Made It!!!!!

Well I made it in one piece. I haven’t started to do anything yet, but I slightly unpacked the van. Tomorrow should be a fun day or organizing and setting up. In the mean time I am going to enjoy this glass of whiskey and relax. Maybe I’ll even read a book. You never know. Things are gonna get wild. Just look at this view:


Prosthecobacter spp.: A story of holdfasts and mustaches

This week I want to highlight Prosthecobacter fusiformis and related species from the genus Prosthecobacter. P. fusiformis is an interesting organism; however I must admit that I discovered it randomly by picking a taxon found in every sample (eight sites total) in one of my datasets. Yes I realize that many may regard this as an odd way to pick a bacterium to write about, but I feel that this was an appropriate way to discover an organism which I knew very little about.

Let’s again start with a little taxonomy (for those into that type of thing):

Phylum – Verrucomicrobia
Class- Verrucomicrobiae
Order – Verrucomicrobiales
Family – Verrucomicrobaiceae
Genus – Prosthecobacter

The Prosthecobacter genus has very few cultured representatives, but it is one of the more interesting groupings I have come across recently. This genus helped to distinguish Verrucromicrobia as a valid phylum of Bacteria. Before the characterization of this group there was little evidence to separate Verrocomicrobia from the other phyla due to the lack of cultured representatives. The inclusion of this second genus (along with molecular evidence of course) which included cultured organisms (even though not many) provided better evidence for the distinction of the phylum. Furthermore, with the use of molecular tools we now know that this phylum is distinct and we have evidence of other (non cultured) organisms that group with Verrucomicrobia. Secondly, all of the cultured representitives of Prosthecobacter are morphologically distinct. This is a rare phenomenon in any group of bacteria. Four species of Prosthecobacters have been carefully characterized and all have distinct standard length and widths as well as curviness and the presence or absence of vibrioid morphology (you may need to look this up for yourself: one of my favorites though) (Figure 1, from Hedlund et al., 1997). Furthermore, in my opinion, P. dejongei should be called the mustache bacteria. Seriously, you can’t look at panel D below and not think of a French mustache. Awesome!!!! I find that this morphology is quite interesting, but I wonder why. Why is there a mustache bacteria? Why are some sister taxa just slightly longer than others? Why are some narrow and straight while others have adapted the vibrioid morphology

So where does this organism get its name? Prosthecobacter refers to the terminal prosthecae found on all of the cells. Prosthecae are a cellular appendage which includes a holdfast that is used to attach to surfaces. Due to the presence of the prosthecae these organisms were originally placed with the Caulobacter (alpha proteobacteria) which are the best known group of prosthecate bacteria. However, it was later discovered that Prosthecobacter do not divide asymmetrically to produce motile (with no prosthecae) and non-motile (with prosthecae) cells. Instead they divide laterally, and thus all daughter cells have prosthecae and remain non-motile. Due to this type of division, Prosthecobacter produce clumps of cells that radiate out along the attached surface. I’m sure that if we were able to image, without disruption, surfaces containing this organism we would be able to find intricate patterns on surfaces. I wonder what the patterns of mustache bacteria would look like?

Ok, so maybe I didn’t only highlight P. fusiformis. Obviously I am more interested in P. dojongei but you still get the point. The genus Prosthecobacter is a great example of the extreme diversity and beauty of aquatic microbes and microbes in general. I still only knew little about this group of organisms, but I find them highly fascinating and I hope you now do as well. Questions, Comments: All welcome!!!!!

Brian P. Hedlund, John J. Gosink & James T. Staley. 1997. Verrucomicrobia div. nov., a new division of the Bacteria containing three
new species of Prosthecobacter. Antonie van Leeuwenhoek 72: 29–38.

Polynucleobacter spp.

If you were to try thinking of a model ‘lake’ bacterium you may consider using a Polynucleobacter spp.

Some taxonomy (if you are into that type of thing):

Phylum – Proteobacteria
Class- Betaproteobacteria
Order – Burkholderiales
Family – Burkholderiaceae
Genus – Polynucleobacter

Members of the genus Polynucleobacter are considered ‘cosmopolitan’, at least in freshwater ecosystems. Common species in this genus are P. necessarius and P. cosmopolitanu. These organisms are globally widely distributed and chances are that next time you jump into your favorite lake or wade across your local stream you will cross paths with a member of this group. Along with their distribution, these organisms are also temporally variable and one study showed that their relative abundance can fluctuate from 4 – >50% of the total microbial community (Hahn et al., 2005 AEM). However, in some Michigan lakes the abundance of this group is <1% showing that there is large spatial variability too (unpublished). Despite this, none would disagree that this group of organisms is fascinating.

In my opinion, the species P. necessariusmay be one of the more interesting in this group (see image below from Bergey’s Manual® of Systematic Bacteriology: Volume Two The Proteobacteria Part C The Alpha-, Beta-, Delta-, and Epsilonproteobacteria). For some time we have known that P. necessarius is an endosymbiont of ciliates (specifically Euplotes spp.). In addition, this interaction is known to be an obligate symbiosis and ciliates that are cleared of their endosymbiont die soon there after. Furthermore, P. necessarius has been implicated as the agent responsible for mate killing among these ciliates. Why does this interaction exist? How did it come to be? If you weren’t captivated by the spatial and temporally variability, I bet you are now.

Feel free to share your thoughts or do a little research of your own (via the web of course).

Bergey’s Manual® of Systematic Bacteriology Volume Two The Proteobacteria Part C The Alpha-, Beta-, Delta-, and Epsilonproteobacteria

Post Field Season Day-to-day

So my field season is now over. I am all done on lakes for this summer and I find myself thinking about what I should do next summer. There must be a way to top my adventure this summer. I will just have to start planning earlier. As I sit here now listening to the rain sprinkling down outside of my office window I find myself reflecting on the summers activities and what my post field season day-to-day will be like. I have spent the recent weeks mostly in the lab; trying to not think much about the piles of data accumulating on my desk and on my hard drive. Some of my lab activities have been fruitful, yet others have been disappointing and thus have taken a strong toll on my motivation. I have a few more days of working in the lab prior to my trek back to campus for the fall and spring. I need to wrap up a few things and prepare my mind for the challenges it will encounter in the next few weeks.

Between classes and teaching I will mostly be working with R. I can see insightful graphs and hours of frustration in my near future. How will I depict my data and what coding errors will I run into? At the moment all I have is the environmental data. The goal will be to apply this data to the biological data, but when will I have said data. Well I have no idea. I have yet to extract any bit of nucleic acid and without that I am left empty handed. I can see long weekends and couch surfing at KBS in my future. I will have to carefully plan my activities so that I will be able to do extractions, purifications, amplifications, purifications, quantifications, and submissions in short one to two day spurts interrupted by long weeks of classes and teachings. This should be fun to say the least.

Aside from my lab activities, I have so many other research activities staring me down. This is like an academic staring contest between me and my work. There is the review sitting on the desk in front of me. That is due by Monday so I have some motivation. Then there is the papers to read and the things to write. How about a draft of this and a outline of that. It all makes sense in my head but when I sit down to actually work there are so many ideas that it is hard to focus, but I try to conquer it one step at a time. A good cup of coffee helps and maybe even a doughnut.

Well the rain is letting up and I see a hint of blue in the sky. Time to make progress on this review and enjoy the rest of the weekend. The post field season day-to-day may not be as exciting as the field work and amazing summer activities that I thoroughly enjoy, but it isn’t the worst thing in the world. I am just going to battle it day by day and hope that I win the staring contest.