Tag Archives: Fungi

Jacques Monod Annual Conference on Bacterial-Fungal Interactions 2013

The first Jacques Monod Conference on Bacterial-Fungal Interactions will be held at Roscoff in Britanny (France) from December 8 to 11, 2013.


The official meeting title will be: “Bacterial-fungal interactions: a federative field for fundamental and applied microbiology“. There is an impressive list of speakers tentatively scheduled to speak.

Register for the conference here and see more information on Francis Martin’s Blog – MycorWeb Fungal Genomics.  The deadline for application to the meeting is September 15th, 2013.

Fungi: The Rotten World About Us

Here’s another video I like to show students and I find it quite entertaining — although from 1980 it’s a little dated.  This version was recorded from VHS, so the image quality isn’t so great.  This video was put together by wildlife producer Barry Paine working with the BBC for its renowned “The World About Us” series and made it’s way to the US and appeared on the PBS show Nature in the early 80’s.

Carbohydrate binding gene family expansion in the amphibian pathogen Batrachochytrium dendrobatidis

You’d have to be living under a rock – as some amphibians do – to not be aware of the massive extinction facing our vertebrate friends living within aquatic habitats.  Researchers still don’t fully understand what is causing the amphibian mass-extinction – stress from habitat loss, increased chemical concentrations in the environment, and an auto-immune degrading infection have all been proposed.  What is known is that the chytrid fungus Batrachochytrium dendrobatidis – opportunistic or not – is infecting and killing a large number of amphibians.

What is not fully understood about B. dendrobatidis is its pathogenicity and what mechanisms it employs to cause infection.  A recent paper, “Species-Specific Chitin-Binding Module 18 Expansion in the Amphibian Pathogen Batrachochyrium dendrobatidis”, published in the mBio journal by John Abramyam & Jason Stajich at UC Riverside, begins to address this pathogenicity.  As the authors point out – more than 100,000 species of fungi have been described to date and very few of them are pathogenic.  This means that the ability to be pathogenic is derived from somewhere: genome expansion events, gene family duplication and diversification events – and we’re only starting to understand horizontal gene transfer events in fungi. This paper addresses the expansion of a gene family across two B. dendrobatidis genomes that are associated with pathogenicity.

When comparing the genomes of B. dendrobatidis with the genomes from other chytrid fungi there has been an expansion of genes within the family Carbohydrate-Binding Module Family 18 (CBM18).  The CBM18 family is a large group of proteins that have been implicated in other fungal pathogenic infections on both plants and animals.  The authors here question whether this interesting lineage specific expansion of CBM18 in B. dendrobatidis could be associated with the virulence of its pathogenicity on amphibians.

The authors used the CBM18 protein family domain HMM to search across the B. dendrobatidis genomes and found an increase in the number of domains when comparing it to genome of its closest relative.  When constructing phylogenetic trees of the CBM18 gene family, three monophyletic and strongly supported clades emerged.  When focusing on divergence of the protein domains, the authors determined that individual domain groups were monophyletic and showed a general pattern with regards to their genome locations.

More specifically, clades of the CBM18 family appears to possess different gene functions, some of which appear to be similar to lectins (LL), tyrosinase/catechol oxidases (TL), and chitin deacetylases (DL).  The function of these genes has yet to be experimentally determined, but the authors make some deductions based on DNA sequences.  The lectin-like genes may be involved in the sequestering of chitin, which could then be disrupting the amphibian immune response.  The tyrosinase/catechol oxidase gene family is associated with melanin synthesis, which could be disrupting the electron transport of the infected amphibians.  Lastly, chitin deacetylases may be involved in suppressing defense mechanisms in place to suppress the fungal infection of the host.  The authors plan to continue to elucidate the pathogenicity of B. dendrobatidis in an attempt to understand the ecology and evolution of its infection on amphibians.

International Society for Human & Animal Mycology Meeting 2012

The 18th Congress of the International Society for Human and Animal Mycology (ISHAM 2012) will be held in Berlin, Germany, from June 11th to 15th, 2012.

The conference organizers have prepared a great selection of speakers in their program.  Check on their website for more information on the meeting.

The Genomes of Two Thermophilic and Biomass-Degrading Fungi, Thielavia terrestris and Myceliophthora thermophila

One of the hurdles to the production of cellulosic biofuel is the economic breakdown plant biomass.  Currently, fungi used to break down plant biomass operate at, or slightly above, room temperature.  Chemical reactions at room temperature proceed slowly, are less efficient, and may be riddled with contaminating fungi which lower the efficiency of the breakdown process.  One scientific goal is to increase the heat in bioreactors with the hopes of speeding up the degradation using efficient fungal enzymes that operate at higher temperatures.

In an effort find thermostable fungal degradative enzymes, researchers have sequenced the genomes of two fungi, Thielavia terrestris and Myceliophthora thermophila, known for their ability to survive at high temperatures, namely 40oC to 75oC.  A report entitled “Comparative Genomic Analysis of the Thermophilic Biomass-Degrading Fungi Myceliophthora thermophila and Thielavia terrestris” has been published online on October 2nd in the journal Nature Biotechnology.  (Image: Myceliophthora thermophila link)

The 38.7 Mbp genome of M. thermophila and the 36.9 Mbp genome of T. terrestris are the first thermophilic eukaryotes to have their genomes sequenced, and contain seven and six complete chromosomes, respectively.  The genome of M. thermophila contains 9,110 protein-coding genes and there are 9,813 such genes in the genome of T. terrestris.  Both filamentous Ascomycetes – placed in the class Sordariomycetes and family Chaetomiaceae – have a similar level of genomic organization, barring numerous translocations and transversions.  When considering the three species with sequenced genomes in the Chaetomiaceae, large portions of the genomes, some of which are greater than 6000 contiguous genes, are shared in syntenous blocks.

Enzymes for the breakdown of plant matter – which can include a wide array of materials from agricultural and forestry waste, recycled pulp and paper products, leaves, etc. – were discovered across the genomes of both T. terrestris and M. thermophila.  These enzymes include numerous carbohydrate-active proteins (CAZymes) which include enzymes in the glycoside hydrolase, polysaccharide lyase, carbohydrate esterase, and glycosyl transferase families.  With some slight differences in regard to the breakdown of specific plant polysaccharides, such as pectin, both fungi can be categorized as general decomposers with regards to their enzyme repertoire.

The researchers then tested the expression of some enzymes identified in these newly sequenced fungal genomes, as well as comparing their diversity to well characterized enzymes from Trichoderma reesei.  Differing from T. reesei, both M. thermophila and T. terrestris have exhibited a proliferation in the GH61 enzyme family, responsible for the degradation of plant cell wall polysaccharides, as well as the GH10 and GH11 xylanase gene families.  The researchers used RNA-Seq to compare the expression of these enzymes on differing plant materials, such as alfalfa and barley straw, which represented characteristic dicot and monocot plants, respectively.  While there are noticeable differences to the degradation of plant material from dicots and monocots by both T. terrestris and M. thermophila, orthologs from both fungal genomes show similar patterns of gene expression, particularly when growing on complex plant substrates.

Research commentaries on this publication can be found here and here.

The Real Threat of ‘Contagion’

In yesterday’s New York Times is a nice opinion piece from Ian Lipkin on real life and real life infectious outbreaks.  You should read it.

Here’s an interesting short film on the “viral” marketing of the movie Contagion.  Obviously, it’s not viral, but bacterial and fungal marketing.

I haven’t seen the movie, so I can’t endorse it one way or another, but I will say Steven Soderburgh has a pretty great track record when it comes to movies.  The above video shows a fascinating way to advertise this movie to audiences (See Jonathan Eisen’s blog post on the subject here).

How Many Species Are There On Earth And In The Ocean?

This week, it’s been hard to miss the new paper, “How many species are there on Earth and in the Ocean?” published by Mora et al. in the August 2011 issue of the journal PLOS Biology.  There have been commentaries or news articles printed in the New York Times, The Economist, The Guardian, Damian Carrington’s Guardian Blog, National Geographic, Yahoo News, AlterNet, MSNBC, Reuters, UNEP, NewsDaily and Ed Yong has posted a commentary on his Google+ page.  Furthermore, some well respected scientists who study biological diversity have joined the debate too: Jonathan Eisen has devoted two blog posts to the paper (one about the actual paper in PLOS Biology and another on the National Geographic commentary) and there is a commentary from Robert May in PLOS Biology about the study and its significance.  Since there is ample information on the study elsewhere, let me communicate a brief summary of the study and some of my feelings about the paper.

It’s quite embarrassing that we have really no clue how much biological diversity is found on this planet.  Adding insult to injury is the fact that we have no concept of the current magnitude of the loss of diversity due to human induced mass extinctions.  This paper seeks to predict total global biological diversity by documenting current taxonomic numbers and extrapolating consistent patterns to estimate the number of species that have yet to be identified.

The methods of the authors essentially consisted of three parts.  First, the authors compiled a list of approximately 1.2 million species pulled from numerous biological databases.  Second, they surveyed a little over 500 taxonomists who were asked to identify the validity of current scientific names and comment on the intensity of current taxonomic efforts to describe new species.  Third, the authors analyzed this data to find the estimated global numbers of biological taxa for each phylum.

The authors show a predictable pattern in the classification of species (at the phylum, class, order, family, and genus level) at least consistently for animals.  By evaluating these patterns using regression, the authors validated this by closely examining 18 taxonomic groups that we think we understand their total biological diversity.  By doing this, the authors come up with a total estimate of 7.7 million species of animals (mostly insects), close to 300,000 species of plants, more than 600,000 species of fungi, and a total estimate of roughly 9 million eukaryotes on Earth.  The authors estimate that 86% of species on Earth and 91% of species in the oceans still have not been formally described.  Previous estimates of species diversity have been wide: anywhere between 3 million to a 100 million species.

This paper is a novel and worthwhile attempt to determine the total amount of species diversity on this planet.  Despite this, I think – and the authors have their own reservations – that there are some serious problems with some of their calculations.

One problem is that the study is based mainly on using animals, and vertebrates for that matter – which are the best described of any phylum, as the baseline for measuring the completeness of species diversity.  I would argue that plants and fungi, and obviously bacteria, archaea, and “the protists” are clearly not well known enough to extrapolate any serious estimate species numbers especially when considering vertebrate animals as a baseline and whose numbers are largely skewed.

Another problem is in our collective definition of species, as well as taxonomic subjectivity of the categorization of other taxonomic hierarchies, which are based on the on the homology of shared characters and, I would argue, are largely incomparable outside of each phylum.  For example, what one taxonomist calls an order in one grouping may not be equivalent to what another taxonomist calls a completely different order in another completely different grouping.

I should point out that the authors don’t ignore these caveats, but they still exist in their study.  In any event, this paper is important because it adds to the dialogue concerning species diversity, the need to estimate, inventory and preserve the massive amount of diversity we share on the planet.

UPDATE: More commentaries in the news can be found here, here, and here.