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Study shows first evidence of bacterial-induced apoptosis in algae

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A new study by UAlberta biologists shows the first evidence of apoptosis, or programmed cell death in algae. The outcomes have broad-reaching implications, from the development of targeted antibiotics to the production of biofuels in industry.

“It sounds odd, but programmed cell death is important to all large organisms. For any cells to differentiate, they have to be able to kill cells. For example, if you injure yourself, your scab is formed with these killed-off cells,” explained Rebecca Case, associate professor in UAlberta ’s Department of Biological Sciences. “Here at the single-cell level, we’ve found that small molecules are passed from bacteria into the host algae. By doing that, the bacteria are able to tell the algae to kill itself.”

Until now, programmed cell death, also known as apoptosis, was thought to only occur in large, multicellular organisms such as animals and humans. This research shows that bacteria that live on single-cellular algae can cause programmed cell death. “It is the first documentation of true apoptosis via bacterial pathogens in microorganisms like algae,” said Case, who conducted the work with PhD graduate Anna Bramucci.

Major potential

One potential application of this research is in drug discovery and development. Unlike traditional antibiotics, which kill all bacteria, this research can be applied to develop drugs with a more fine-tuned approach, turning individual bacteria or cells on and off. Previously Case and colleagues have used this approach to find antibiotics that are effective at concentrations up to 1,000 times lower than traditional antibiotics.

“In interactions like these that occur in close proximity you can find molecules that are effective in very small concentrations,” said Case. “Going forward, that’s what we want—really potent molecules.”

Another area of interest is in natural fuels derived from living matter, called biofuels. “Algae can also be used to create lipids for biofuels,” explained Case. “If we can better understand their life cycles, we can find ways to keep them alive for longer, to produce more fuel for industry.”

Read the paper: Scientific Reports

Article source: University of Alberta

Image credit: Anna Bramucci/ University of Alberta

In Frontiers in Plant Science: Natural plant defense genes provide clues to safener protection in grain sorghum

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Weeds often emerge at the same time as vulnerable crop seedlings and sneak between plants as crops grow. How do farmers kill them without harming the crops themselves?

Seed and chemical companies have developed two major technologies to avoid crop injury from soil- and foliar-applied herbicides: genetically modified herbicide-tolerant crops; and safeners, chemicals that selectively – and mysteriously – protect certain crops from damage. In a new University of Illinois study, researchers identify genes and metabolic pathways responsible for safener efficacy in grain sorghum.

The discovery goes a long way in explaining how safeners work. According to Dean Riechers, weed scientist in the Department of Crop Sciences at U of I and co-author on the Frontiers in Plant Science study, scientists serendipitously discovered safeners in the late 1940’s. Greenhouse-grown tomato plants were inadvertently exposed to a synthetic plant hormone during an experiment. The tomatoes showed no symptoms of exposure to the hormone itself, but when a herbicide was sprayed later, they were unharmed. Without fully understanding how they worked, researchers began experimenting to find more “herbicide antidotes” before commercializing the first safener (dichlormid) for corn in 1971.

Today, after nearly 50 years of commercial use in corn, rice, wheat, and grain sorghum, safeners remain a mystery. The existence of synthetic chemicals that selectively protect high-value cereal crops and not broadleaf crops or weeds is fascinating but doesn’t make intuitive sense, according to Riechers. Figuring out how the protective mechanism switches on in cereal crops could one day help scientists induce protection in broadleaf crops, like soybeans and cotton.

“Finding a safener that works in dicot crops would be the Holy Grail,” Riechers says.

The first step, however, is understanding what happens inside cells of cereal crops when exposed to safeners. In previous trials with grain sorghum, the research team noticed a massive increase in production of glutathione S-transferases (GSTs). These important enzymes, present in all living organisms, quickly detoxify herbicides and other foreign chemicals before they can cause damage. But that didn’t narrow the haystack very much.

“These cereal crops have up to 100 GSTs, and we didn’t know if one or more was providing the protective effect,” Riechers says. “We also couldn’t tell why GSTs were increased.”

The team used an approach known as a genome-wide association study. They grew 761 grain sorghum inbred lines in a greenhouse and compared plants treated with safener only, herbicide only, or both safener and herbicide. Scouring the genome for differences, they found specific genes and gene regions that were switched on in the safener-treated plants. Not surprisingly, they were genes that coded for two GSTs.

“Although we suspected GSTs were involved, this technique seemingly pinpointed the gene responsible for safening sorghum, SbGSTF1, along with a second tandem GST gene,” Riechers says.

In addition to finding this key gene for detoxification, the researchers also analyzed the RNA molecules expressed in safener-treated plants and revealed a plant defense pathway pulling double duty.

According to Riechers and co-author Patrick Brown, sorghum is well-known for producing allelochemicals, or chemical defenses, against insects and pathogens. One of these, dhurrin, is a chemical with a cyanide group. When it is under attack, sorghum releases a “cyanide bomb,” killing the insect or pathogen. It turns out some genes involved in dhurrin synthesis and metabolism were triggered in response to safeners, too.

“This link to dhurrin was kind of a clue – maybe the safener is tapping into a chemical defense pathway the plant is already using to protect itself,” Riechers says. “This is a new concept no one has ever proposed before in sorghum. It’s giving us some insight why the safener might be eliciting this response in the plant.”

The ability to turn on defenses and protective pathways with safeners could have all sorts of applications, according to Riechers. “It doesn’t seem logical there would be a pathway that’s only specific for synthetic herbicides,” he says. “Maybe safeners could be deployed to protect crops against insect herbivores, chemical pollutants, or environmental stresses. The possibilities and applications are very promising.”

The researchers have plans and funding to expand the experiment to wheat, and ultimately hope to identify more precise safener-herbicide-crop combinations that could eventually translate to broadleaf crops.

Read the paper: Frontiers in Plant Science

Article source: University of Illinois

Image credit: You Soon Baek/University of Illinois

Plant immunity cut to size

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An international team based in Ghent, Belgium VIB-UGent Center for Plant Systems Biology and Basel, Switzerland (University of Basel) found a link between a class of enzymes and immune signals that is rapidly triggered upon physical damage in plants. This new discovery will increase our understanding of the plant immune system and might be exploited to improve crop health and yield in the future.

As a universal process in all multicellular organisms, including humans and plants, damaged cells send out signals to alert the surrounding tissue of the wound. These signals can activate the immune system to prevent infection and promote tissue regeneration, eventually leading to wound healing. In plants, short protein fragments or peptides play an important role in the immune system. These peptides are produced from precursor proteins that are ‘cut into shape’ by so-called proteolytic enzymes or proteases.

The problem is that there are a lot of proteases, which means that it is essential to identify which ones perform which roles in the plant immune system. By wounding leaves of the thale cress, Arabidopsis thaliana, the teams of Thomas Boller (Prof. emeritus, University of Basel), Frank Van Breusegem VIB-UGent Center for Plant Systems Biology and Kris Gevaert (VIB-UGent Center for Medical Biotechnology) found that a class of proteolytic enzymes called metacaspases played an important role in the plant’s response which involves the release of calcium and the peptide precursor protein PROPEP1. They checked their findings by producing a plant with a mutation in the gene coding for an important metacaspase. This plant was unable to release the immune signal.

To understand the speed and extent of the immune response in Arabidopsis, Simon Stael, the postdoc who led the efforts, damaged the roots with lasers. The targeted plant cells responded quickly. Simon Stael says: “We were really excited to see those first laser shots followed by calcium waves and PROPEP1 signal dispersion.” The newly uncovered process can be summarized as follows: damage elicits high calcium levels in the cell interior that activate metacaspases. These metacaspases go to work on PROPEP1, which regulates the immune response and associated damage limitation efforts.

This opens up new avenues of research since proteases usually cleave more than one protein. So, which other plant processes are influenced by metacaspases and contribute to wound response and immunity? We can now also use the laser ablation technique to look at a variety of other responses in the damaged cells and their surroundings, to learn more about the details of local wound response. Finally, crop breeding strategies mostly select for optimal growth, yield and quality of food or feed in combination with intensive pesticide use, potentially crippling the plant immune system. Metacaspases now emerge as potential targets for improved breeding techniques and better crop immunity.

Read the paper: Science

Article source: VIB-UGent Center for Plant Systems Biology

Image credit: Wikimedia Commons

New Plant Breeding Technologies for Food Security

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An international team, including researchers from the University of Göttingen, argues in a perspective article recently published in “Science” that new plant breeding technologies can contribute significantly to food security and sustainable development. Genome editing techniques in particular, such as CRISPR/Cas, could help to make agriculture more productive and environmentally friendly. The researchers advocate the responsible use and support of these new technologies.

“Plant breeding and other agricultural technologies have contributed considerably to hunger reduction during the last few decades”, says Matin Qaim, an agricultural economist at the University of Göttingen and one of the article’s authors. But the resulting high intensity in the use of agrochemicals has also caused serious environmental problems. Future technologies need to reduce the negative environmental footprint and make agriculture more resilient to climate stress. Predictions suggest that small farms in Africa and Asia will suffer especially from the effects of climate change.

“Genome editing allows us to develop crop plants that are more resistant to pests and diseases and more tolerant to drought and heat”, says Shahid Mansoor from the National Institute for Biotechnology and Genetic Engineering in Pakistan. This can help to reduce crop losses and chemical pesticide sprays. In genome editing, certain DNA sequences are changed or “switched off” in a very precise way without foreign genes being introduced. Hence, genome-edited crops are different from transgenic genetically modified organisms (GMOs). “The new methods are already being used in various cereals and also to improve neglected food crops such as pulses or local vegetables,” Mansoor explains.

“We should be careful not to repeat the mistakes that were made with GMOs”, says Qaim. “The limited public acceptance and the high regulatory hurdles for transgenic GMOs have contributed to a concentration of biotech developments in only a few major crops and in the hands of only a few multinationals. We need more diversity and more competition,” adds Qaim. “Genome-edited crops do not contain foreign genes; as the breeding techniques are more precise, these crops are as safe as conventionally bred crops. Hence, genome-edited crops should not be regulated as if they were transgenic GMOs”.

In Europe, regulations for genome-edited crops are still being debated. In July 2018, the EU Court of Justice ruled that these crops would fall under the existing GMO law, which is disappointing according to the authors of this position paper. “This will hold up future applications” says Qaim. The regulation of new breeding technologies in Europe also has a major impact on developing countries, carrying the risk that the enormous potential of genome editing for food security cannot be fully harnessed, the researchers fear.

Read the paper: Science

Article source: University of Göttingen

Image credit: CCO Public Domain / Markus Spiske in Pixabay

New, more efficient way to reduce water use and improve plant growth

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A team of scientists has revealed a new, sustainable way for plants to increase carbon dioxide (CO2) uptake for photosynthesis while reducing water usage.

The breakthrough was led by a team of plant scientists at the University of Glasgow and has been published in the journal Science. The researchers used a new, synthetic light-activated ion channel, engineered from plant and algal virus proteins, to speed up the opening and closing of the stomata – pores in the leaves of plants – through which carbon dioxide (CO2) enters for photosynthesis.

Stomata are also the main route for water loss by plants. Previous attempts to reduce water usage by manipulating these pores has generally come at a cost in CO2 uptake.

Consequently, the plants engineered at Glasgow showed improved growth whilst conserving water use.

The scientists’ modified plants grew as normal and substantially better under light conditions typical of the field, fixing more CO2 while losing less water to the atmosphere.

Crop irrigation accounts for roughly 70% of fresh water use on the planet and its use has expanded at unsustainable rates over the past three decades. Scientists have been trying to find ways to make plants grow with less water. Until now, much of the research has reduced water consumption, but at a potential cost in reduced CO2 uptake and plant growth. This is not a satisfactory approach overall, given the growing demands on agricultural food production.

This new research now offers a different approach that can successfully improve growth without compromising water use efficiency.

The researchers studied the plant Arabidopsis, a member of the mustard family. Using the light-activated ion channel, called BLINK, the plant’s stomatal responses were accelerated and better synchronized when grown under fluctuating light – conditions which are typical of the natural environment (e.g. when clouds pass overhead or when shaded by neighboring plants). The engineered plants demonstrated improved growth and biomass production whilst also conserving water.

Co-corresponding author Prof John Christie, from the University’s Institute of Molecular, Cell and Systems Biology, said: “Our findings demonstrate the feasibility of improving the efficiency of water use by plants while making gains in photosynthetic CO2 assimilation and plant growth.”

Prof Mike Blatt added: “Previous efforts to improve plant water use efficiency have focused on reducing stomatal density, despite the implicit penalty in CO2 uptake for photosynthesis. Alternative approaches, like the one we have used, circumvent the carbon-water trade-off and could be used to improve crop yield, particularly under water limiting conditions.”

Lead author Maria Papanatsiou said: “Plants must optimize the trade-off between photosynthesis and water loss to ensure plant growth and yield. We adopt a well-established approach used in neuroscience, called optogenetics, to better equip stomata that are essential in balancing CO2 uptake and water loss.

“We used a genetic tool that acts as a switch allowing stomata to better synchronize with light conditions and therefore enhance plant performance under light conditions often met in agricultural settings.”

Read the paper: Science

Article source: University of Glasgow

Image credit: University of Glasgow

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).

Income

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