Holy Moly! - Obsidian Pool

Holy Moly, Friday just may have been one to high points of my scientific career. Melody, Dan and I finally made it to Obsidian Pool in the Mud Geyser region of YNP. Last time we travelled out here a herd of bison and elk prevented us from visiting - we got as close as the opposite side of the lake you can see the background of this blog's main image (also see: The thing about nature...  ). For those that don't know, Obsidian Pool is where modern microbial ecology really hit its straps (Heart Lake and searching for OP's). In one paper (Hugenholtz et al., 1998), effectively doubled the known diversity of microbial life.   

Anyway the Fanboy in me had to go and visit. 

It was great. 

One thing to note is that the physicochemistry of Obsidian Pool has changed a fair bit since the 1990's; In the Hugenholtz paper, the temperature was >85C, the pH was ~6.5 and the spring was a black colour. On Friday, the temperature was 75C, pH 4.8 and was the colour of tea. The microbial community has changed accordingly and now represents reflects the acidification of the spring (Meyer-Dombard et al., 2005) - An overt pointer of this acidification is the movement of 'Tar Pit' (see video below), an acidic mud pot that is progressively moving towards Obsidian Pool and will one day consume it. 

Here's some pictures (actually a lot) - click on them to get the full image:

and here's some videos in case you haven't seen enough....

Arriving at the Obsidian Pool area with good news


'Tar Pit' - The mud geyser that will eventually consume Obsidian Pool.

Churning Caldron: The turbulence is all gas - the temperature is only 74C, so isn't boiling!


Hugenholtz P, Pitulle C, Hershberger KL, and Pace NR. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology 180(2), 366-376.

Meyer-Dombard DR, Shock ER, and Amend JP. 2005. Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA. Geobiology 3 (3), 211–227.

Small Perpetual Spouter & a road trip

I've just got back from a road trip to see colleagues and researchers in San Francisco and Portland. It was a great, but fast, trip. I visited a number of Biotechnology Start-ups in SF. The thing that struck me most about these companies and the work they do (and the general attitude in SF) was the can-do attitude and that no barrier seemed to be too high. The groups are highly focussed with young staff and big plans. It is a completely different environment to what I'm used to. 

While in Portland, I caught up with Anna-Louise Reysenbach - one of the leading figures in thermophile research at present. We're working on some joint microbiology projects from New Zealand. One of the projects is an undergraduate metagenomic study where final year university students get experience piecing together microbial genomes from hot spring metagenomes. These weren't run-of-the-mill genomes from boring 'garden variety' bacteria, rather genomes from uncultured and sometimes deep-branching (evolutionarily ancient) bacteria and archaea. What a great experience for the undergraduates - I so wish I had the opportunity to do something like this when I was a student. We're hoping to publish manuscripts on each of the genomes and for the students to get authorship.

As a side note, Melody Lindsay (a doctoral student in Eric's lab) found a historical reference to the 'new' hotspring I've been documenting in a number of blogs (see: Where'd you come from Bro'?). It looks like the spring has come and gone over the years as it appears in a photo in the definitive Yellowstone National Park hotspring survey reference book: Hot Springs of the Yellowstone National Park (Allen & Day, 1935). Word from the Geyser Gazers (a group of people that monitor geyser activity in the Park) is that the spring has been noted in the 1930's, 1970's and early 1980's, but is absent at other times. I've scanned the image taken sometime between 1925-1935 where you can see a spring called 'Small Perpetual Spouter' in the foreground in front of Cinder Pool. I took a photo from about the same location as the 1930's image and edited and cropped to look similar (see below - what do you think?). We're pretty sure it is the same spring, but it's clear that the activity of the spring was much more in the 1925-30's image with geysering to what looks like about 90cm than what it is today.


Allen ET, and Day AL. (eds.) In: Hot Springs of the Yellowstone National Park. Vol 466. Carnegie Institution of Washington, Washington. 1935. 

Cinder Pool

Cinder Pool would have to be one of the strangest hotsprings I've ever encountered. It is part of the trifecta of microbial ecosystems that Dan Colman and Eric Boyd are monitoring this Summer/Fall to observe the microbial community variation with any geochemical and physical changes.  The springs are all in 100 Springs Plain in the Norris Geyser Basin and we've been visiting the springs weekly (see previous blogs - Where'd you come from Bro?, Where'd you go Bro' etc.).

The is about 10m in diameter and is rimmed in silica sinter and kaolinite. It varies in temperature (we've witnessed 80-92C) and is ~pH 4. The spring water is milky white with black 'cinder' precipitates that float on the surface. The contrast of the black floating cinder against the white spring water gives a yin-and-yan feel to it. The 'cinder' is actually small spheroids of sulphur with about 1% pyrite entrained which gives it the black colour. A close look at them (see main blog image above) shows that each of the spheroids have burst. 

So what are the black cinder bubbles and what makes the white milky colour? The consensus (Xu et al., 2000) at present is that the spring is about 20m deep. At the bottom of the spring is a layer of molten sulphur (about 120C). Gas bubbles move through the molten sulphur and get coated in sulphur. As the bubble rises in the water column cools to less than 112C (where sulphur sublimes) and goes hard. Along the way, (and this is speculation) gas escapes and iron reacts with soluble sulphide to form pyrite that gets entrained in the solidified bubble. The spring water is white because of the suspended fine sulphur particles. 

As to the more important questions what microbes live there and what do they do for a living? This is still being investigated, but Eric has written a nice paper that is starting to unravel these questions (Urschela et al., 2015) and hopefully Eric, Dan and the team will unravel it further. 


Xu Y, Schoonen MA, Nordstrom DK, Cunningham KM, Ball JW. 2000. Sulfur geochemistry of hydrothermal waters in Yellowstone National Park, Wyoming, USA. II. Formation and decomposition of thiosulfate and polythionate in Cinder Pool, Journal of Volcanology and Geothermal Research 97: 407–423.

Urschela MR, Kuboc MD, Hoehlerc TM, Peters JW and Boyd ES. 2015. Carbon source preference in chemosynthetic hot spring communities. Applied and Environmental Microbiology 81 (11): 3834-3847.

Heart Lake and searching for OP's

Last Friday Dan and I made a trip to Heart Lake in the south of YNP. Heart Lake is one of the more isolated parts of the Park and involves a nine mile hike into Witch Creek which is underneath Mt Sheridan. The valley has a wide range of neutral-alkaline springs as well as some acidic features at the top of the valley. The reasons for making this hike are multiple: the first-and-foremost reason was that I'd been told by Mircea Podar (from the National Labs) that one of the alkaline springs along Witch Creek reportedly had a high concentration of bacteria related to the candidate phylum OP1 (or Candidatus "Acetothermia"). This phylum is quite elusive and is one of the most deeply-branching (ancient) bacteria phylum known. No strains of this phylum have ever been cultivated and maintained in laboratory conditions. I am keen to learn more about this phylum as it pops up rarely in a number of our favourite springs in NZ (see here and here for examples). The second reason was that the valley contained a number of springs that had very similar physicochemical conditions to those in New Zealand. Extracting and comparing the microbial communities and their function are a primary objective of my Fulbright Fellowship. Unfortunately, the springs I had identified from the RCN database were now at different temperatures to what was previously noted in the RCN database, so I couldn't sample it.  The third reason for visiting Heart Lake was that Dan had some data from his former supervisor Tina Takacs-Vesbach, that Chthonomonas-like bacteria had been detected in some of the features in the valley. Unfortunately, we ran out of time to look for these features and flagged it - In retrospect, this was a good idea as it was a long walk out getting us to the truck by 6:30pm. Luckily, we were able to grab a couple of (possible) OP1 samples along with a couple of other interesting samples for Dan to look at as well. It was a great day.

A couple of side notes:

1. We rented a economical car to get to and from the park and instead received a 5.2L RAM Truck. It even had 120AC V power outlets. I now know what it is like to drive a tank.  

2. We passed Isa Lake on the drive in/out. Isa Lake literally sit on the American continental divide and has two outlets; one going east (to the Missouri then the Mississippi Rivers and then out to the Gulf of Mexico) and one going west (to the Snake River and out to the Pacific). So you can't walk the continental divide and keep your feet dry!

PS thanks (really) to everyone whom sent in the newspaper report of the man mauled by the same Grizzly Bear twice in one day,... much appreciated, especially as I walked past Mt Sheridan (renown for its bears!).

FYI: I'm pretty excited about tomorrow. Dan, Melody and I are going to Obsidian Pool in the Mud Volcano district of the YNP. For those of you that don't know about Obsidian Pool, it is the site where (arguably) the modern era of microbial ecology really started in earnest. In the mid-1990's, Phil Hugenholtz, Norman Pace and colleagues extracted DNA from Obsidian Pool and detected 11 new candidate bacterial phyla (OP1-OP11) and an additional candidate archaeal phyla (Korarchaeaota) (see references below), effectively doubling the number of microbial phyla at that point of time. This was done without needing to cultivate the cells in the lab and was the precursor to all the molecular work in microbial ecology being done today. And yes, the OP1 mentioned in the previous paragraph is one and the same phylum as the one originally discovered in Obsidian Pool. 


Barns et al., 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hotspring environment. Proc Nat Acad Sci USA 91(5), 1609-1613.

Hugenholtz, et al., 1998.Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180(2), 366-376.

Where'd you come from bro'? II

So we returned to Norris Geyser Basin this week to resample the three springs as per normal and to see whether the new spring was still there and whether the disappearing spring in the middle of Tantalus Stream (see Blog post 'Where'd you go bro'?') had resumed normal function. The weather was sunny (or at least there was no rain) all week, so if both of these features were truly temporary due to the previous week's rain, then we'd expect that the features would have changed. 

Cinder Pool had returned close to its normal self the temperature back close to boiling and much of the black cinder floating over the top of the spring, and the filaments at Dragon Spring had returned. Also, the spring in the middle of Tantalus Stream was still withdrawing water as per the previous week.

The new spring was thankfully still there and looked like it had matured over the proceeding seven days. The spring had cooled off slightly (down from 82C to 68.5C), the conductivity had reduced (down from 4.1 uS/cm to 3.7 uS/cm) and the flow rate has reduced to around 1-2 L/sec. The diameter of the spring had also contracted a couple of inches and but most interestingly, more than 50% of the spring sediment surface was now covered in elemental sulphur. This bodes well for an established a microbial population. We sampled it again and hope to observe changes reflecting the spring physicochemical conditions. 



Where'd you go bro'?

I forgot to mention that there were other changes to the Norris Geyser Basin on the day we discovered the formation of the new spring (Where'd you come from bro'? post). Of note, we also observed that one of the more active springs in Talantus stream had changed from a vigorous (ebullition >2 inches in height) and hot geothermal spring with substantial iron deposition to an ambient temperature spring, that intermittently expelled gas and then withdrew Talantus stream water underground.  Much of the iron deposits had bleached; if you look hard at the associated image, you can see some of the red iron hydroxides on the underside of the rocks in the spring. The video below shows the spring withdrawing water rather than expelling it.

....This part of Norris appears to be in flux at the moment.


The Tantalus Stream spring which appears to be withdrawing water rather than expelling it


Sentinel Meadows

I got my first taste of circumneutral springs in YNP today when I accompanied Melody, Max and Dan to Sentinel Meadows in the Lower Geyser Basin. Sentinel Meadows is about a mile hike from the trail head at Fountain Flat Freight Road and is a large grassed plain with five significant geothermal features; Flat Cone, Steep Cone, Mound, Queen's Laundry Springs and Bison Pool. Unfortunately (but to my secret delight), there was a large herd of bison congregating in the vicinity of the springs, potentially restricting our access for sampling. 

Flat Cone, Steep Cone and Mound Springs are hot (+85C) and alkaline (pH 9.5) and have substantial silica sinter aprons extending away from the spring proper. These aprons are 30-40m in diameter and in the case of Steep Cone Spring, is an elevation of 10m above the meadow. Unfortunately due to the proximity of the bison herd, we were unable to access Steep Cone Spring, but luckily were able to circumnavigate to the east and visit Bison Pool where Melody was undertaking research on the Thermocrinis streamers in the outlet stream. As we were packing up at the end of the day, the bison moved away and we were able to visit both Steep Cone and Mound Springs. This brought about the two highlights of the day: The first was experiencing the geysering of Flat Cone Spring which generates an unnerving 'knocking' sound that can be heard and felt (see the video below - neither Max nor I had experienced the 'knocking' before - unfortunately you can't hear the 'knocking' on the video audio). The second highlight was watching a second herd of bison migrate into Sentinel Meadow from Steep Cone Spring. 

Steep Cone Spring in the foreground and bison herds in the background.

Flat Cone Spring geysering and our reaction to the knocking.


What are they?

One of the sub-objectives I have during this Fulbright Fellowship is to investigate whether a thermophilic bacterium, Chthonomonas calidiroseathat we regularly detect and cultivate from New Zealand geothermal ecosystem is present in Yellowstone. While this doesn't seem like much of a bold objective, up until this date, and despite the massive amounts of microbial community sequencing data available online, the strain hasn't been detected outside New Zealand. It is tempting to speculate that Chthononmonas is endemic to NZ particularly as the four strains we've previously isolated have very similar genomes and physiologies (see reference below). However, I really doubt that they are endemic and suspect Chthonomonas spp. are resident in geothermally-heated soils in Yellowstone... it's just that nobody has really gone looking for them.

So as a side project to the main objective of comparing the diversity and microbial populations of identical NZ and YNP springs, I'm playing around with trying to cultivate Chthonomonas from geothermally-heated soils I find here at Yellowstone. The image above are some colonies subcultured from an initial enrichment of a geothermal soil at Rabbit Creek. The colonies are on a solid medium called Phytagel and were grown in an oven at 60C.  At first glance they look like fungi which would be a turn-up considering that the maximum reported temperature for fungi is about 56C. However, I suspect that instead they are a filamentous bacterium called Thermogemmatispora from the phylum Chloroflexi.

I haven't yet grown anything that looks like Chthonomonas. Fingers crossed.


Lee KC, et al. 2016. The Chthonomonas calidirosea genome is highly conserved across geographic locations and distinct chemical and microbial environments in New Zealand's Taupo Volcanic Zone. Appl Environ Microbial 82, 3572-3581.

First impressions of Yellowstone National Park

I went along with Dan Colman, a Post-doc in Eric Boyd's Geobiology laboratory at MSU, to the 100 Springs Plain in the Norris Geyser Basin and got my first taste of Yellowstone National Park yesterday.

Dan is running a field experiment to understand how microbial communities change to reflect changing environmental conditions. He's monitoring three geothermal springs weekly colloquially known as Dragon, Cinder Pool and HFS. All are acidic (~pH 3.1), hot (78-92C) and within 200m of each other. Visually, the springs are vastly different from each other; Dragon is a small seep, and low flow with beautiful yellow, red-orange and green microbial-mineral zonations around the outflow channel (image). FHS on the other hand is a large (2m), clear, very active spring with substantial ebullition (gas and water being pushed above the height of the spring), minor silica sinter edging and no outflow. Cinder Pool is completely different from both of these and is perhaps the most mind-bogglingly interesting geothermal feature I have even seen. I will blog about it separately later on, because there is so much to say about it. However briefly, it is about a 10m in diameter pool with a bone white water column and a silica sinter rim. It, like HFS, is highly active with significant ebullition and has a temperature that gets close to boiling (~93C in YNP). But, what makes it visually striking is that it has black, cinder-looking substrates floating on a significant proportion of the pool. The black cinder reminds me very much of welding slag and it contrasts the bone white pool dramatically - kind of a yin and yan hot spring. 

Dan is monitoring the microbial populations, the physical conditions (pH, temperature and conductivity) and chemistry (ferrous iron and sulphide in the field, and suite of soluble metals analyses in the laboratory) of the three springs on a weekly basis and has been doing so since early June. The aim is to catch environmental condition variations that leads to parallel changes in microbial populations in the individuals springs.

So what are my first impressions of YNP and the springs? Well as a generalisation I'd group all the acidic springs in New Zealand as turbid (non-transperant), gassy, sulphurous, and generally muddy affairs. The acidic springs in Norris are almost polar opposite. The majority (with the exception of Cinder Pool) are clear, iron rich and not particularly gaseous. The latter struck me as particularly different; in NZ if I were to stand in the steam zone of an acidic spring my gas monitor would scream 'blue murder' and would show elevated concentrations of hydrogen sulphide (H2S) and carbon dioxide (CO2). Here in Norris, my monitor didn't even register a beep. There is also WAY more iron precipitate at the peripheries of the springs in Norris that I've even seen in NZ. I suspect that the low gas, high iron content and spring clarity are all related and probably account for some significant differences in microbial populations between the two countries. Hopefully, Dan, Eric and I will be able to tease these differences out over the next couple of months.


Blog Post #1

Welcome to my first blog post documenting my time at Montana State University. I'm at MSU as a Fulbright Scholar and will be working with Dr Eric Boyd whom leads a laboratory group similar to mine at GNS Science in New Zealand. I hope to be spending much of my time learning new geobiology techniques, exchanging ideas with other microbiologists and ecologists, and undertaking research at Yellowstone National Park. 

So what do I hope to achieve?

Well my stated research objectives are to compare the microbial community composition and function of as close to physicochemically identical hot springs in New Zealand and YNP. My hypothesis is that while the microbial taxa making up the individual ecosystems most likely are different, the broader community functionality should be the same. What I mean by community function is that the genes the community expresses as a response to the environmental conditions experienced should be the same or similar. For example, if a hot spring emits hydrogen gas, then we'd expect to see hydrogenase enzymes (enzymes that metabolise H2) expressed in both the NZ and YNP systems irregardless the microbial taxa present. Thus if we summed the total community function responses to their environments, that should be similar despite being geographically distant (see Research Goals tab for a more detailed explanation). 

Outside my stated objectives, I'm hoping to getting a greater insight into environmental microbiology research in the US, learn new techniques, come up with new research directions, and also impart some of my knowledge concerning the New Zealand geomicrobiology and science systems to my US colleagues. Of course, living in a new country and experiencing life outside the research land will also be a great learning experience. My family are living here on campus with me and my two kids, Lily and Luca are attending the local elementary school. Mel, my wife and Lily are both blogging about their day-to-day experiences which will be a whole lot less stale than my microbiology posts. So I hope you enjoy this blog. Let me know what you like/dislike and any questions you have, particularly if I'm not explaining things well enough.