Tag Archives: Ascomycete Fungi

Drought-Induced Decline in Mediterranean Truffle Harvest

Some of my favorite foods are truffles, and perhaps the best tasting truffle – in my humble opinion – is the famous Périgord Black Truffle, also known as Tuber melanosporum, which is known as a prized delicacy capable of fetching a pretty penny.

me holding truffle

Tuber melanosporum is an important ectomycorrhizal fungus that can be cultivated with crop trees such as Hazelnut, and other truffles can be cultivated with other nut trees such as Pecan.  Despite a concerted effort to understand the biology of T. melanosporum, both through a genome sequence and other molecular tools to understand population biology – as well as government efforts to promote cultivation with nut trees – harvests of the Périgord Black Truffle have been declining since the 1970s.  There has been no agreement in what has been causing this decline from a community of researchers.

truffle climate change paper header

In a brief report entitled “Drought-Induced Decline in Mediterranean Truffle Harvest” in the journal Nature Climate Change, Büntgen et al. recently described how climate change may be affecting truffle production, either directly, or by affecting the biology of the truffle’s host trees.  Such measurements are challenging in numerous regards; inspecting climate data is difficult enough, but reports of truffle harvesting are scarce for many reasons, one of which is the fact that many successful truffle collectors are reluctant to give information about their productive grounds.

truffle climate paper figure

The authors correlated climate details from 12 climate models with truffle harvests from various parts of Europe (namely Aragón in Spain, Périgord in southern France, and Piedmont and Umbria in Northern Italy).  They observed that tree ring growth in Oak trees and truffle production were correlated and showed that increased measurements of summer evapotranspiration could explain both the reduction in plant growth and truffle production.

The authors hypothesize that tree and fungus competition for summer soil moisture may be reducing the production on truffle sporocarps.  Unless the present course of climate change is reversed, it is expected that truffle harvests in Europe will continue to decline.  This is bad news not just for the truffles and trees, but the people who enjoy both.

UPDATE: The New York Times have posted an article (December 20th) entitled “$1,200 a Pound, Truffles Suffer in the Heat

Fungal Meningitis Outbreak

Sorry for the lack of posts as of late, I’ve been a little swamped lately with writing and researching; unfortunately this blog has to suffer sometimes.

I don’t have time to write a complete post right now – maybe soon in the future – but I’ve been closely following the cases of fungal meningitis derived from contaminated injections of the steroid methylprednisolone acetate.  Looks like the main culprit is Exserohilum rostratum, although one person has been infected with a species of Aspergillus. Both of these fungi are extremely common in soils and are plant pathogens.

Here’s some links from the CDC on the current infections:

CDC fungal infections page

CDC information on fungal meningitis

CDC page on the current fungal meningitis ourbreak

As of today, October 12th, the number of infections have been reported from numerous states:

map of fungal meningitis cases

Here’s a quick informational video on fungal meningitis:

Here are some links to news articles published over the few weeks:

CDC: Multistate Meningitis Outbreak Investigation

NYT: Interactive Map – Tracking an outbreak

Meningitis: Top 10 Things CDC Says You Should Know

Fungal Meningitis From Injections: Not Even Close To Over

Republicans Grill FDA Chief On Meningitis Outbreak

Despite Antifungal Treatment, More Woes For Some Meningitis Patients

Pharmacy Owners Had No Hand In Meningitis Outbreak: Lawyers

Second Illness Is Infecting Those Struck by Meningitis

Fungal Meningitis: 404 Cases, 29 Deaths

More bacteria, fungi in drugs from Mass pharmacy

Elio Schaechter’s Small Things Considered: Fungal Meningitis

‘Worried Sick’: Meningitis Risk Haunts 14,000

Documents in Meningitis Case Show Complaints in 1999

Meningitis Outbreak: FDA re-releases list of customers

Meningitis Outbreak Spurs Calls To Strengthen FDA

Meningitis spreads to 19th state, sickens 347

PDF of Food & Drug Administration Assessment of Pharmacy Sterility

FDA: Mold seen in 83 vials of the steroid linked to fungal meningitis outbreak

FDA: Meningitis-linked Pharmacy Knew of Bacteria

Records Show Problems at Steroid Pharmacy as Far Back as ’06

Investigators visit office tied to meningitis cases

Steroid shot near spine gives illness an opening

Fungal meningitis outbreak tied to steroid shots isn’t the first, reports show

NBC News – Experts: Many ways for fungi to taint drugs / Four more die in fungal meningitis outbreak

Sterility Found Lacking at Drug Site in Outbreak

FDA warns of further risk from tainted drugs

Meningitis outbreak rises to 205 cases: CDC

Meningitis: 5th case reported in Minnesota, all women

Another death reported in meningitis outbreak

Legal recriminations begin over major U.S. meningitis outbreak

Lawmakers focus on small drugmakers as meningitis death toll rises

Rare fungal meningitis outbreak spreads to six states

Seven deaths reported in growing meningitis outbreak; second fungus found

U.S. meningitis deaths rise, prompting call for tighter drug rules

Meningitis cases raise questions about steroid shots

CDC: 12 more people infected with fungal meningitis linked to Framingham pharmacy

F.D.A. says avoid drugs from company tied to meningitis

When leaf mold gets in your steroid injection

Meningitis outbreak: 13,000 got suspect steroid shots

Epidural steroid shots debated amid meningitis scare

Rare fungal meningitis outbreak rises; 7 dead, 64 sick

Meningitis outbreak kills seven; continues spreading to ninth state

Fungal meningitis: Know the subtle symptoms

More patients linked to fungal meningitis infections, CDC says

Meningitis outbreak 2012: Steroid related fungal meningitis cases rise to 47

Seven deaths reported in growing meningitis outbreak; second fungus found

U.S. fungal meningitis infections rise to 47

CDC: Death toll in rare fungal meningitis outbreak linked to steroid injections rises to 7

Boston: Former regulator calls for more oversight of compounding pharmacies

UPDATE (December 21st, 2012): CDC Recommends Assertive Clinical Evaluation of Potential Fungal Meningitis Patients

UPDATE (December 21st, 2012): Tainted steroids cause spine infections in addition to meningitis; all patients face grueling recovery

UPDATE (January 6th, 2013): Massachusetts governor offers new pharmacy rules

Common Toolbox Based On Necrotrophy In A Fungal Lineage

One of the most exciting aspects of the genomic revolution in biology is understanding the genetic mechanisms behind an organisms natural history.  Within the fungi it has been fascinating to begin to tease apart how seemingly similar life histories can be explained by disparate genomic landscapes, or opposingly, how completely different modes of survival can be explained by a common set of genes.  There has been a steady increase in research over the last few years documenting a large array of tools in the genomic toolbox.

A recently published paper in the journal PLOS One, authored by Andrew et al., entitled “Evidence for a Common Toolbox Based on Necrotrophy in a Fungal Lineage Spanning Necrotrophs, Biotrophs, Endophytes, Host Generalists and Specialists” comes from the Kohn Lab at the University of Toronto, which has long studied the fungal family Sclerotiniaceae.  The Sclerotiniaceae is a group of Ascomycetes known for being typically necrotic pathogens which are host generalists or specialists.

This is a great group of fungi to address questions like: why is one species necrotic while another is just biotrophic? …and why are some fungi specialists, while others generally infect plants without regard to taxonomy?  To address these questions the authors sampled across 52 strains of fungi in the Sclerotiniaceae representing 30 taxa covering the spectrum of host specificity/generality and trophic types.  They chose a suite of genes responsible for both general cell housekeeping (controls, etc.) and associated with pathogenicity and constructed phylogenies of these genes to observe relationships between these 52 strains.  Evidence of positive selection acting on these genes, as well as site-specific selection, was also assessed.  Lastly, the authors assessed the pathogenicity of these strains by initiating infection studies on Arabidopsis thaliana plants.

The authors found that there are at least two origins of biotrophy from a necrotrophic ancestor in the Sclerotiniaceae and that there is evidence of selection on all the genes associated with pathogenicity tested in this study.  The housekeeping genes in this study were used to control for the phylogenetic analysis and showed no evidence of positive selection as opposed to the pathogenicity genes.  Furthermore, likelihood analyses showed no statistical differences in the genes of strains from different trophic lifestyles, as well as host generalists and specialists.

Within this study on the Sclerotiniaceae, it appears that there is a common tool box of genes shared by the fungal strains studied here.  The level of expression of genes differed in this study, which could explain trophic and host specificity differences exhibited by these fungi.  It will be interesting when we have more genome sequences from this family to see how genome structure and rearrangements have contributed to the expression and diversity of genes associated with necrotrophy in this family of fungi.

Human Pathogenic Types of the Fungus Fusarium Detected in Plumbing Drains

I recently wrote about a paper that surveyed the diversity of bacteria in public restrooms using metagenomic techniques.  While that paper focused on bacteria on bathroom surfaces, another recent paper – “Widespread Occurrence of Diverse Human Pathogenic Types of the Fungus Fusarium Detected in Plumbing Drains”, authored by Dylan Short and colleagues – focused specifically on probing the diversity of the large Ascomycete genus Fusarium found in sink drains, with specific focus on isolates that are human pathogens.

The authors sampled 471 drains – more than 95% of which were from public bathroom sinks – from 131 buildings throughout the mid-eastern to southern United States (and California too).  They selectively isolated Fusarium species from sink drains using cotton swabs and then streaked petri plates of Nash-Snyder Agar, which is a semi-selective medium containing the fungicide pentachloronitrobenzene.  The plates were inspected after the fungi had some time to grow, were propagated, and then verified as Fusarium species using microscopic morphology and DNA sequencing.

Six different loci – translation elongation factor (TEF), the internal transcribed spacer region (ITS) into the large ribosomal subunit (LSU), the nuclear rDNA intergenic spacer region (IGS), the RNA polymerase II large subunit (RPB2), portion of the alpha-tubulin (TUB) gene, and calmodulin (CAM) – were identified using Sanger sequencing to assess the diversity of Fusarium in the sink drains.  The sequence data was compared to an extensive database of the genus Fusarium maintained by the Geiser Lab and others.

Fusarium species were extremely common in sink drains; 66% of the sink samples – and 82% of all the buildings sampled – yielded at least one isolate.  These isolates could largely be placed within three Fusarium species complexes: the Fusarium solani species complex (62% of samples), the F. oxysporum species complex (28%), and the F. dimerum species complex (8.5%).  Sink drains from 91% of private residences and 80% of public buildings yielded Fusarium isolates.  Of all the buildings that yielded Fusarium within sink drains, approximately 80% contained one of the six major isolates recognized from human infections.

It is interesting to note that human infections from Fusarium species are rare, but the six most common Fusarium isolates found in sink drains are also the six most common involved in human infection.  The authors note that it’s apparent that people are in constant contact with these fungi within indoor environments.  It’s also notable that novel species complexes were identified using these techniques and that there was a wide phylogenetic breadth to the Fusarium isolates that were sampled from sink drains.

This paper is a substantial contribution to the growing literature documenting the indoor environment for fungi.  The next step would be to use metagenomic techniques – and marker loci for fungi to encompass a meta-taxonomic assessment – to identify all the fungi found in sink drains.

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.