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Study provides clues on how trees evolve to survive

The towering, hundreds of years old Sitka spruce trees growing in the heart of Vancouver Island’s Carmanah Valley appear placid and unchanging.

In reality, each one is packed to the rafters with evolutionary potential.

UBC researchers scraped bark and collected needles from 20 of these trees last summer, sending the samples to a lab for DNA sequencing. Results, published recently in Evolution Letters, showed that a single old-growth tree could have up to 100,000 genetic differences in DNA sequence between the base of the tree, where the bark was collected, and the tip of the crown.

Each difference represents a somatic mutation, or a mutation that occurs during the natural course of growth rather than during reproduction.

“This is the first evidence of the tremendous genetic variation that can accumulate in some of our tallest trees. Scientists have known for decades about somatic mutations, but very little about how frequently they occur and whether they contribute significantly to genetic variation,” said Sally Aitken, the study’s lead researcher and a professor of forestry at UBC. “Now, thanks to advances in genomic sequencing, we know some of the answers.”

The researchers chose the Sitka spruce because it’s among the tallest trees growing in the Pacific Northwest, and sampled the exceptional trees in Carmanah Walbran Provincial Park.

“Because these trees live so long and grow so tall, they’re capable of accumulating tremendous genetic variation over time,” explained Vincent Hanlon, who did the research as part of his master of science in the faculty of forestry at UBC.

“On average, the trees we sampled for the study were 220 to 500 years old and 76 metres tall. There’s a redwood tree in California that’s 116 metres tall, but these Sitka spruce were pretty big.”

The researchers say more time and further studies will be needed to understand exactly how the different somatic mutations will affect the evolution of the tree as a species.

“Most of the mutations are probably harmless, and some will likely be bad,” explained Aitken. “But other mutations may result in genetic diversity and if they’re passed onto offspring they’ll contribute to evolution and adaptation over time.”

Studying somatic mutation rates in various tree species can shed light on how trees, which can’t evolve as rapidly as other organisms like animals due to their long lifespans, nonetheless survive and thrive, Aitken said.

“We often see tree populations that adapt well to local climates and develop effective responses to changing stresses such as pests and bugs,” she added. “Our study provides insights on one genetic mechanism that might help make this possible.”

Read the paper: Evolution Letters

Article source: University of British Columbia

Image: TJ Watt

For thousands of years, plants have produced food for humans, but with genetic tweaks, they can also manufacture proteins like Ebola vaccines, antibodies to combat a range of conditions, and now, cellulase that is used in food processing and to break down crop waste to create biofuel. In Nature Plants, a team from Cornell University and the University of Illinois announced that crops can cheaply manufacture proteins inside their cellular power plants called chloroplasts—allowing the crops to be grown widely in fields rather than restrictive greenhouses—with no cost to yield.

“This research shows the potential to improve people’s quality of life by producing medicinal and industrial proteins at costs that are orders of magnitude cheaper than current production methods,” said Justin McGrath, a research scientist at the IGB, whose work was supported by the IGB Fellows program. “Currently, protein production can cost hundreds to thousands of dollars per gram, but we estimate that this new approach would reduce costs to just a few dollars per gram, allowing production to expand exponentially to help meet market demand.”

Typically, these proteins are produced using cell cultures, where yeast or other microbes manufacture proteins in batch production. The genes that encode for these proteins are located in the nuclei of tobacco leaf cells—but each tobacco leaf cell has only one nucleus with one DNA copy to manufacture protein, limiting the amount of protein that can be produced. These plants must be grown in sealed greenhouses to prevent gene escape from their pollen.

In this study, the team engineered tobacco to produce cellulase proteins in the crop’s chloroplasts, where plants turn sunlight and carbon dioxide into energy through the process called photosynthesis. Each leaf cell contains about one hundred chloroplasts that contain thousands of copies of chloroplast DNA—which is separate from nuclear DNA—that can produce an enormous amount of protein.

“Given the huge health costs inflicted on global society, the idea of growing any more tobacco is not just bad, but ugly. But, this overlooks the fact that tobacco—as a crop bred to produce large quantities of leaves—could be a factory for good,” said Stephen Long (BSD/CABBI/GEGC), the Ikenberry Endowed University Chair of Crop Sciences at Illinois. “Chloroplasts are not present in pollen, making it possible to cultivate this engineered tobacco in fields and transform land once used for cigarette and cigar production into protein factories that can improve our health and industrial efficiency.”

However, chloroplast DNA encodes proteins essential for photosynthesis, which provides the energy for all plant growth and production—including protein production. This study asked whether protein production in the chloroplast compromises photosynthesis and growth.

To find out, the team grew tobacco engineered to produce cellulase in real-world, agronomic conditions over two years at Illinois’ Energy Farm. While they detected a slight effect on photosynthetic capacity in one year, there were no detectable differences in yield in either year.

“We showed, for the first time, that large amounts of recombinant protein can be produced in field cultivation and that this does not compromise photosynthesis or crop productivity,” McGrath said. “This study opens the door to much wider testing of chloroplast protein production, and ultimately, tobacco fields that would do good for society.”

Read the paper: Nature Plants

Article source: University of Illinois

Image: Cornell University / University of Illinois

Some fungi and bacteria live in close association, or symbiosis, with tree roots in forest soil to obtain mutual benefits. The microorganisms help trees access water and nutrients from the atmosphere or soil, sequester carbon, and withstand the effects of climate change. In exchange, they receive carbohydrates, which are essential to their development and are produced by the trees during photosynthesis.

More than 200 scientists from several countries, including 14 from Brazil, collaborated to map the global distribution of these root symbioses and further the understanding of their vital role in forest ecosystems. They identified factors that determine where different kinds of symbionts may emerge and estimated the impact of climate change on tree-root symbiotic relationships and hence on forest growth.

They concluded that the majority of ectomycorrhizal trees will decline by as much as 10% if emissions of carbon dioxide (CO2) proceed unabated until 2070, especially in cooler parts of the planet. Ectomycorrhizae are a form of symbiotic relationship that occurs between fungal symbionts and the roots of various plant species.

The authors of the study, featured on the cover of Nature, included Brazilian researchers Carlos Joly and Simone Aparecida Vieira, both professors at the University of Campinas (UNICAMP) and coordinators of the FAPESP Research Program on Biodiversity Characterization, Conservation, Restoration and Sustainable Use (BIOTA-FAPESP), as well as plant ecologist Luciana Ferreira Alves, now at the University of California, Los Angeles (UCLA) in the United States.

“We’ve long known that root-microorganism symbiosis is key to enable certain tree species to survive in areas where the soil is very poor and nutrients are released slowly by the decomposition of organic matter. The mapping survey helps us understand the distribution of these relationships worldwide and the factors that determine them,” Vieira told Agência FAPESP.

The researchers focused on mapping three of the most common groups of tree-root symbionts: arbuscular mycorrhizal fungi, ectomycorrhizal fungi, and nitrogen-fixing bacteria. Each group comprises thousands of species of fungi or bacteria that form unique partnerships with different tree species.

Thirty years ago, botanist David Read, Emeritus Professor of Plant Science at the University of Sheffield in the United Kingdom and a pioneer of symbiosis research, drew maps to show locations around the world where he thought different symbiotic fungi might reside based on the nutrients they provide to fuel tree growth.

Ectomycorrhizal fungi provide trees with nitrogen directly from organic matter, such as decaying leaves, so Read proposed that these fungi would be more successful in forests with cooler and drier seasonal climates, where decomposition is slow and leaf litter is abundant.

In contrast, Read argued, arbuscular mycorrhizal fungi should dominate in the tropics, where tree growth is limited by soil phosphorus and the warm, wet climate accelerates decomposition.

More recently, research by other groups has shown that nitrogen-fixing bacteria seem to thrive most in arid biomes with alkaline soil and high temperatures.

These hypotheses have now become testable thanks to the data gathered from large numbers of trees in various parts of the globe and made available by the Global Forest Biodiversity Initiative (GFBI), an international consortium of forest scientists.

In recent years, GFBI-affiliated researchers have built a database comprising information from more than 1.1 million forest plots and have inventoried 28,000 tree species. They surveyed actual trees located in over 70 countries on every continent except Antarctica.

The inventories also contain information on soil composition, topography, temperature and carbon storage, among other items.

“The plots inventoried by researchers linked to BIOTA-FAPESP are located in areas of Atlantic rainforest, including the northern coast of São Paulo State, such as Caraguatatuba, Picinguaba, Cunha and Santa Virgínia, and the southern coast of the state, such as Carlos Botelho and Ilha do Cardoso,” Joly said. “We also inventoried a substantial part of the Amazon region via projects in collaboration with other groups.”

Data on the locations of 31 million trees from this database, along with information on the symbionts associated with them, were fed by the GFBI team into a computer algorithm that estimated the impacts of climate, soil chemistry, vegetation and topography, among other variables, on the prevalence of each type of symbiosis.

The analysis suggested that climate variables associated with organic decomposition rates, such as temperature and moisture, are the main factors influencing arbuscular mycorrhizal and ectomycorrhizal symbioses, while nitrogen-fixing bacteria are likely limited by temperature and soil acidity.
“Climate changes occurring in the Northern Hemisphere may displace ectomycorrhizal fungi to other regions, leading to a drastic reduction in the density of these symbiotic relationships or their total loss,” Vieira said.

“This can affect nutrient cycling and above all carbon fixation, which depends on these symbiotic associations if forest vegetation is to absorb nutrients that are scarce or not available in the requisite form.”

Effects of climate change

To gauge the vulnerability of global symbiosis levels to climate change, the researchers used their mapping survey to predict how symbioses may change by 2070 if carbon emissions continue unabated.

The projections indicated a 10% reduction in ectomycorrhizal fungi and hence in the abundance of trees associated with these fungi, corresponding to 60% of all trees.

The researchers caution that this loss could lead to more CO2 in the atmosphere because ectomycorrhizal fungi tend to increase the amount of carbon stored in the soil.

“CO2 limits photosynthesis, and an increase in atmospheric carbon could have a fertilization effect. Faster-growing plant species may be able to make better use of this rise in CO2 availability in the atmosphere than slower-growing plants, potentially leading to species selection. However, this remains to be seen,” Joly said.

The researchers are also investigating the likely impact of increased atmospheric CO2 and global warming on plant development. Plants must expend more resources on respiration in a warmer climate, so photosynthesis will accelerate. What the net outcome of this growth effect will be is unclear, according to the researchers.

“These questions regarding tropical forests are still moot. Continuous monitoring of permanent forest plots will help us answer them,” Joly said.

Read the paper: Nature

Article source: By Elton Alisson | Agência FAPESP

Image: bere von awstburg / Pixabay

Dominant, non-native plants reduce wetland biodiversity and abundance more than native plants do, researchers report in the journal Ecology Letters. Even native plants that dominate wetland landscapes play better with others, the team found.

The researchers analyzed 20 years of data collected by expert botanists from hundreds of randomly selected sites in Illinois. This allowed them to track changes in the variety and abundance of different plants in the same locations over time.

The dominant non-natives are not just choking out many other plants, the researchers report. They also have a broad ecological footprint, taking over wetlands on a regional level, rather than just in individual sites. This negatively affects populations of birds and insects that rely on the native wetlands.

“The more dominant they are, the less room is available for other species,” said Illinois Natural History plant ecologist and botanist Greg Spyreas, who conducted the research with INHS plant ecologist David Zaya and colleagues from the U.S. Geological Survey. “These non-natives become more dominant over time and their impact on the rest of the community is fundamentally different,” Spyreas said. “They outcompete better. And that’s across hundreds of sites.”

For example, a European cultivar of reed canary grass has taken hold in many parts of North America. It grows extremely fast, reduces the light available to other plants, produces enormous numbers of seeds and sends out underground stems to quickly colonize a site, Spyreas said.

“It creates this very thick thatch of dead material on the ground that other plants can’t penetrate – but it can,” he said. “It tolerates drought and flooding very well, whereas a lot of native plants cannot.”

Another offender, a non-native common reed, Phragmites, “is notable in its aggressiveness,” Zaya said. It can quickly crowd out other wetland species, including native Phragmites.

Not all non-native plants reduce the ecological richness of wetlands, Zaya said.

“There are non-natives that sit in the background and don’t affect the wetland community,” he said. “Also, many native plants will dominate wetland communities.”

Some researchers have hypothesized that it doesn’t matter if a dominant plant is native or non-native: Both can drive down the diversity and abundance of other species, Zaya said.

But the new study shows that dominant, non-native species are much more likely to radically diminish the biological diversity of a locale than their native counterparts will.

“When I see native- versus non-native-dominated wetlands, it looks like two totally different worlds,” Zaya said. “Each native wetland has its own personality, with a different little flower or forb or rare grass or sedge. No two are the same. But the non-native wetlands tend to look alike. They’re the same here as they are in Ohio.”

The data also offer insights into how to best maintain wetland diversity, the researchers said.

“If you have a massive database of wetland plants like we do in Illinois, if you look at the numbers, you can isolate the species that are the most problematic,” Spyreas said. Five non-native wetland plants are on the “worst offender” list, he said: reed canary grass, a non-native cattail, invasive Phragmites and two European buckthorns.

“If you can eliminate those, you’ve eliminated 90 percent of the non-native wetland species problem,” Spyreas said.

Read the paper: Ecology letters

Article source: University of Illinois at Urbana-Champaign, News Bureau

Image: Greg Spyreas, Michael Jeffords and Susan Post

Native forests make up 1% of the landscape in South Africa but could play a key role in reducing atmospheric carbon and identifying sustainable development practices that can be used globally to counter climate change, according to a Penn State researcher.

“As we think about pathways for reducing atmospheric carbon dioxide concentrations, one of the available approaches is to use the natural world as a sponge,” said Erica Smithwick, professor of geography and director of the Center for Landscape Dynamics at Penn State.

The challenge, according to Smithwick, is to use forests to store carbon while also meeting local community needs. As trees grow, they absorb and store carbon through photosynthesis. Carbon makes up about half of a tree’s mass, but amounts vary by species. To find its carbon stock, scientists use equations based on the tree’s diameter and other variables, like height and wood density, rather than cutting down and weighing each species.

In 2011, Smithwick tagged and measured trees in the Dwesa-Cwebe nature reserve in the Eastern Cape Province with help from students in Penn State‘s Parks and People study abroad program. She remeasured the trees five years later while in South Africa on a Core Fulbright U.S. Scholarship and analyzed the forests’ carbon content. The results of the study, one of the first to quantify carbon content in Africa, appear in a recent issue of the journal Carbon Management.

Smithwick found that the coastal, indigenous forests store a moderate to large amount of carbon. They are also a biodiversity hotspot and thus important for conservation. The local communities depend on the forests for resources such as medicinal plants, fuelwood and timber, as well as their spiritual needs, Smithwick added.

“As we move toward the sustainable development of these places, we need to think about how the local communities are able to value and work with these characteristics of the forests,” said Smithwick, who also holds an appointment in Penn State’s Earth and Environmental Systems Institute. “Understanding what is an optimal level of productivity extraction from the natural system so we’re not degrading the system is an area of interest. We’re trying to figure out what the balance between forest productivity and resource extraction is.”

Smithwick noted that the large amount of forest productivity, or how quickly the forests grow, and small amount of human use of forest resources suggest that humans are not negatively influencing the Dwesa-Cwebe forests. She added that access to the nature reserve is limited, and other reserves see more resource extraction.

The South African government manages Dwesa-Cwebe but plans eventually to hand over management of the park to the surrounding local communities. Smithwick said that conservation of the area must integrate human interactions and values into a development model that recognizes how humans can benefit a forest system if managed in a sustainable way.

“We have to recognize the importance of these natural forests and their biodiversity and carbon values, but we also have to situate that in a sustainable development challenge,” said Smithwick, who is also director of the Huck Institutes of Life Sciences Ecology Institute and associate director of the Institutes of Energy and the Environment. “The forest in South Africa is a good case study for how we start to think about balancing these considerations. The lessons learned from this hopefully can resonate to how we think about these challenges in other parts of the world.”

Read the paper: Carbon Management

Article source: Penn State

Image: Erica Smithwick Lab / Penn State

The sweet, starchy orange sweet potatoes are tasty and nutritious ingredients for fries, casseroles and pies. Although humans have been cultivating sweet potatoes for thousands of years, scientists still don’t know much about the protein makeup of these tubers. In ACS’Journal of Proteome Research, researchers have analyzed the proteome of sweet potato leaves and roots, and in the process, have revealed new insights into the plant’s genome.

The sweet potato (Ipomoea batatas, Lam.) is a staple food in some parts of the world, in addition to being used for animal feed and industrial products, such as biofuels. The plant has a surprisingly complex genome, encoding more predicted genes than the human genome. Sweet potato also has a complex chemical composition, with a low protein content in the roots (the part that people eat) and many secondary metabolites in the leaves, making it difficult to extract sufficient quantities of proteins for analysis. Sorina and George Popescu and colleagues wanted to see whether a “proteogenomics” approach — analyzing both protein and genetic data together — could help them gain a better understanding of the compositions of sweet potato roots and leaves.

The team extracted proteins from root and leaf samples using two different methods and cut them into peptides, which they analyzed with liquid chromatography and mass spectrometry. The researchers identified 3,143 unique proteins from sweet potato leaves and 2,928 from roots. When they compared the proteomic data with the genome of the sweet potato, they identified some regions in the published genome sequence where their data could provide enhanced information. For example, the analysis predicted 741 new protein-coding regions that previously were not thought to be genes. The group says the results could be used to help further characterize and biofortify the tuber.

Read the paper: Journal of Proteome Research

Article source: American Chemical Society

Image: Iva Balk/Pixabay

Wetlands are an important part of the Earth’s natural water management system. The complex system of plants, soil, and aquatic life serves as a reservoir that captures and cleans water. However, as cities have expanded, many wetlands were drained for construction. In addition, many areas of land in the Midwest were drained to increase uses for agriculture to feed a growing world.

Draining wetlands disconnected the natural flow and retention of water, a system that had worked well for millennia. One solution to wetland draining was to rebuild these wetlands in another area (more convenient to humans). These are referred to as “constructed wetlands.” In other cases, constructed wetlands are built to rebuild an area no longer used for agriculture.

How these constructed wetlands are built and managed can make a big environmental impact. Karla Jarecke and researchers from several universities have been studying wetlands’ impact on the greenhouse gas methane.

“Globally, wetlands are the largest natural source of methane to the atmosphere,” says Jarecke. “Methane has a much bigger impact than carbon dioxide on global warming – an impact 25 times greater.”

Both natural and constructed wetlands emit methane. Due to their nature – wetlands are, after all, wet – soil microbes and plants are forced to metabolize under anaerobic conditions. And, this leads to methane production.

The soil microbes are responsible for the production of methane in wetlands. The methane then gets to the atmosphere via diffusion, transport through plant tissue, and the episodic release of gas bubbles. The hydrologic stability of wetland soils, as well as the transport efficiency through plants, can affect how much and how often methane is released from the soil.

“Understanding the conditions under which methane is produced and released in wetlands could lead to solutions to reduce methane emissions,” says Jarecke.

The study focused on two common wetland plants and their potential role in methane emissions: swamp milkweed and northern water plantain. Plants and soils were collected from a constructed wetland in Dayton, Ohio. They were then transported to Lincoln, Nebraska to create wetland mesocosms. The Dayton site had formerly been drained and used for agriculture and was rebuilt as wetland in 2012.

The researchers harvested seedlings of swamp milkweed and northern water plantain from the wetland and transplanted them into soils collected in PVC pipe. They covered individual plants with clear acrylic cylinders during gas sampling. This helped them measure and quantify methane emissions from the soil-plant mesocosms. The study was performed in the summer of 2013.

Besides comparing the emissions of the two plant species, the researchers studied the effects of hydrology – or the saturation of the soil. “While the controls of hydrology and plant species on methane emissions are individually well-studied, the two are rarely studied together,” says Jarecke.

This recent study concluded that water level and saturation influenced methane emissions more than the type of plant species. While methane emissions differed between laboratory mesocosms with water plantain and mesocosms with swamp milkweed, methane emissions did not differ in field mesocosms with each of the two species. In the field, soil saturation had a greater effect on methane emissions.

Finding plant species that reduce microbial methane production could be a key to better wetland management. For example, plants that deliver oxygen to the rooting zone can suppress microbial methane production. In addition, future research is needed to understand how varying soil saturation affects methane emissions. This information could be valuable for designing wetland topography that creates hydrologic conditions for increased carbon storage and reduced methane emissions.

Read the paper: Soil Science Society of America Journal

Article source: American Society of Agronomy

Image: Karla Jarecke