Tag Archives: Bacteria

Cas9 – The Good, The Bad, and The Ugly of a Viral Hunter

The CRISPR/Cas9 system for viral defense in bacteria is a recently discovered system that is really fascinating.  Cas9 is useful for genome engineering and currently getting a lot of attention in this area.

Greene Lab Studios (a subsidiary of the Greene Lab) put together this video to the title music from the soundtrack of the film  The Good, The Bad, and The Ugly composed by Ennio Morricone.  The video briefly explains how the CRISPR/Cas9 system works in recognizing and cleaving foreign nucleotides in a cell.

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.

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.

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).

Activity of Abundant and Rare Bacteria in a Coastal Ocean

It’s been a busy summer, but I’m back to focusing on some recent research.  In fact, there’s been a flurry of recent papers which I plan to highlight here.  I’m exploring fungal and bacterial abundance in forest soils using pyrosequencing techniques with my own research, so I was interested to read this paper on bacterial activity in oceans off the Delaware coast.

In a study from the July 18th early online edition of the journal PNAS, researchers from the University of Delaware and University of Southern California sequenced the bacteria in seawater off the Delaware coast every month over the course of three years.  The research, authored by Barbara Campbell and her colleagues, measured both 16s rDNA and rRNA using next generation pyrosequencing techniques.  By measuring both the presence of DNA (a marker for species presence and overall abundance) and RNA (a marker for relative activity or, more accurately, ribosome activity) in this constantly shifting ecosystem, the authors hoped to explore and understand abundance of both rare and frequently found bacteria in a coastal ocean environment.  I already told you about an article featuring the Rappemonad bacteria, some of which were studied in this paper.

It has been hypothesized in ocean ecosystems that abundant bacteria are found frequently because they have high growth rates and are better at competing against slower growing bacterial.  Conversely, rare bacteria have long been considered to have slower growth rates, just be poor competitors to the more abundant bacteria, or have more streamlined genomes which are better suited to wait in dormancy until the right factor, most likely a specific nutrient, comes into play.

More than 600 OTUs (Operational Taxonomic Units – a term for individuals observed from the environment) were observed and these organisms formed a typical rank abundance curve that we have come to expect from environmental sampling, so there were no surprises in that finding.

What was more surprising, or should I say interesting, was what the authors found by comparing both DNA and RNA from their samples.  After the quality control of their 454 pyrosequencing reads, the authors included more than 500,000 nucleotide samples in their analysis.  More than half of the individual bacteria cycled between abundant and rare during the three years of sampling.  Interestingly, almost half of the bacteria were always considered rare, and close to 12 percent remained rare and inactive, and less than 5 percent were considered to be always abundant throughout the sampling.  The researchers used quantitative RT-PCR to validate specific DNA and RNA concentrations for five separate OTUs to verify the findings from the pyrosequencing portion of the study.

Also quite interesting was that the authors did not observe a pronounced seasonally affected microbial component or an environmental factor that could explain the abundance or scarcity in this ocean environment.  It appears by all accounts that the microbial community observed in this study is constantly changing and may not be regulated by many other factors except the community itself.  See here for a press release from the University of Delaware on this study.

Horizontal Gene Transfer In Ascomycete Fungi

Horizontal Gene Transfer (HGT) goes against what we typically consider the normal transfer of genetic material from parent to offspring.  HGT involves the transfer of genetic material from one organism to another.  Within the bacteria, whose mode of survival typically depends on phagocytosis, there is a fairly amount of HGT.  Events of HGT have been rarely observed in Eukaryotes because numerous barriers exist to prevent foreign nucleotides from entering a cell’s nucleus.  Some of these barriers in the Fungi include a substantial cell wall made of chitin, multiple cell and nuclear membranes to cross, and the secretion of metabolic enzymes to the outside of the cells and subsequent uptake of the nutrients.  Despite these barriers, there is now evidence of multiple occurrences of HGT in the fungi.

In a recent article published in the journal Current Biology, Jason Slot and Antonis Rokas, both of Vanderbilt University, provided evidence of HGT in two Ascomycete clades.  In this study, the authors identified a 23-gene cluster from the genus Aspergillus which relocated to the genus Podospora.  Genes that are in this cluster synthesize the toxic compound, Sterigmatocystin, which is a precursor to aflatoxins, noted for their production in Aspergillus.  Both genera are located in the subphylum Pezizomycotina, so each clade is not distantly related, but HGT was observed using different methods.

While it’s easy to observe genetic material passed from generation to generation, recognizing HGT is a little more difficult.  The main way the researchers have identified HGT is using phylogenetic methods to identify gene clusters whose homology cannot be explained by lineage alone.

Thomas Richards points out in his commentary on the Slot & Rokas paper (also in Current Biology), that because fungi do not phagotrophically consume their food they are less likely to incur HGT event.  There are two notable hypotheses to why we do see HGT in the fungi.  First, many secondary pathway genes in Eukaryotes are encoded in gene clusters, and the fungi have a fair amount of these clusters.  Gene clusters, which are more functional in a natural selection sense, are therefore more likely to persist upon transmission, as opposed to individual genes.  Data from HGT studies in fungi support this hypothesis.  Second, fungi are naturally, from the basis of their biology and natural history, intimately tied to other organisms, and fulfill roles as saprobes, pathogens, or symbionts.  This close intimacy increases the opportunity for genes to transfer from one organism to another.  Data suggests that this hypothesis is true also, as many of the recorded instances of HGT in fungi have been observed in organisms with overlapping environments.

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.