Complete world map of tree diversity: New statistical model eliminates blank spaces

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The biodiversity of our planet is one of our most precious resources. However, for most places in the world, we only have a tiny picture of what this diversity actually is. Researchers at the German Centre for Integrative Biodiversity Research (iDiv) and Martin Luther University Halle-Wittenberg (MLU) have now succeeded in constructing, from scattered data, a world map of biodiversity showing numbers of tree species. With the new map, the researchers were able to infer what drives the global distribution of tree species richness. Climate plays a central role; however, the number of species that can be found in a specific region also depends on the spatial scale of the observation, the researchers report in the journal Nature Ecology and Evolution. The new approach could help to improve global conservation.

Around the world, biodiversity is changing dramatically and its protection has become one of the greatest challenges mankind is facing. At the same time, we still know very little about why some places are biologically diverse while others are poor, and where are the most biodiverse places on Earth. Also, the reasons why some areas are more species-rich than others are often unclear: what role do environmental factors like climate play, and how important are historical factors like past ice ages for the biodiversity we are observing today? Our knowledge is based on scattered local surveys and is full of gaps; especially in tropical regions, where biodiversity can be particularly high. Closing all gaps by comprehensively surveying the whole planet, is, however, simply impossible.

Satellite imagery can close some data gaps; for example, when collating information on forest cover, but these techniques have their limits. “We don’t have to just count the trees, we also need to identify what species they are,” explains Dr Petr Keil, lead author of the new study. “In the tropics, we find hundreds of different tree species in a single hectare. We can identify these only on site. Therefore, most areas haven’t been surveyed for biological diversity – and probably never will be.” Keil and co-author Prof Jonathan Chase are scientists at the German Centre for Integrative Biodiversity Research (iDiv) and at the Martin Luther University Halle-Wittenberg (MLU).

Despite the patchy data, Keil and Chase wanted to create a world map of tree species richness. In a first step, they compiled well over 1,000 lists of tree species. These came either from small forest plots which had been surveyed in previous studies, or from whole countries. For most countries in the world, it is known which tree species can be found there, but not where exactly, and also it is often unclear whether specific species are rare or common. In order to be able to calculate the number of tree species for the extensive blank spaces on the map, the researchers developed a statistical model. The trick is that the model combines the available patchy information on the surveyed plots with the information on the country level and also integrates established data on environmental factors like climate. The result is a complete map of biodiversity in all the forested areas in the world.

“It was like a 1000-piece puzzle that we only had a few pieces of, and we didn’t even know what the big picture was,” says Jonathan Chase. “With our approach, we were able to calculate the missing pieces and put the puzzle together.” Using the new method, the researchers can calculate the number of tree species for areas of different sizes; a nature reserve, a country or an entire continent. This enabled them to investigate the underlying causes of the variation of tree diversity on our planet. Their analysis revealed that climate is the most important factor; the highest number of tree species can be found in the hot, humid tropics. Nevertheless, the number of tree species also varies across different places with the same climate, in some cases quite substantially. In southern China, for example, the researchers see a much higher diversity than in other regions with a similar climate.

Importantly, however, just how much ‘extra’ diversity one finds in places like China depends on the view of the observer. “If you’re standing in a forest counting the number of species around you, you might not even notice the difference between China and other climatically similar areas. However, when you move from one site to the next and add up species observed across many sites, the difference really pops out”, Jonathan Chase says.

This disparity between adjacent areas is called beta diversity. Within a larger region it leads to a high total diversity. Keil and Chase have shown in their analysis that this measure of diversity is particularly high in the dry (not wet) tropics, especially in mountainous areas like in southern China, Mexico, or in the Ethiopian highlands. One reason for this high beta-diversity might be events in the geological past, like ice ages. “During the last glaciation, the trees could survive only in mountain valleys, and different populations were isolated from each other as a result,” explains Petr Keil . “If you stand in one of these valleys today, you see a medium number of tree species. But if you climb over the ridge and hike down into the neighbouring valley, you find different tree species, and still others in the next valley.”

Keil and Chase are primarily concerned with understanding how biodiversity is distributed on the planet and what factors are driving it. But their model can also be useful for developing strategies for conservation, especially in forests where tree diversity has not been heavily influenced by humans. For example, in the case of the mountains of China, protecting only one valley is not enough; it is the diversity of different valleys which gives this area its high biological value. “In order to really understand and protect biodiversity, we have to look at the local and regional scale at the same time,” says Keil. “That is, we need both the perspective of a naturalist standing in a forest and the big picture of an entire country. Our approach now enables that”.

Read the paper: Nature Ecology and Evolution

Article source:German Centre for Integrative Biodiversity Research (iDiv)

Image credit: Petr Keil and Jonathan Chase

Researchers describe new tubular structures at plant-fungal interface

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For hundreds of millions of years, plants and fungi have formed symbiotic relationships to trade crucial nutrients, such as phosphate and fatty acids. This relationship is extremely important to the growth and survival of both organisms, and solving the mystery of how they transfer molecules to each other could eventually help reduce the use of fertilizer in agriculture.

Now, researchers at the Boyce Thompson Institute (BTI) have uncovered structural networks of tubules at the plant–fungal interface that could shed light on the mechanisms of this natural partnership. Details of the study were published in Nature Plants.

An estimated 80% of vascular plant families form symbioses with a type of soil fungi called arbuscular mycorrhizal fungi. The fungi penetrate the outermost cells of a plant’s roots and grow intricate branch-like structures called arbuscules. Each host plant cell then grows a membrane that envelops an arbuscule, and nutrient exchange takes place within the space between the plant membrane and the fungal cell wall.

In an attempt to understand the fundamental interaction between plants and the fungi, BTI faculty member Maria Harrison and postdoctoral scientist Sergey Ivanov joined forces with R. Howard Berg, director of the Donald Danforth Center’s Integrated Microscopy Facility. They used advanced electron microscopy techniques to image arbuscules present in the roots of the legume Medicago truncatula colonized by the fungus Rhizophagus irregularis, and were surprised by the results.

“Our understanding of the sub-cellular structural basis of the interaction relies on studies performed 30-40 years ago. Many of them indicated that the material around the fungus but inside the plant membrane would be an amorphous matrix of carbohydrate material,” said Harrison, the paper’s corresponding author. Instead, the researchers found a network of round, tubular and dumbbell-shaped structures constructed of lipid membranes, nearly all of which appeared to connect back to the plant cell’s membrane.

The researchers were further surprised to find another network of membrane tubules in the space between the fungal cell membrane and the fungal cell wall. “It was totally unexpected to see such an extensive proliferation of fungal membrane, particularly knowing that the fungus is starving for lipids,” explains Ivanov, the paper’s lead author.

Harrison and Ivanov speculate that the networks are related to the transfer of lipids.

“Somehow lipids are released from the plant cell and fed to the fungus, and we wondered how they move through what we thought was an aqueous matrix between the plant cell membrane and the fungal cell wall,” says Harrison. “But maybe this space isn’t so aqueous after all, and perhaps this membrane-rich environment facilitates the movement of lipids between the organisms.”

Given the plant and fungal membrane networks’ close physical proximity to each other, the fungal network could be involved in lipid absorption in order to optimize the process. The researchers suspect the network is not involved with transferring phosphate to the plant because the membrane networks are more abundant near the larger branches of the arbuscule, whereas phosphate uptake likely occurs near the smaller branches.

Harrison believes that newer technologies are to thank for finding these networks of tubules. “High-pressure freezing fixation of samples gives better membrane preservation than older techniques. I think that is the reason that these extensive membranes were not seen before,” she says. “Plus, 3D electron tomography is very powerful and let us visualize the networks, which didn’t look connected on 2D images.”

Ivanov, worked closely with Berg, who has expertise with cryofixation and electron microscopy, and Jotham Austin II at the University of Chicago, who is an expert in tomography.

Another research group led by Uta Paszkowski of the University of Cambridge in the UK performed similar imaging studies in rice colonized with R. irregularis, and found similar structures. Those results were published in the same issue of Nature Plants.

Read the paper: Nature Plants

Article source:Boyce Thompson Institute

Image credit: Jotham Austin II and R. Howard Berg

Scientists have discovered that grasses are able to short cut evolution by taking genes from their neighbours

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The findings suggest wild grasses are naturally genetically modifying themselves to gain a competitive advantage.

Understanding how this is happening may also help scientists reduce the risk of genes escaping from GM crops and creating so called “super-weeds” – which can happen when genes from GM crops transfer into local wild plants, making them herbicide resistant.

Since Darwin, much of the theory of evolution has been based on common descent, where natural selection acts on the genes passed from parent to offspring. However, researchers from the Department of Animal and Plant Sciences at the University of Sheffield have found that grasses are breaking these rules. Lateral gene transfer allows organisms to bypass evolution and skip to the front of the queue by using genes that they acquire from distantly related species.

“Grasses are simply stealing genes and taking an evolutionary shortcut,” said Dr Luke Dunning.

“They are acting as a sponge, absorbing useful genetic information from their neighbours to out compete their relatives and survive in hostile habitats without putting in the millions of years it usually takes to evolve these adaptations.”

Scientists looked at grasses – some of the most economically and ecologically important plants on Earth including many of the most cultivated crops worldwide such as: wheat, maize, rice, barley, sorghum and sugar cane.

The paper, published in the journal Proceedings of the National Academy of Sciences, explains how scientists sequenced and assembled the genome of the grass Alloteropsis semialata.

Studying the genome of the grass Alloteropsis semialata – which is found across Africa, Asia and Australia – researchers were able to compare it with approximately 150 other grasses including rice, maize, millets, barley and bamboo. They identified genes in Alloteropsis semialata that were laterally acquired by comparing the similarity of the DNA sequences that make up the genes.

“We also collected samples of Alloteropsis semialata from tropical and subtropical places in Asia, Africa and Australia so that we could track down when and where the transfers happened,” said Dr Dunning.

“Counterfeiting genes is giving the grasses huge advantages and helping them to adapt to their surrounding environment and survive – and this research also shows that it is not just restricted to Alloteropsis semialata as we detected it in a wide range of other grass species.”

“This research may make us as a society reconsider how we view GM technology as grasses have naturally exploited a similar process.

“Eventually, this research may also help us to understand how genes can escape from GM crops to wild species or other non-GM crops, and provide solutions to reduce the likelihood of this happening.

“The next step is to understand the biological mechanism behind this phenomenon and we will carry out further studies to answer this.”

Read the paper: PNAS

Article source: University of Sheffield

Image credit: University of Sheffield

Cell division in Plants: How cell walls are assembled

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Plant researchers at Martin Luther University Halle-Wittenberg (MLU)_ are providing new insights into basic cell division in plants. The scientists have succeeded in understanding how processes are coordinated that are pivotal in properly separating daughter cells during cell division. In the renowned scientific publication “The EMBO Journal “, they describe the tasks of certain membrane building blocks and how plants are impacted when these building blocks are disrupted.

For their study, the plant researchers examined the roots of the thale cress plant, Arabidopsis thaliana. They cultivated normal plants and plants in which they artificially switched off certain enzymes that affect the composition of the membranes. “We wanted to find out which membrane building blocks are important for cell division and why,” explains Professor Ingo Heilmann from MLU.

For plants to develop, their cells have to divide. First, the genetic material located in the cell nucleus divides. Two whole new cell nuclei are formed from the duplicated genetic material. The other components of the cell, for example the chloroplasts and mitochondria, are distributed between the two future daughter cells. All this takes place in the parent cell.

Only then the daughter cells will be separated by a new cell wall. The whole process can be compared to a construction site. First, a temporary scaffold made of protein fibres, the so-called phragmoplast, forms in the middle of the cell. Like railway tracks, these fibres guide the building materials needed for the cell wall. Small bubbles gradually transport new cell wall material along the rails. This is assembled together by a complex fusion machinery to form a larger structure: the cell plate. The cell plate continues to grow at its edges from the centre of the cell outwards until a cell wall disc completely separates the daughter cells from one another. “The fusion machinery has to correctly coordinate the protein fibres for everything to function properly, otherwise the freight cars will transport the cell wall material to the wrong spot or at the wrong time and cell plate formation will cease,” explains Heilmann.

Using biochemical and cell biology experiments, his research group was able to show that PI4P, a membrane building block, plays two roles during cell division: PI4P not only controls the activity of the fusion machinery, it also ensures the new material is transported in the right direction. For the first time, the researchers were able to show that PI4P helps to ensure that the protein scaffold of the phragmoplast is assembled and disassembled in the right places. In normal plants, this results in regular cells that fit together perfectly and give the plant its needed stability.

In mutated plants, however, the scientists observed severe defects in cell division: They found enlarged cells containing several cell nuclei as a result of the unsuccessful separation of the daughter cells. Some cells were unable to divide completely, the cell tissue was chaotic, and there were enormous differences in the sizes of the individual cells. “This is not happy tissue. It makes the entire plant more unstable, reduces its size and impacts how it adapts to environmental stimuli,” explains Heilmann.

The results of the research group from Halle help to better understand the dynamics of the plant’s cytoskeleton of microtubules. The cytoskeleton not only determines the direction of cellular transport processes during cell division, but also directs general plant growth. Therefore, the new findings could have far-reaching consequences, for example on the deposition of cellulose in plant cell walls and thus on biomass and cellulose production. However, it must first be determined whether the findings can also be applied to other plants and how the activity of the enzymes investigated here can be specifically regulated.

Read the paper: The EMBO Journal

Article source:Martin-Luther-Universität Halle-Wittenberg

Image credit: Ingo Heilmann (The EMBO Journal)

Genetic blueprint for extraordinary wood-munching fungus

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A relatively unknown fungus, accidentally found growing on an Acacia tree in the Northern Cape, has emerged as a voracious wood-munching organism with enormous potential in industries based on renewable resources.

The first time someone took note of Coniochaeta pulveracea was more than two hundred years ago, when the South African-born mycologist Dr Christiaan Hendrik Persoon mentioned it in his 1797 book on the classification of fungi.

Now C. pulveracea has had its whole genome sequenced by microbiologists at Stellenbosch University (SU) in South Africa, and henceforth made its debut in cyberspace with a few tweets and a hashtag. All because this relatively unknown fungus has an extraordinary ability to degrade wood – hence the descriptor “pulveracea”, meaning powdery.

In the age of biotechnology, biofuels and the usage of renewable raw materials, this is an important fungus to take note of, says Prof Alf Botha, a microbiologist in the Department of Microbiology at SU.

Over the past 25 years, there has been a number of reports on the ability of species in the Coniochaeta genus to rapidly degrade lignocellulose into fermentable simple sugars. But thus far Prof Botha‘s lab is the only one to be working on C. pulveracea.

The work started in 2011, when he quite randomly snapped a brittle twig, covered in lichen, from a decaying Acacia tree. At the time, he was holidaying with family on a farm in the Northern Cape. “At the time we were looking for fungi and yeasts that can break down wood, so I knew this was something special when I decided to keep the twig,” he explains. But to date, despite numerous attempts, they have not been able to find it again.

However, back in the lab there was great excitement when they observed that this species in the Coniochaeta genus was literally munching its way through birchwood toothpicks. Even more astounding was its ability to change form between a filamentous fungus and a yeast, depending on the environment.

“This is highly unusual for a fungus. We’d typically expect this kind of behavior from some fungal pathogens,” explains Botha.

Over the past decade Botha and his postgraduate students focused on unraveling this yeast-like fungus’ behavior. In 2011 Dr Andrea van Heerden found that it produced enzymes that degraded the complex structures of wood into simple sugars, feeding a community of surrounding fungi that do not have the ability to degrade wood. In 2016, she published the results of her investigation into its ability to switch to a yeast-like growth. Understanding this process would be important to the potential use of this fungi in industrial processes.

In the latest study, MSc student CJ Borstlap worked with Dr Heinrich Volschenk, an expert molecular biologist, and Dr Riaan de Witt from the Centre for Bioinformatics and Computational Biology at SU, to produce the first draft genome sequence of C. pulveracea. With a genome size of 30 million nucleotides and over 10 000 genes, this was no easy task. In the process he picked up the necessary coding skills to identify and name all 10 053 genes, and to identify those responsible for the wood-degrading character of the fungus.

Dr Volschenk says the next step is to understand the fungus’ mechanism of breaking down wood and producing sugars on a molecular level: “With the genetic blueprint now available, we can study the network of genes and proteins the fungus employs to convert wood and other similar renewable resources into more valuable products,” he explains.

The sequence data for C. pulveracea have been deposited at the DNA Data Bank of Japan (DDBJ), the European Nucleotide Archive (ENA) at Cambridge, and GenBank in the United States of America, under the accession number QVQW00000000 and is freely available to all researchers in this field.

Read the paper: Microbiology Resource Announcements

Article source: Stellenbosh University

Image credit: Heinrich Volschenk

Plants can skip the middlemen to directly recognize disease-causing fungi

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Scientists at the Max Planck Institute for Plant Breeding Research in Cologne have revealed that direct physical associations between plant immune proteins and fungal molecules are widespread during attempted infection. The authors’ findings run counter to current thinking and may have important implications for engineering disease resistance in crop species.

Fungal diseases collectively termed powdery mildew afflict a broad range of plant species, including agriculturally relevant cereals such as barley, and result in significant reductions in crop yield. Fungi that cause powdery mildew deliver so-called effector molecules inside plant cells where they manipulate the host’s physiology and immune system. In response, some plants have developed Resistance (R) genes, usually intracellular immune receptors, which recognize the infection by detecting the fungus’ effectors, often leading to plant cell death at the site of attempted infection to limit the spread of the fungus. In the prevailing view, direct recognition of effectors by immune receptors is rather a rare event in plant-pathogen interactions, however, and it has been thought instead that in most cases recognition proceeds via other host proteins that are modified by the pathogen.

In barley populations, one of the powdery mildew receptors, designated mildew locus a (Mla), has undergone pronounced diversification, resulting in large numbers of different MLA protein variants with highly similar (>90%) DNA sequences. This suggests co-evolution with powdery mildew effectors, but the nature of the evolutionary relationship and interactions between immune receptor and effectors remained unclear.

To address these questions, Isabel Saur, Saskia Bauer, and colleagues from the department of Paul Schulze-Lefert first isolated several effectors from powdery mildew fungi collected in the field. Except for two, these proteins were all highly divergent from one another. When the authors expressed the effectors together with matching MLA receptors this led to cell death not only in barley but also in distantly related tobacco cells, already suggesting that no other barley proteins are required for recognition. Using bioluminescence as a marker for direct protein-protein interactions, the scientists indeed found specific associations of effector-MLA pairs in extracts of tobacco leaves. Similarly, a protein-protein interaction assay in yeast also revealed interactions only of matching effector-MLA pairs. These results suggest that highly sequence-related MLA receptor variants directly detect unrelated fungal effectors.

Plant disease is a major cause of loss of yield in crops. Transfer of plant R genes between species is a potentially powerful approach to generate disease-resistant crops. The authors’ discovery that multiple variants of the same resistance gene are able to bind dissimilar pathogen proteins, also in distantly related plant species, underlines the potential of this approach and chimes in with the earlier finding that wheat versions of Mla, Sr33 and Sr50, provide disease resistance to the stem rust isolate Ug99, a major threat to global wheat production.

Paul Schulze-Lefert sees further exciting applications on the horizon: “Our discovery that direct receptor-effector interactions are widespread for MLA receptors suggests that it may be feasible to rationally design synthetic receptors to detect pathogen effectors that escape surveillance by the plant immune system.”

Read the paper: eLife

Article source:Max Planck Institute for Plant Breeding Research

Image credit: Takaki Maekawa

World’s biggest terrestrial carbon sinks are found in young forests

By | Climate change, Forestry, News

More than half of the carbon sink in the world’s forests is in areas where the trees are relatively young – under 140 years old – rather than in tropical rainforests, research at the University of Birmingham shows.

These trees have typically ‘regrown’ on land previously used for agriculture, or cleared by fire or harvest and it is their young age that is one of the main drivers of this carbon uptake.

Forests are widely recognised as important carbon sinks – ecosystems capable of capturing and storing large amounts of carbon dioxide – but dense tropical forests, close to the equator have been assumed to be working the hardest to soak up these gases.

Researchers at the Birmingham Institute of Forest Research (BIFoR) have carried out fresh analysis of the global biosphere using a new combination of data and computer modelling in a new study published in the Proceedings of the National Academy of Sciences of the United States of America (PNAS). Drawing on data sets of forest age, they were able to show the amount of carbon uptake between 2001 and 2010 by old, established areas of forest.

They compared this with younger expanses of forest which are re-growing across areas that have formerly experienced human activities such as agriculture or logging or natural disturbances such as fire.

Previously it had been thought that the carbon uptake by forests was overwhelmingly due to fertilisation of tree growth by increasing levels of carbon dioxide in the atmosphere.

However, the researchers found that areas where forests were re-growing sucked up large amounts of carbon not only due to these fertilisation effects, but also as a result of their younger age. The age effect accounted for around 25 per cent of the total carbon dioxide absorbed by forests. Furthermore, this age-driven carbon uptake was primarily situated not in the tropics, but in the middle and high latitude forests.

These forests include, for example, areas of land in America’s eastern states, where settlers established farmlands but then abandoned them to move west towards the end of the 19th century. The abandoned land became part of the US National Forest, along with further tracts abandoned during the Great Depression in the 1930s.

Other significant areas of forest re-growth include boreal forests of Canada, Russia and Europe, which have experienced substantial harvest activity and forest fires. Largescale reforestation programmes in China are also making a major contribution to this carbon sink.

Dr Tom Pugh, of the Birmingham Institute of Forest Research (BIFoR), explained: “It’s important to get a clear sense of where and why this carbon uptake is happening, because this helps us to make targeted and informed decisions about forest management.”

The research highlights the importance of forests in the world’s temperate zone for climate change mitigation, but also shows more clearly how much carbon these re-growing forests can be expected to take up in the future. This is particularly important because of the transient nature of re-growth forest: once the current pulse of forest re-growth works its way through the system this important part of the carbon sink will disappear, unless further reforestation occurs.

“The amount of CO2 that can be taken up by forests is a finite amount: ultimately reforestation programmes will only be effective if we simultaneously work to reduce our emissions,” explains Dr Pugh.

Read the paper: PNAS

Article source:University of Birmingham

Image credit: CCO Public domain