Monthly Archives: February 2011

XV International Congress on Molecular Plant-Microbe Interactions

The XV International Congress on Molecular Plant-Microbe Interactions has shaped up to be an amazing meeting.  A stellar group of researchers will be presenting at the meeting.  Registration is open now.

Directly from the meeting website:  “The XV International Congress on Molecular Plant-Microbe Interactions is recognized as the most important international meeting for plant-microbe interactions to discuss research and network with colleagues from around the world.  This meeting is the global venue for presenting and discussing new research and developments in molecular plant-microbe interactions.  Through plenary lectures, concurrent sessions, special workshops and various events, attendees experience innovative plant-microbe interactions research.  The meeting features hundreds of abstracts and provides networking and professional development opportunities.”

First Steps Toward Learning the Language of Mycorrhizal Communication

I’ve already talked about mycorrhizal associations numerous times (here and here), so if you’re not already used to hearing about mycorrhizae, you will if you continue to read this blog.  In this recent paper, entitled “Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza“, published online in the journal Nature, the authors Maillet et al address plant and fungal interactions of arbuscular mycorrhizal associations.  Using the Glomus intraradicesMedicago truncatula model system, the researchers identify diffusible chemical signals produced by the fungus during initiation of the mycorrhizal association with the plant.

It has been hypothesized that both fungi and bacteria interacting with plant roots do so using similar genetic mechanisms.  It has already been shown that rhizobial bacteria – particularly the nitrogen fixing microbes associated with leguminous plants – produce lipochitooligosaccharide (LCO) signals used in the  communication with host plants.  The authors of this study discovered that the fungus Glomus intraradices, like the nitrogen-fixing bacteria, secretes an array of sulfated and non-sulfated simple LCOs which stimulated the formation of arbuscular mycorrhizae in disparately related plants, such as Medicago (Fabaceae), Daucus carota (Wild Carrot; Apiaceae), and Tagetes patula (French Marigold; Asteraceae).  These compounds were found in Glomus intraradices both interacting with plant roots and in free-living resting spores in the soil.

Comparing the genes involved in the transduction of the LCO signals in both rhizobial bacteria associated with legumes and arbuscular mycorrhizal fungi associated with land plants yielded similar gene expression pathways.  In order to validate the role of LCOs in mycorrhizae formation, the researchers genetically engineered non-plant interacting bacteria to produce the LCOs from Glomus.  These engineered bacteria increased mycorrhizae formation in plants already associated with Glomus.  Fungal LCOs were also found to induce root branching, a trait long associated with the formation of mycorrhizae in plants.  There is a nice commentary on this research article located here.

Lessons Learned from Ectomycorrhizal Fungal Genome Sequencing

Genome sequencing has provided us with an amazing amount of information regarding organismal biology and mycorrhizal fungi are some of the most interesting of the organisms who have had their genomes sequenced.  Maybe I am a little partial to these fungi because I study them intimately, but new sequencing technology has made this an exciting time for people like me.

Ectomycorrhizal fungi are a polyphyletic group of organisms which form a symbiotic association with the roots of tree species (the word ‘mycorrhizal’ literally means plant-fungal unions).  This association has typically been recognized by the exchange of nutrients and water from the fungus to the plant and the exchange of sugars derived from photosynthesis from the plant to the fungus.  Although ectomycorrhizal fungi only form mycorrhizae  with 3% of plant species (arbuscular and other mycorrhizal fungi associate with approximately 92% of plants), these associations are with a diverse array of plant lineages, including the Betulaceae, Cistaceae, Dipterocarpaceae, Fabaceae, Fagaceae, Myrtaceae, Pinaceae, and Saleceae.  Plants in these families cover almost the entire portion of boreal, temperate, Mediterranean, and sub-tropical woodlands, so their importance is significant.  It’s very interesting to note that these associations have independently arisen at least eight times within the angiosperms and between six and eight times in the gymnosperms.  Mycorrhizal associations are thought to have originated when plants and fungi climbed onto land together (more on that here).

The sequencing of both fungal and plant genomes over the last few years has led to greater understanding of how these organisms interact during their mutualistic associations.  Although genome sequencing has addressed some long established questions, there are many more questions that have arisen from these sequencing efforts.  This recent review in Trends in Genetics by Jonathan Plett and Francis Martin of INRA-Nancy, two of my collaborators, addresses the current state of our knowledge of  the ectomycorrhizal symbiosis and poses directions for future research in this vital research area.

Currently, only two ectomycorrhizal fungal genomes (Basidiomycete mushroom Laccaria bicolor & Ascomycete truffle Tuber melanosporum) have been sequenced, but other fungi (see the Mycorrhizal Genomes Project) are scheduled to be sequenced by the Martin Lab through JGI.  With a genome size of 65 Mb Laccaria bicolor has the largest amount of protein coding regions of any sequenced fungus, and Tuber melanosporum has the largest genome of any sequenced fungus at 125 Mb but has one of the least dense genomes.

The nature of mutualistic symbiotic relationships imply that both organisms benefit from the association and both ectomycorrhizal fungi and their host plants fulfill this criteria.  Unlike saprotrophic fungi, ectomycorrhizal fungi are very poorly suited to degrade cellulosic plant material, but they are able to access soil nutrients via a large biological toolbox of secreted proteases and phosphorus transporters.  Both Laccaria bicolor and Tuber melanosporum, which have very different genomes, exhibit a very similar suite of symbiosis-induced nutrient cycling enzymes, which suggest that providing nutrients to the host plant is a key defining feature of ectomycorrhizal fungi.  Interestingly, Laccaria bicolor and Tuber melanosporum rely on differing mechanisms of interacting with their host and acquiring carbon from the environment.  Laccaria bicolor appears to be less dependent on the host and more active at acquiring carbon from the soil substrates and, as a result, may act as a weak saprotroph in the environment.  Tuber melansporum is more aggressive in its colonization of plant roots and does not appear to be able to acquire carbon from the soil and therefore is more dependent on the host for its survival.

Information gathered from fungal genomes suggests that a majority of the biochemical and genetic control over the initiation of the mycorrhizal association comes from the fungal partner, which makes sense given that the fungus has more energy to gain from the association.  Most mycorrhizal fungi are unable to acquire carbon from the environment so they are completely reliant on hand outs from their host plants.  It appears that mutualistic fungi share similar mechanisms with pathogenic fungi and bacteria when interacting with plants, including the use of small secreted proteins which interact directly with plant cells.

With the sheer amount of genomic data being generated it’s an exciting time to be a scientist, especially one who studies mycorrhizal fungi.  Over the next few years, especially with sequencing projects scheduled for completion, we will have even more data to shed light on the amazing biological associations of plants and microbes.

(Above Photo: section of Populus/Laccaria ectomycorrhizal root – JM Plett © INRA)

Bioenergy Trees – An Upcoming New Phytologist Symposium

Fuels derived from cellulosic biomass are increasingly becoming a priority as we focus both on reducing the large amount of greenhouse gases we introduce into the atmosphere and our dependence on unsustainably sourced fossil reserves.  Liquid or solid biofuels derived from cellulosic materials, such as trees, will address these criteria while also assisting agricultural development in rural areas by promoting sustainable coppice harvesting on marginal lands not suitable for consumption crop production.  The use of next-generation genomics technologies, as well as more traditional biological research methods, will help develop and enhance tree growth in no- to low-input environments.  Additionally, genomic resources will contribute to understanding the process of cell wall formation in woody plants and allow researchers to optimize the composition of plant cell walls for bioenergy concerns.

In the upcoming meeting “Bioenergy Trees” – sponsored by the journal The New Phytologist in their ongoing series of symposia – will address the development of trees and other woody biomass for bioenergy purposes.  This meeting will be held at INRA-Nancy, in Nancy/Champenoux, France, from May 17th to 19th, 2011.  Registration is now open.  In addition to this very pertinent research topic, Nancy is truly a magical place, so it’s with great excitement that I tell you about this meeting.

In addition, The New Phytologist has announced the next round of symposia for 2012 here.

Newly Identified Branch of Marine Eukaryotes on the Tree of Life

We’re only just now starting to get a grasp on the sheer amount of global biological diversity, most of which has been very difficult to observe with conventional observational means.  Changes in technology and sampling strategies have resulting in the acquisition of information regarding many previously undocumented forms of biological life.  Along with microorganisms associated with plant roots – the strict focus on my research interests – phytoplankton represent a large group of organisms that we still know little about.  For selfish reasons I was interested in this study because I wanted to see how these authors addressed ways of learning more about a previously unknown lineage of ocean phytoplankton.  As evidenced by next generation sequencing efforts, there are many unknown and undescribed fungi in soils and there is a huge amount of commonality of the diversity of microbial life in soils and oceans.

Published in the Proceedings of the National Academy of Sciences, a study entitled “Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life”, by Kim et al, describes a recently identified and previously uncultured marine and freshwater microalgal lineage of Eukaryotic organisms.  The researchers title this group of phytoplankton the rappemonads, from the initial paper (authored by Rappé et al 1998) that reported unknown DNA sequences from this lineage.  The researchers designed nucleotide primers and fluorescent probes from initial DNA sequences (from the Rappé et al study) and used these molecular diagnostics to observe marine and freshwater samples for their presence or absence of these unknown organisms.

Phylogenetic analysis of environmental nucleotide sequences revealed that rappemonads are related to both haptophyte and cryptophyte algae but constitute a diverse and independent lineage.  To resolve the phylogenetic position of the rappemonads the authors designed specific nucleotide primers spanning the 18S-ITS1-5.8S-ITS2-28S rRNA genes and sequenced this gene cluster.  The authors used maximum likelihood algorithms to construct a phylogeny, which resolved the rappemonads between the haptophyte and cryptophyte algae.  It should be made clear that there is low branch support (at around 50) for some of these clades, so more data is needed for strict resolution of the red plastid algae.

Probes for fluorescent in situ hybridization were developed to observe rappemonads.  Rappemonads were described to be relatively large in size – approximately 6 µm in diameter versus the smaller picophytoplankton (2 to 3 µm) – significantly larger than open-ocean phytoplankton.  Rappemonads appear to contain two to four plastids and are putatively photosynthetic.

Using quantitative PCR methods, the authors identified high concentrations of rappemonads in late-winter blooms along the surface waters at a site in the Sargasso Sea.  Rappemonads were rare or absent in stratified summertime conditions, when concentrations of chlorophyll containing microorganisms are at their highest in deep waters.  Rappemonads were frequently found in North Pacific anticyclonic eddy samples, which are characterized by colder more nutrient-rich waters that have been brought to the sea surface.  When considering water characteristics (such as depth, salinity, phosphate, nitrate, and nitrite), there were no statistical significance between samples containing rappemonads and those where they were absent.  In addition, rappemonads were found in both marine and freshwater conditions, bringing into question when and where one may find these organisms and which would warrant further study.

Comparative Genomics Of Eukaryotic Microorganisms Meeting

I’m not sure if I am going to be able to make this meeting, but I thought I would pass on the information to you.  The list of speakers is excellent and it’s in a beautiful location.  This is a biannual meeting on the comparative genomics of Eukaryotic microorganisms sponsored by the European Molecular Biology Organization (EMBO).

Registration and meeting information is located here.