of Sciences

Article source: Yale School of Forestry & Environmental Studies (F&ES)

Image credit: Sean Mattson

Transcription Factor Network Gets to Heart of Wood Formation

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North Carolina State University researchers have uncovered how a complex network of transcription factors switch wood formation genes on and off. Understanding this transcriptional regulatory network has applications for modifying wood properties for timber, paper and biofuels, as well as making forest trees more disease- and pest-resistant.

“We’re building a complete story, so to speak, of how wood formation functions – all the intricate components, how they interact and how they fit together to regulate wood formation inside the cell walls of woody plants,” says Jack Wang, assistant professor in the College of Natural Resources and co-lead author of a Plant Cell article about the work.

Researchers with NC State’s Forest Biotechnology Group used transgenic black cottonwood (Populus trichocarpa), a species they’ve studied intensively, to identify interactions in a transcriptional regulatory network directed by a key transcription factor, PtrSND1-B1. The researchers documented four levels of interactions in the network, from DNA to enzyme levels. The work is an extension of two previous studies, in which functions of PtrSND1-B1 were discovered using a wood-forming cell system. These early studies were published in PNAS and Plant Cell by co-authors Quanzi Li, Ying-Chung Lin and Wei Li of the Forest Biotechnology Group, led by Vincent Chiang.

“Transcription factors – a complex network of them – regulate which wood formation genes are turned on or off,” Wang says. “Essentially these are high-level regulatory switches.

“Understanding this network allows us to identify single switches inside that complex network of transcription factors that could simultaneously control multiple wood-forming genes. Instead of working with one, two or three genes at a time, which is our current limit, plant biologists could work with tens of genes at a time.”

The new study upends ideas about transcriptional regulatory networks inferred from work with nonwoody species, such as Arabidopsis thaliana, a model plant.

“This network of transcription factor regulation in woody tissues is almost completely different from the regulatory processes in Arabidopsis and other plants,” says Hao Chen, co-lead author of the article and a postdoctoral researcher at NC State.

“Of 57 regulatory interactions we identified, 55 were specific to woody plant tissue, showing that herbaceous plants like Arabidopsis cannot stand in for woody plants.”

The study provides an extensive look at a transcriptional regulatory network in woody plants. Researchers’ goal is to provide a toolkit for building trees with specific properties needed for commercial timber, paper, biofuel production and conservation needs.

Plant biologists tested 42 of the interactions they found in lines of transgenic black cottonwood, verifying the function of about 90 percent. The network revealed which genes are common targets for specific transcription factors. As a result, researchers found nine new protein-protein interactions involved in forming lignin, a component in the cell wall that gives wood its strength and density.

Wang says several recent studies show that lignin is related to disease and insect resistance in trees, a major concern. A 2012 U.S. Forest Service report estimated that 7 percent of the nation’s forests are in jeopardy of losing more than a quarter of their tree vegetation by 2027. The amount of threatened vegetation rose by 40 percent in just six years.

“Studies like this that look at lignification and wood formation will have great value in helping to understand how trees can be made to be more robust and to improve forest health in general,” Wang says.

Read the paper: Plant Cell

Article source: North Carolina State University

Image credit: Jack P. Wang and Ilona Peszlen

Disappearing rice fields threaten more global warming

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All over China, a huge change has been taking place without any of us noticing. Rice paddies have been (and are being) converted at an astonishing rate into aquaculture ponds to produce more protein for the worlds growing populations. This change risks creating an unexpected impact on global warming.

International researchers, including Prof Chris Freeman from Bangor University, have found conversion of paddy fields to aquaculture is releasing massive amounts of the greenhouse gas methane into the atmosphere.

The UN Intergovernmental Panel on Climate Change (IPCC), have warned the planet will reach the crucial threshold of 1.5 degrees Celsius above pre-industrial levels by as early as 2030, precipitating the risk of extreme drought, wildfires, floods and food shortages for hundreds of millions of people. Freeman commented “Another source of methane is the last thing we need”.

It was always assumed that because rice paddies are already a huge source of atmospheric methane, nothing could happen to make a difficult situation worse.

When describing their work which appears in “Nature Climate Change”, Prof Chris Freeman commented: “We were amazed to discover that methane production from the converted rice paddies was massively higher than before conversion.”

Prof Freeman of the Bangor University‘s School of Natural Sciences explains:

“Paddy fields produce huge quantities of methane when decaying plant material is broken down by microbes called methanogens in the oxygen-free waterlogged paddy soils. But in the aquaculture ponds that are replacing the paddy fields, vast quantities of food are added to feed the crabs and fish that are being grown in them, and that massively increases the amount of rotting material for the methanogens to produce even more methane.”

Prof Freeman added: “We have known for some time that rice paddies were bad for global warming. But the realisation that there’s a “hidden” new source of problems is taking these threats to whole new level.”

There is also hope revealed in their studies though. Their research shows that if modifications were made to aerate the aquaculture ponds, much of the harmful methane could be eliminated before it reached the atmosphere. The IPCC warn global net emissions of carbon dioxide would need to fall by 45% from 2010 levels by 2030 and reach “net zero” around 2050 in order to keep the warming around 1.5 degrees C. The race is now on to ensure these changes are introduced before the current increasing rate of land use change exacerbates the global warming situation further.

Read the paper: Nature Climate Change

Article source: Bangor University

Image credit: CCO Public domain

Large and branched root systems can speed up growth of spruces

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According to a study by the Natural Resources Institute Finland (Luke), strong growth rate of spruces can be due to the structure of their root system. A large and branched root system offers a major benefit when competing for water and nutrients, and it can boost the growth of fast-growing spruces when compared to slow-growing ones already from the early stages.

The growth rate of trees varies: some trees grow slower and others faster by nature. The amount of nutrients and water a tree receives depends on its root system and the symbiotic mycorrhizal fungi growing in the root system. Earlier studies have determined that fast-growing spruce clones have more diverse selection of symbiotic fungi in their root systems. One cannot determine based on this result whether the diversity is the underlying reason for the fast growth rate or its consequence, however.

– Our goal was comparing the root systems of seedlings before the growth differences appear to find out whether small seedlings already show any external characteristics that anticipate good growth. We utilised Luke’s tree breeding data on the origins of fast- and slow-growing spruces, explains Taina Pennanen, Principal Scientist at Luke.

Fast-growing spruces grow extensive root systems already as seedlings

The 54 spruce seedlings that were included in the study were grown at a nursery garden and examined when they were 1.5 years of age and their sprouts were of the same height. Even though there were no differences in the height of the sprouts or the weight of the roots, the structures of the fast- and slow-growing spruces’ root systems were already clearly different

– Interestingly enough, there were more branches in the root systems of the fast-growing seedlings than in those of the slow-growing ones. There were more root tips than in the slow-growing seedlings and more lateral branches farther away from the base of the seedling than in the slow-growing seedlings, and the total length of the lateral branches was higher, explains Leena Hamberg, a Senior Scientist at Luke.

The large number of root tips farther away from the base of the seedling may allow the fast-growing seedlings to obtain, over the course of time, more diverse fungal contacts and more nutrients from the forest soil where neither nutrients nor fungi are evenly spread. This also enables good nutrient and water carrying capacity.

– Trees are highly long-lived plants, and the differences in the structural characteristics of the roots may become even more pronounced over time. We already know based on our previous studies that the characteristics of the roots of a spruce are hereditary. This phenomenon may, in part, explain the different growth rates of spruces, Taina Pennanen says.

Read the paper: Tree Physiology

Article source: Natural Resources Institute Finland (Luke)

Image credit: CCO Public domain