Monthly Archives: December 2011

Old Time Fungal Virulence?

I recently came across an article I found interesting about a widespread geological mystery I was not previously aware of: the presence of filamentous microfossils found worldwide in sediments from the Permian-Triassic boundary transition.  It’s been previously debated that these fossils could be the descendant of either filamentous Ascomycete fungi or freshwater Zygnematateous algae based on their morphology and chemistry.  Either choice represents drastically different scenarios for environmental change that occurred 250 million years on a global scale.  Could the predominance of this organism be the cause of massive plant destruction or the effect of plant destruction from flooding, which is also characteristically found at the end of the Permian period?

In a paper entitled “Fungal virulence at the time of the end-Permian biosphere crisis?”, published in the journal Geology, a group of researchers push the argument toward identifying these fossils – the morphospecies named Reduviasporonites stoschianus – as ancient relatives of the asexually reproducing fungus Rhizoctonia.

Levels of 13C in the fossils do not exclude them from being either fungi or algae, and nitrogen isotope composition would point to a fungal lifestyle.  Cellulosic walls of known filamentous green algae are usually not geologically preserved as well as those identified as Reduviasporonites.  Since there has been no conclusive chemical studies of these microfossils the authors hare rely on microscopic morphological comparisons.

Reduviasporonites stoschianus is found in more than 90% of many geological formations at the time of the Permian–Triassic boundary.  These organisms formed a characteristic “barrel” shaped filaments anywhere between 10 and 90 μm, which look like monilioid hyphae that are typified by Rhizoctonia.  This article states that Rhizoctoniaare mostly Basidiomycota, but some represent Ascomycota” which is incorrect.  Rhizoctonia are placed in the family Ceratobasidiaceae, which is in turn placed in the order Cantharellales of the Basidiomycetes.

It’s certainly difficult to tell the extent of pathogenicity on a host from fossilized material as there few real observations of the invasion of plant tissues.  Furthermore, by observing fossils you are not certain if the presence of these putative fungi is the cause of plant death or a symptom of decline.  While it’s difficult to determine virulence based on fossil evidence, this paper introduces some interesting speculative evidence.

The Medicago Genome Provides Insight Into the Evolution of Rhizobial Symbioses

Legumes are a very successful lineage of plants which have developed associations with soil microbes, most notably endosymbiotic nitrogen fixing bacteria.  Nitrogen fixation is found in specialized plant root structures called nodules.  Published online on November 16th in the journal Nature was the article “The Medicago genome provides insight into the evolution of rhizobial symbioses” by Young et al. (Another paper concerning the Medicago genome recently appeared in the journal PNAS).  Medicago truncatula, the plant sequenced in this paper, is related to the economically important crop alfalfa (Medicago sativa) and is a commonly used model plant to study above and below ground plant biology, most notably interactions with symbiotic microorganisms.

The Medicago genome (like most genomes) is still in the draft stage.  Through the use of bacterial artificial chromosomes (BACs) and direct sequencing of genomic DNA, the researchers estimate the genome of Medicago is upwards of 350 Mb in length.  As an estimation of the completeness of the M. truncatula genome, approximately 94% of expressed genes (as ESTs) map to the draft genome.  An estimated number of genes for M. truncatula is 62,388, with an average gene size of 2,211 base pairs per gene, and an average of 4 exons per gene.  These numbers seem to be in the same “ballpark”, or perhaps larger, than the genomes of Poplar, Rice, and Arabidopsis.

The sequencing of numerous plant genomes, including M. truncatula here, indicates a whole genome duplication event which occurred prior to the split of the rosids from the asteroids at approximately 150 million years ago.  Another whole genome duplication event occurred at approximately 60 million years ago in the Legumes, which yielded several subclades, with Medicago being placed in the Hologalegina clade.

Significant synteny is shared between Medicago and the genomes of other sequenced legumes, Glycine max and Lotus japonicus.  A common ancestor of the legumes underwent a whole genome duplication event, occurring approximately 58 million years ago, and as a result, specific euchromatic regions of Medicago share synteny with numerous regions in each of the Lotus and Glycine genomes, as well as other regions of the Medicago genome.  Additionally, due to a pre-Rosid whole genome duplication event, the genome of Medicago shows synteny to the grape genome in at least three elongated regions.

There has been a high rate of local gene duplication events – some by tandem duplication – in the Medicago genome, and these events are approximately three fold higher than Glycine and one and a half times greater than both Populus and Arabidopsis.  Gene duplication events in Medicago could explain the average to above average number of genes observed in the genome.  Based on the estimated time of origin for the legumes, Medicago has undergone synonymous substitutions at a rate almost twice that of the average rate of vascular plants.

Production of a specialized organ, the root nodule, in many members of the legumes is a trait with both ecological importance and human agricultural interest.  Through the structure of the root nodule, leguminous plants harbor anaerobic actinorhizal bacteria which are capable of fixing atmospheric nitrogen.  It appears that the trait of nodulation has evolved numerous times in the Fabales, and was reliant on whole genome duplication events which allowed the emergence of novel gene functions from redundant genes.

There are numerous plant genomic features present in the Legumes with regard to signaling with rhizobial microorganisms, such as nitrogen fixing bacteria and mycorrhizal fungi.  Duplicated genes have evolved roles in nodulation formation (the genes NFP and ERN1) and mycorrhizal colonization (the genes LYR1 and ERN2).  The researchers used RNA-Seq data from six different plant organs to differentiate gene expression of putative whole genome duplicated paralogs.  Not surprisingly for Medicago, roots had the highest amount of differential expression of paralogous genes, followed by flower, nodule, leaf, seed, and flower bud.  Transcription factors, putatively responsible for tissue differentiation in gene expression, were estimated to be 6% of all Medicago genes.

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.

Microbial Biogeography Of Public Restroom Surfaces

A very interesting paper recently appeared in the PLOS ONE journal, authored by Flores et al. entitled “Microbial Biogeography of Public Restroom Surfaces”.  This study, conducted by the Noah Fierer and Rob Knight labs at University of Colorado – Boulder, addressed the diversity of bacteria found at various places in public restrooms.  The novel aspect of this research is the use of culture-independent next-generation sequencing to determine bacterial species found in discriminating locations in public restrooms.

The restroom has been one of the greatest inventions in human history – especially from a public health perspective.  Without toilets and sinks – not failing to mention the plumbing infrastructure to get waste away from living spaces – disease causing bacteria (and let’s not forget other infectious organisms of the human gut, such as intestinal worms) associated with human waste easily spread from human to human, especially in close living quarters.  A fascinating brief overview of the microbial history of toilets (including some great anecdotes featuring toilet visionary Sir Thomas Crapper) and a commentary of this scientific paper, written by Rob Dunn, can be found on the Scientific American Blogs site.

Using barcoded pyrosequencing of the 16S rRNA gene marker, Flores et al. observed bacterial species on ten different surface types (door handles & stall handles – both in and out, faucet handles, soap dispenser, toilet seat, toilet flush handle, floor around toilet and floor around sink) in twelve different (six male and six female) restrooms on the UC-Boulder campus on a single day.

The researchers identified 19 different bacterial phyla on all of the surfaces sampled.  The majority of sequences (approximately 92%) could be placed within four phyla, including the Actinobacteria, Bacteriodetes, Firmicutes, and Proteobacteria.  Human-associated bacteria were found strongly associated with restroom surfaces, which is not surprising for indoor environments.

Bacterial communities could be categorized by the surfaces they inhabited.  On toilets, gut-associated bacteria were the dominant group.  Skin-associated bacteria were – not surprisingly – found on surfaces touched by hands, such as door handles.  The restroom floor held the greatest diversity of bacteria – some of which were found in low abundance – as these surfaces contained soil associated, as well as human associated, bacteria.  Quite interestingly, the researchers found that some of the toilet flush handles contained soil associated bacteria, implying that some restroom users flush toilets with their feet to avoid directly touching the handles.

There were no statistically significant differences between bacterial communities found in female and male restrooms, although the relative abundances of some bacterial groups were gender associated.  The bacterial family, Lactobacillaceae, found associated with vaginas, were – not surprisingly – more abundant in and around female restroom toilets than male counterparts.

The authors used the newly developed software package, Source Tracker, to determine the similarity of bathroom surfaces to communities from expected and previously published sources, such as human skin, the human gut, urine, soil, and faucet water.  It was predicted that human skin was the primary source of restroom surface bacteria.  Human gut was a source of bacteria found on and around toilets.  Despite the presence of many typical soil bacterial groups found on restroom floors, soil was not identified as a statistically significant source, probably because soil typically contains a highly diverse taxonomic array of species, many of which are rare.  The authors state that custodial mops and ventilation systems may also have some influence on the floor surfaces but were not directly addressed in this study.

The authors show here that human-associated bacteria are the most common microbes found in public restroom surfaces.  Human influenced source patterns can be determined from the bacterial community structure within the biogeography of restrooms.  This study underscores the importance of hand washing, particularly when using public restrooms, and the techniques used in this paper could be used to track or determine likely pathogenic bacteria found on surfaces during incidents of infectious outbreaks.