It’s Microbial Sciences Friday on

The American Society of Microbiology (ASM) has been assembling a team of writers for a new blogging network. I am excited to say that I am a part of this group and will be writing primarily for the Microbial Sciences blog there.

Other budding blogs in the network are bLogphase from ASM CEO Stefano Bertuzzi and Zika Diaries by Vincent Racaniello. Articles are also coming in from Elio Schaecter’s Small Things Considered – which just hit its 10-year anniversary as the original ASM blog.

For me this starts today with “Mystery of the Spring-Smelling Microbes” – an article inspired by an incubator on my floor that smells like dirt. It’s the story of how I learned about the molecule geosmin and the microbes that produce it.

I will continue to write mostly photography and travel related articles here on Animalcule. But most of my online essays about microbes from this point will be within the “umbrella” (or maybe the better metaphor is, within the, biofilm) and cross-linked here.

Things are just getting started, but we plan to publish a Microbial Sciences article at least once every week, on this, the first, Microbial Science Friday. We are an enthusiastic group of microbiologists with months of interesting topics in the works! So definitely look for updates and check out what is developing on!


A mid-October trip to Woods Hole

WHOI Woods Hole Scott Chimileski


Yesterday I traveled from Boston down to Woods Hole to give a talk for Virginia Edgcomb’s group at the Woods Hole Oceanographic Institute (WHOI). On one hand, I am surprised it took me so long to visit this storied mecca of biological research, right here in New England. But on the other hand, it is exciting to have just now discovered this truly special place, home not only to WHOI, but also to the Marine Biological Laboratory.

It was a beautiful autumn day there, and I had a bit of time to photograph the village and surrounding areas after my talk. I have a strong feeling I will be spending more days here in the future!


Scott Chimileski Woods Hole sunset
I caught this astonishing mid-October sunset just outside of the village of Woods Hole.


Scott Chimileski Woods Hole sunset


Bringing the Microbial World into our Natural History Museums

Scott Chimileski Harvard Museum of Natural History HMNH
The Harvard Museum of Natural History

A quick post to link an article I wrote for ASM’s great blog, Small Things Considered:

I have to send many thanks to Elio Schaechter for his extraordinary editorship of this and many other articles on Small Things!

In the article I ask why microbes are typically a minor component of natural history museums, argue why it’s important that we change this, and offer some solutions for presenting the microbial world for the public. I also discuss our project to bring the microbial world into the Harvard Museum of Natural History, in an exhibit to open in 2017!

Scott Chimileski Microbes

Block Island flower and insect photography: testing the Canon 5DS and MP-E 65mm macro


Scott Chimileski - Block Island
I happened upon this Block Island blue-spotted leopard moth.


I am out on Block Island this week and—while I am trying to avoid working to some extent—I can at least use this vacation as a perfect opportunity to test my brand new camera setup. I recently upgraded to the Canon 5DS, along with a new Canon MP-E 65mm macro lens. The MP-E 65mm effectively converts my 5D into a field dissecting microscope, ranging from 1:1 to 5X magnification. This may be one of the best macro setups possible at this time, with the new 50.6 megapixel sensor representing the state of the art for DSLRs (at least for a few months, until there is something better!). In fact, the capabilities of the 5DS now overlap with what would previously only be attainable with medium format cameras. I am very excited about what I plan to do with this camera in the next few years, especially because I actually plan to use every last one of these pixels for producing large format prints.

Here are a few test shots I took this week on Block Island, Rhode Island:

Scott Chimileski - Block Island Leopard Moth
Increasing the magnification. Quite the face on this little guy, but you need to look close to see it …


Scott Chimileski Block Island Berries
The wild berries growing within the island dunes made for great macro subjects.
Scott Chimileski Block Island Berries
Bringing the berry into focus … Despite being less than 1 centimeter in diameter, here the berry looks like a giant monument.  

Scott Chimileski Block Island Berries


Scott Chimileski - St. john's wort.
St. John’s wort grows everywhere you look in the island meadows.


Scott Chimileski - Block Island


Scott Chimileski - Dandelion Block Island
The common dandelion seed head – a wonderfully evolved and beautiful structure that is easily overlooked.


Scott Chimileski - Block Island meadow
This final photo from within an island meadow was not taken with the MP-E 65mm, but rather a 50mm prime lens.

Roland Thaxter’s 19th century drawings of myxobacteria

Scott Chimileski Animalcule - Roland Thaxter Myxobacteria
Roland Thaxter observed and sketched many social behaviors for myxobacterial species long before they were experimentally characterized. Bot. Gaz. 17(12):389-406 (1892). (Public Domain).

I now sit within a secluded nook of the Sterling Memorial Library at Yale University, working alongside my sister, Lindsay. I am writing my dissertation (or perhaps more accurately, writing a blog article), while my sister puts together quizzes for an herbal medicine class she teaches. I find the occasion ideal to highlight these remarkable drawings of myxobacterial social behaviors by Roland Thaxter, who collected some of his samples here in New Haven. I was recently led to Thaxter’s images indirectly while reading E.O. Wilson’s 1975 book, Sociobiology.

Scott Chimileski Animalcule - Thaxter myxobacteria
There is little doubt that in this image, Thaxter has drawn swarming myxo cells moving out from the periphery of the colony. This phenomenon is strikingly reminiscent of modern studies of predataxis behavior.

Thaxter published these drawings in the Botanical Gazette in 1892, in “On the Myxobacteriaceae, a New Order of Schizomycetes.” Though Schizomycetes is an archaic botanical term for bacteria, Thaxter’s classification was among the first to separate myxobacteria from fungi, the branch of life in which they had previously been grouped. The drawings shown in this post represent species from the genera Chondromyces, Stigmatella, Archangium and Myxococcus.

“A few years since while collecting fungi at Kittery and in several other localities in New England and the southern states, the writer’s attention was attracted by a bright orange-colored growth occurring upon decaying wood, fungi and similar substances, which, although in gross appearance it seemed somewhat highly organized, was found, when examined in a presumably mature condition, to consist of apparently amorphous material, without signs of hyphae or spores of any kind. Its general appearance and the character of the substance which composed it suggested an immature condition of some myxomycete which had become dried while in the act of rising from the substratum to form its fruitification.”                                                                                                                                                                                                                   – Roland Thaxter, 1892

G.P. Clinton wrote a biography of Roland Thaxter for the National Academy of Sciences in 1935.  Thaxter was born in New England and spent most of his life here (like me, so far at least). In addition to New Haven, he collected samples in Kittery Point, Maine, where he spent many summers, and in Cambridge, MA, where he worked as a professor at Harvard for the bulk of his career.

Thaxter-Myxobacteria-3 copy

As a botanist, Thaxter’s attention was drawn to structural detail. This could explain how he was able to single out and produce the first descriptions of some of the most developmentally complex bacterial groups to be discovered, even to this day. According to Clinton, he was very much of the “pure science” type—less interested in practical applications for botany. It seems the division between these two ways of approaching science was already palpable in 1933.

Clinton also suggests that Thaxter’s success as a scientist was linked with his artistic creativity. The fact that these sketches are relevant and inspirational to me, a microbiologist studying social behaviors over 100 years later, is another testament to Thaxter’s artwork.

Scott Chimileski- Thaxter - Sociomicrobiology Myxobacteria
E.O. Wilson highlighted these drawings of fruiting body development in his 1975 book, Sociobiology.


Writing  within the historic Sterling Memorial Library at Yale University!

Yale Sterling Library

Yale Sterling Library

While I was talking to an old man …

“While I was talking to an old man (who leads a sober life, and never drinks brandy or tobacco, and very seldom any wine) my eye fell upon his teeth, which were all coated over; so I asked him when he had last cleaned his mouth? And I got for an answer that he’d never washed his mouth in all his life … I took some of the matter that was lodged between and against his teeth, and mixing it with his own spit, and also with fair water (in which there were no animalcules), I found an unbelievably great company of living animalcules, a-swimming more nimbly than any I had ever seen up to this time.”
               – Antonie van Leeuwenhoek, Letter 39, September 17, 1683

The Tiny Giants exhibit from Bigelow Laboratory

photo (18)3

I had a chance to visit the Tiny Giants: Marine Microbes Revealed on a Grand Scale exhibit this week, at the Portland Public Library in Maine. Produced by scientists from the Bigelow Laboratory for Ocean Science, the exhibit features photomicrographs of phytoplankton and zooplankton, focused on diatoms and dinoflagellates. Images on display were collected through both light microscopy and electron microscopy.

If you are within driving distance of Portland, I highly recommend visiting the exhibit (on display until March 31).

photo 5 (1)
A variety of microscopic crustaceans and unicellular algae.


photo (22)
“Predator in Pink.” A predatory dinoflagellate, Protoperidinium, with a natural pink tinge. Photo credit: Dr. Peter Countway


photo 4 (2)
Marine snails: Limacina helicina. Photo credit: Laura Lubelczyk


More information about the exhibit:


A fantastic sunset on an early spring night in Portland, Maine.
A fantastic sunset on an early spring night in Portland, Maine.

The first @ASM meeting on sociomicrobiology

photo 1 (9)

This weekend I was fortunate to be one of fifty microbiologists at the first @ASM meeting: a new conference format held at the headquarters of the American Society of Microbiology in Washington, D.C. Not only was this the first @ASM meeting – it was also the first ASM Conference on Mechanisms of Interbacterial Cooperation and Competition, or effectively (as noted by many of the participants): sociomicrobiology.

ASM headquarters: located in a beautiful brick building in Washington, D.C.
ASM headquarters: located in a beautiful brick building in Washington, D.C.

Each and every talk was truly excellent, but of course I did have some favorites, biased no doubt by my own interests:

  • Both Peter Greenberg and Kevin Foster presented a broad context for the concept of sociomicrobiology, as it is developing into a new science. Peter Greenberg framed his talk around quorum sensing, while Kevin Foster is doing some amazing work from the perspective of the evolution of social behaviors and particularity in the application of computational modeling of biofilm formation. In many ways microbes are ideal organisms for empirically testing the first principles of social interactions.
  • Susanne Mueller, a research scientist from the Kirby Lab at the University of Iowa, gave a fascinating talk based on two recent papers on Myxococcus/Bacillus interactions. B. subtilis forms a newly discovered form of biofilm called the megastructure only in response to Myxo predation. Megastructures are filled with spores and are not dependent on the same genes involved in colony biofilm formation, suggesting a unique mixture of unknown matrix components.
  • Elizabeth Shank presented work from her group at the University of North Carolina, advancing previous studies visualizing matrix expression and unique functional cell types in B. subtilis biofilms. She has shown that matrix expression in B. subtilis can be triggered by other sympatric species: induced by particular metabolites (for example, Thiocillin).
  • Paul Straight’s talk on chemical interfaces between Streptomyces and B. subtilis colony biofilms included some great photographs. His work shows that two colony biofilms grown adjacent to each other are engaged in a complex exchange of chemical information.
  • There were also many talks on type VI secretion systems (T6SS; by and large the major theme of the conference): a mechanism for effector secretion that is structurally homologous to bacteriophage components. These began with a great keynote talk by John Mekalanos, whose group discovered T6SS in 2006. It was amazing to see how such a transformative discovery can open up an entire field in less than a decade.
  • Harry Mobley discussed the history of swarming in Proteus mirabilis, in what was a very informative but also very entertaining talk (I think he gets the award for most laughter). He focused on the formation of Dienes lines between successive layers of swarming cells in this species, and how these characteristic boundary layers are now known to be mediated by T6SS.

Based on the success of this meeting, plans for the next ASM sociomicrobiology meeting are already underway.  It remains to be determined whether the conference will be expanded in size, or left at the extremely small 50 person level. I can say that 50 people was very nice; I met essentially everyone, and the poster session was excellent: incomparable to the field of posters at the general meeting.

A quick run past the white house on a cloudy day!
A quick run past the white house on a cloudy day!

Ten grams of DNA

Scott Chimileski-DNA extraction- Haloferax volcanii
Ten+ grams of crude DNA, extracted from 5 liters of Haloferax volcanii culture.

Almost all biologists extract DNA for one reason or another. But for just about every routine application, plasmid preps, sequencing, and the like–we are used to dealing with nanogram or microgram concentrations–delicately resuspended from the most minuscule pellets, barely visible on the side of a microtube. This is not a tale of nanograms or micrograms.

For my first project as a PhD student, I studied the idea of extracellular DNA (or eDNA) as a nutrient in haloarchaea: a group of “extremophilic” archaea that live at very high salt concentrations. We knew from population genetic studies that haloarchaeal species were promiscuous in natural hypersaline sites, able to readily exchange genes horizontally (that is, independent of vertical inheritance through reproduction). But it was unclear how they were doing this: which actual cellular mechanisms mediated gene transfer. One possibility was natural uptake of eDNA, a process that had not been studied in haloarchaea (or essentially any species within the domain Archaea for that matter). So, inspired by discussions with my advisor and by earlier work on eDNA as a nutrient in bacterial species, I began my investigation of DNA uptake by asking whether the species Haloferax volcanii could “eat DNA.”

I needed DNA to provide as a possible growth substrate–a lot of DNA. I quickly found that typical DNA extractions were not going to be of much help. I was testing many replicates, DNA isolated from a range of species, several related conditions, and trying to figure out whether DNA could act as a carbon, nitrogen and/or phosphorus source (after all, DNA offers all three of these essential elements of life).

I did what any scientist would do: I scaled-up … and scaled-up, and scaled-up. The fact that I needed highly purified DNA meant I needed even more to start with, because of course some is lost with each purification step. I finally ended up with a purification process that began with an ethanol extraction from 5 liters of spun-down liquid culture. Adding the ice cold ethanol in 2 liter flasks was always exciting at the end, when gobs of DNA (a bit of RNA too) would precipitate instantaneously: a slurry that you could probably spool with a baseball bat. Even after several subsequent phenol-chloroform extractions to remove contaminating protein, RNA digestions, and removal of low molecular weight fragments and other impurities, I was able to yield several grams of pure DNA.

I share these photographs from one of my extractions back in 2010, as I wonder whether many others have seen so much DNA in one place. Beyond literally intending to use it as “food,” it is difficult to imagine other experimental contexts requiring grams of DNA.

This work ended up leading to into a great story that is still unfolding. Extracellular DNA turned out to be a nice thread (no pun intended) into my next project too: considering it is also component of haloarchaeal biofilms.

This post if part of a series of articles reflecting back on my work as a PhD student–in anticipation of my (tantalizingly forthcoming) thesis defense in 2015.  

3D print of a biofilm from confocal microscopy data

Scott Chimileski animalcule 3D print
A 500x 3D print of a section of mature Haloferax volcanii biofilm

3D printers may soon be common household items. Or at least – hopefully  – common laboratory items. I recently converted confocal data from a biofilm into a 3D print.

The biofilm print features one of the larger tower structures I have observed for this archaeal species, Haloferax volcanii, which lives at high salt concentrations. A 3D reconstruction of the same image stack was recently published in an article in BMC Biology. The data was collected in 2012 at the Center for Biofilm Engineering at Montana State University.     

Scott Chimileski animalcule Leeuwenhoek biofilm 3D print

At 7.5 cm in height, the print is five hundred times larger than the actual size of the biofilm. This would be equivalent to making a print of a person taller than the empire state building.

I chose to print in sandstone because it is one of the more economical materials. It also has a nice natural feel, unlike plastic. My second choice was ceramic. However, each material comes with its own practical guidelines: ceramic is both more delicate (as you might expect) and preserves less detail.

Scott Chimileski Haloferax volcanii biofilm 3D print
Each 3D model build depends on the specific properties of the printed material.

There is a great potential for this sort of work. I think that any form of scientific data that has a three dimensional element can and should be 3D printed. 3D glasses allow a virtual sense of three dimensions by playing a kind of trick on human stereovision. But this is not an intuitive experience. Having something physical to see and touch is ultimately the best way to appreciate and understand anything in 3D – especially something invisible.


A video showing the model used to create the 3D print: