Tag Archives: DNA

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.

Epigenetics And The Inheritance Of Acquired States

Epigenetics as a scientific field has undergone an explosion in productivity arising from genome sequencing projects.  We are now starting to understand how environment factors – such as nutrition and various stresses – regulate how DNA is modified as well as how genes are turned on and off.  We are also learning how epigenetic factors relate to the development of stem cells and cancer.  Evidence of this is that there are numerous meetings on the immediate horizon addressing epigenetics.

I recently mentioned one meeting here, but another is this symposium sponsored by the academic journal Cell.  Some of the topics for discussion at this meeting include: chromatin and its replication, the role of RNA in epigenetic inheritance, the inheritance of cellular states of stem cells, methylation, and mechanisms of epigenetic gene silencing.

Registration for this symposium is now open.