Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Retracing the Roots of Fungal Symbioses

27.02.2015

Understanding how plants and fungi developed symbiotic relationships

With apologies to the poet John Donne, and based on recent work from the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, it can be said that no plant is an island, entire of itself. Unseen by the human eye, plants interact with many species of fungi and other microbes in the surrounding environment, and these exchanges can impact the plant’s health and tolerance to stressors such as drought or disease, as well as the global carbon cycle.


Francis Martin, INRA

Mycorrhizal fungi include some of the most conspicuous forest mushrooms, such as the iconic fly agaric (Amanita muscaria), one of the fungi sequenced for this project. Recent studies indicate that mycorrhizal fungi also play a significant role in belowground carbon sequestration, which may mitigate the effects of anthropogenic CO2 emissions.

Mycorrhizal fungi live in the roots of host plants, where they exchange sugars that plants produce by photosynthesis for mineral nutrients that fungi absorb from the soil. They include some of the most conspicuous forest mushrooms, including the iconic, flaming red “fly agaric,” Amanita muscaria, and are of interest to bioenergy researchers, because they play roles in maintaining the health of candidate feedstock crop trees. Recent studies indicate that mycorrhizal fungi also play a significant role in belowground carbon sequestration, which may mitigate the effects of anthropogenic CO2 emissions.

To understand the basis for fungal symbiotic relationships with plants, a team of DOE JGI researchers led by Igor Grigoriev and longtime collaborators at the French National Institute for Agricultural Research (INRA) and Clark University conducted the first broad, comparative phylogenomic analysis of mycorrhizal fungi, drawing on 49 fungal genomes, 18 of which were sequenced for this study. The 18 new fungal sequences included 13 mycorrhizal genomes, from ectomycorrhizal fungi that penetrate the host roots, and including species that comingle with orchid and heathland (which include blueberry, heather, and heath) plant roots. In the February 23, 2015 online edition of Nature Genetics, these researchers describe how the comparative analyses of these genomes allowed them to track the evolution of mycorrhizal fungi. The results help researchers understand how plants and fungi developed symbiotic relationships, and how the mutualistic association provides host plants with beneficial traits for environmental adaptation.

Starting with previously sequenced mycorrhizal fungi

“Mycorrhizal symbioses are highly complex, but analyses of the 49 genomes indicate that they have evolved independently in many fungal lineages,” said INRA’s Francis Martin, one of the study’s senior authors. To understand the genetic shifts underlying the repeated origins of mycorrhizal lifestyles, the researchers focused on enzymes that degrade plant cell walls from 16 gene families associated with plant cell wall degradation. They took their cue from the first sequenced ectomycorrhizal fungus, Laccaria bicolor and the first sequenced arbuscular mycorrhizal fungus Rhizophagus irregularis– all work done at the DOE JGI–which illuminates the origins and evolution of these enzymes, knowledge to be applied in collaboration for improving biomass breakdown for biofuels production.

Through molecular clock analyses, which combine genome-scale molecular data with fossil calibrations, the team could work backwards to estimate when saprotrophic and mutualistic lineages last shared common ancestors based on the amount of divergence.

The analyses of the fungal genomes and fossils suggested that in comparison to brown rot fungi and white rot fungi that evolved over 300 million years ago, ectomycorrhizal fungi emerged fairly recently from several species and then spread out across lineages less than 200 million years ago. The team also found that up to 40 percent of the symbiosis-induced genes were restricted to a single mycorrhizal species.

Fungi evolving to break down plant cell walls

David Hibbett of Clark University, another of the study’s senior authors, compared the work to a previous collaboration with the DOE JGI detailed in Science to trace the evolution of white rot fungi, which are capable of breaking down cellulose, hemicellulose and lignin in plants. Prior to the emergence of white rot fungi hundreds of millions of years ago, fungi were not capable of breaking down lignin, and the undecayed plant mass became the basis of large coal deposits.

“Together these studies tell a story about how mushroom-forming fungi evolved a complex mechanism for breakdown of plant cell walls in ‘white rot’ and then cast it aside following the evolution of mycorrhizal associations, as well as the alternative decay mechanism of ‘brown rot,’” Hibbett said. “The other major part of the story is that in mycorrhizal lineages there is a huge turnover in genes that are upregulated in the symbiosis-many of these have no homologs in even closely related species, suggesting that the evolution of the symbiosis is associated with massive genetic innovation.”

Martin chimed in: “Many of these genes are likely used to control plant immunity during the massive colonization of root tissues by the fungus.”

DOE JGI’s Igor Grigoriev also pointed out, “This first large-scale study of mycorrhizal genomics is also the first step in both broader and deeper exploration of mycorrhizal diversity, their interactions with host plans, and roles in forest ecosystems using genomics tools, which are the focus areas for the JGI Fungal Genomics Program.”

Martin, leader of the Mycorrhizal Genomics Initiative, a DOE JGI Community Science Program project, is presenting on “Harnessing Genomics for Understanding Tree-Microbe Interactions in Forest Ecosystems” at the 10th Annual Genomics of Energy & Environment Meeting, set for March 23-26, 2015 in Walnut Creek, California. To register for the meeting, and to see the rest of the agenda, go to http://usermeeting.jgi.doe.gov . Annegret Kohler, the first author on the Nature Genetics paper, will present on aspects of this work at the fungal workshop that precedes the meeting: http://usermeeting.jgi.doe.gov/2015-workshops/ .

For those interested in exploring new project submissions, the 2016 Community Science Program call for letters of intent deadline is April 16, 2015. More information can be found at http://bit.ly/JGI-2016-CSP 

The U.S. Department of Energy Joint Genome Institute, User Facility of Lawrence Berkeley National Laboratory supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov

Contact Information
David Gilbert
Public Affairs Manager, DOE Joint Genome Institute
degilbert@lbl.gov
Phone: 925-296-5643

David Gilbert | newswise

Further reports about: Genome Institute JGI Laboratory Roots analyses cell walls fungal fungi genes genomes mycorrhizal mycorrhizal fungi plant cell species

More articles from Life Sciences:

nachricht Quality control in immune communication: Chaperones detect immature signaling molecules in the immune system
20.09.2019 | Technische Universität München

nachricht Moderately Common Plants Show Highest Relative Losses
20.09.2019 | Universität Rostock

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: 'Nanochains' could increase battery capacity, cut charging time

How long the battery of your phone or computer lasts depends on how many lithium ions can be stored in the battery's negative electrode material. If the battery runs out of these ions, it can't generate an electrical current to run a device and ultimately fails.

Materials with a higher lithium ion storage capacity are either too heavy or the wrong shape to replace graphite, the electrode material currently used in...

Im Focus: Stevens team closes in on 'holy grail' of room temperature quantum computing chips

Photons interact on chip-based system with unprecedented efficiency

To process information, photons must interact. However, these tiny packets of light want nothing to do with each other, each passing by without altering the...

Im Focus: Happy hour for time-resolved crystallography

Researchers from the Department of Atomically Resolved Dynamics of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg, the University of Hamburg and the European Molecular Biology Laboratory (EMBL) outstation in the city have developed a new method to watch biomolecules at work. This method dramatically simplifies starting enzymatic reactions by mixing a cocktail of small amounts of liquids with protein crystals. Determination of the protein structures at different times after mixing can be assembled into a time-lapse sequence that shows the molecular foundations of biology.

The functions of biomolecules are determined by their motions and structural changes. Yet it is a formidable challenge to understand these dynamic motions.

Im Focus: Modular OLED light strips

At the International Symposium on Automotive Lighting 2019 (ISAL) in Darmstadt from September 23 to 25, 2019, the Fraunhofer Institute for Organic Electronics, Electron Beam and Plasma Technology FEP, a provider of research and development services in the field of organic electronics, will present OLED light strips of any length with additional functionalities for the first time at booth no. 37.

Almost everyone is familiar with light strips for interior design. LED strips are available by the metre in DIY stores around the corner and are just as often...

Im Focus: Tomorrow´s coolants of choice

Scientists assess the potential of magnetic-cooling materials

Later during this century, around 2060, a paradigm shift in global energy consumption is expected: we will spend more energy for cooling than for heating....

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Optical Technologies: International Symposium „Future Optics“ in Hannover

19.09.2019 | Event News

Society 5.0: putting humans at the heart of digitalisation

10.09.2019 | Event News

Interspeech 2019 conference: Alexa and Siri in Graz

04.09.2019 | Event News

 
Latest News

Quality control in immune communication: Chaperones detect immature signaling molecules in the immune system

20.09.2019 | Life Sciences

Moderately Common Plants Show Highest Relative Losses

20.09.2019 | Life Sciences

The Fluid Fingerprint of Hurricanes

20.09.2019 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>