Thursday, May 31, 2007


I enjoyed spending time taking pictures on the microscope last night and hopefully some readers will also enjoy seeing what is in the bay from time to time. I don't have DIC on my little scope so don't expect to be seeing any thing like this.

I actually saw a relative of these last night but they were attached to an ostracod and it was moving too fast for me to get a picture. Check out all of the great pictures at the Olympus site, and anyone interested in contributing to my new microscope fund, please drop me a line.

Wednesday, May 30, 2007

In the bay 30 May 2007*

The marine diatom
Asterionellopsis glacialis

Check out some better picures here and here.

*I am still experimenting with sample collection locations and and I hope to get access to a better microscope/camera setup, but I intend to make "In the bay" a regular feature of the blog. This image was taken on an old Bausch & Lomb compound microscope at ~100x with an inexpensive 0.3 megapixel digital camera. Water was collected with a fine meshed plankton net in a shallow cove on the north end of Aquidneck Island in Narragansett Bay, RI (see the red arrow below).

Tuesday, May 29, 2007

All of us

John Dennehy, the Evilutionary biologist, put up a post last week about an article in Science News reviewing research on the abundance and diversity of microbes associated with the human body. It presents a nice summary. Some fact culled from that article and elsewhere that are worth contemplating:

> There are 10 time (TEN TIMES) as many bacterial cells as mammalian cells in your body. If you like to contemplate zeros the number is estimated to be ~ 1014 bacterial cells to a measly 1013 mammalian.

> The bulk of these microbes live in our gut where densities can reach 1011 to 1012 cells ml-1 making the gut the ecosystem with the highest density of bacterial cells yet described.

> These are diverse communities 400 or so species but with two only 2 divisions (Fermicutes and bacteroides) accounting for 98% of total population)

>As with other microbial communities a very small fraction of the total number of species present are conducive to culture so most of what we know about them is from extracting and sequencing their genetic material.

> At birth the gut is sterile and must be colonized by bacteria ingested from the environment.

I do have one nit to pick with the Science News article. In the section describing the metagenomic efforts directed at sequencing the 'community genome' this is said:

"Called metagenomics, this form of analysis doesn't produce a list of bacteria but instead describes the metabolic activities going on within a microbial community. These activities include energy conversion and the transport and break down of carbohydrates and amino acids."

Generating sequence data from the DNA present in a microbial community is useful and worth doing. It provides information about what genes are present and about the metabolic potential of the community. But in isolation, it provides no information about what metabolic activities are actually occurring. The only real way to know what activities are occurring is to measure the activity directly There are practical limitations to doing direct measurements of all enzymatic activities of potential interest so the genetic data is very valuable but its limitations are worth keeping in mind.

Sunday, May 27, 2007

The name

I chose the name Mixotrophy because it suggests the blog will contain a varied diet of thoughts and ideas. Some original and some recycled.

Within biology, the term is used in at least two distinct ways. The more common usage (and the first one I encountered in my studies) describes a large, diverse group of photosynthetic organisms that are capable of acquiring energy from sunlight (autotrophy) and from the degradation of preformed organic compounds (heterotrophy). This definition from the Smithsonian Environmental Research Center gives an idea of how broadly the term is applied.
Mixotrophic organisms gain their nutrition through a combination of photosynthesis and uptake of dissolved or particulate organic material. However, they vary widely in their photosynthetic and heterotrophic capabilities. Some mixotrophs are mainly photosynthetic and only occasionally use an organic energy source. Others meet most of their nutritional demand by phagotrophy, but may use some of the products of photosynthesis from sequestered prey chloroplasts.

The other usage is limited to prokaryotes* and is much more specific in its meaning. Here, mixotrophy refers to organisms that are capable of acquiring energy from the oxidation of inorganic compound but are unable to fix carbon. This means they must obtain organic carbon for biosynthesis. A relatively well know example of an organism in this group is Beggiatoa

*Yes I am going to continue using the term and, at the risk of contributing nothing of substance to the discussion, I will probably put up a post about it later in the week

Saturday, May 26, 2007

Thank you evolution

While a substantial amount of human ingenuity has gone into developing the molecular techniques employed in modern biology, all of these tools have at their root genes and gene products provided to us by the organisms we study. The DNA polymerase used in PCR was isolated from a hyperthermophilic bacteria, the reverse transcriptases used to make expression libraries come courtesy of RNA viruses and the multitude of cloning vectors, transposons and antibiotic cassettes are all derived from DNA isolated from natural sources. Other examples are luminescent compounds from fireflies or soft corals and fluorescent proteins from jellyfish.

Friday, May 25, 2007

ASM general meeting

I have been in Toronto all week at the annual American Society for Microbiology meeting. These big meetings can be a bit overwhelming given the numerous concurrent talks and poster sessions running every day. In reflecting on the many topics I learned about (some new and some quite familiar to me), I am struck by how ubiquitous the use of molecular techniques has become. When the information generated with these techniques is combined with biochemical and physiological data, incredible insight can be gained into the mechanisms by which microbes survive and thrive in diverse environments.

Examples include relatively old techniques such as the generation of mutant strains by random or site directed mutagenesis and the rescuing of these mutants by complementation. This reductionist approach provides information about the role specific genes play in the survival of microbes in different environments, in the utilization of specific food sources or the resistance to stresses.

Newer innovations such as 454 sequencing combined with modern computing power and bioinformatics software allow researchers to approach the same questions more broadly. For example, the technique can be used to sequence the entire genome of multiple strains of the same species of bacteria or to generate enormous databases of the specific genes expressed by microbes grown under specific culture conditions.

These approaches are revolutionizing microbial ecology.

Thursday, May 24, 2007


Welcome to mixotrophy. I set of the template quite a while ago but with all the interesting blogs out there that I spend time reading and commenting on, I have not found the time to post anything here. Hopefully that will change. Please check back soon