This week we took some of our first year Animal Behaviour and Conservation Biology students to watch a Dartmoor Pony (Equus ferus Boddaert) dissection at Dartmoor Zoo, which is a relatively short drive from the University and is just on the south tip of Dartmoor, surrounded by beautiful countryside. Dartmoor ponies are an essential part of the moor’s ecosystem and are semi-feral at present. In order to conserve the moor’s ecosystem, it is vital that the ponies are preserved in a viable and healthy state. Because of the small gene pool getting even smaller, there is a scheme under way to cull individual female ponies that consistently deliver deformed or ill foals. This sounds quite an extreme means to deal with the problem but it’s really the only way.

To ensure this is a waste-free process, once the animals have been slaughtered, the zoo butchers the meat for use as feed for zoo animals such as tigers and lions. They also enjoy the occasional horse’s head but the public tends not to like to have to see that, so it’s kept to an occasional treat! The skin is used for leather or to make toys for the big cats to train with - as are the tails. The bones and offal are sent to be rendered into tallow and gelatine for non-human use, such as in laboratories.

In this photo, the underside of the horse has been opened and the digestive tract is spilling out. The bright yellow matter is adipose (fat) tissue under the skin of the pony. The large structure hanging to the floor is the cecum - in humans this is a small pouch at the junction of the small and large intestines, but in some animals like this pony that eat a lot of cellulose (in plant material), the cecum is much larger. This is because it is the location in which hind-gut fermentation takes place, where anaerobic Bacteria ferment cellulose to enable it to be digested. 

Simply put, without its cecal Bacteria, this horse would not be able to survive on its diet of grass and plant matter since it would not be able to digest the cellulose present at all. 

Autotrophic Mycobacterium spp. - whatever next?!

One of the many genera within the Bacteria that I have worked on is Mycobacterium. When I tell people this, they often say “Oh, you work on TB?” and the answer is no. I’ve never worked on the tubercle bacillus, as TB stands, though I did apply to do a Ph.D on TB at the National Institute of Medical Research - I even went and had my TB vaccination done because I’d never been vaccinated (growing up in the Styx, it wasn’t necessary so we never had it done). The Mycobacterium strain that I worked on was called (by my own invention) DSQ3 and I’ll say a bit more about it in a minute. I read an article this past week in Frontiers in Microbial Physiology and Metabolism, our newest microbial physiology journal concerning autotrophic growth of two Mycobacterium spp. at the expense of elemental sulfur. This is very exciting as although autotrophy at the expense of hydrogen has been found in Mycobacterium spp. before (Lukins & Foster, 1963), the prospect of them using sulfur opens up a whole new set of doors…but I’m not really that surprised. You see - Mycobacterium is one of those genera (like Bacillus) that is just full of surprises and metabolic diversity (usually by way of pinching genes from other bugs) - it never ceases to amaze me. I myself discovered methylated amine use as a sole carbon and nitrogen source in Mycobacterium sp. DSQ3 (Boden et al. 2008) so I’ve seen first hand just how adaptable these bugs can be.

The genus Mycobacterium has been known about for over 100 years now, but diseases caused by some of its members have been around for far longer than that. Leprosy and tuberculosis are caused by M. leprae and M. tuberculosis (in man anyway, M. bovis in cattle) respectively and are probably two diseases that are immediately associated with particular periods of world history or particular parts of the globe. M. tuberculosis is the type species of the genus though M. leprae is an excellent example of an important organism that we can easily identify in its environment (living organisms!) but can’t actually grow in the lab (outside of a laboratory animal). The names of these species are rather boringly just Latinisations of “of [disease name]” but Mycobacterium itself tells you a lot about the genus. It very literally means “fungal rodlet” and that’s pretty much what the little swines look like - small rods and there’s something distinctly fungal about them. When they’re growing on solid media in the lab their colonies look very much more fungal than bacterial and the produce floating mats on complex broths which look a lot like fungi.

Now, the main thing about the Mycobacterium genus is that it’s stupidly large as genera go. There are at present 154 species of Mycobacterium, which is frankly idiotic and there are numerous non-Code divisions within the genus such as “fast”/”slow” and different “complexes” relating to different disease causing groups. What it really needs is a good spring-clean and a good sort out but, even as a taxonomist, I ain’t touching it. It’s way too far gone to get any real sense out of without moving some clinically important strains into different genera, which won’t help with diagnostics and, although it’ll make things systematically “right”, it could complicate things more in other ways. The species that I worked with was M. fluoranthenivorans, the type strain of which degrades fluoranthene (a polyaromatic hydrocarbon from coal tar), though my strain was never tested on it - mine grows pretty well on dimethylamine hydrochloride though (Hormisch et al., 2004; Boden et al., 2008) and came from the sediments of the River Thames.

The strains that have just been shown to grow on elemental sulfur are from the species M. cosmeticum and M. pallens and were isolated from sandstone at the Angkor Wat in Cambodia (Kasumi et al., 2011). The former was originally isolated from a sink in a nail salon in Atlanta and also from an infection under the skin of a Venezuelan woman who had undergone a minor invasive cosmetic procedure (Cooksey et al., 2004) - the name “cosmeticum” refers to cosmetics in general. The latter species came from soil in Hawaii and takes the name “pallens” from its pale yellow colour (Hennessee et al., 2009). In the original studies on these species, there is nothing to really make it obvious that the whole species could grow on sulfur - in fact, it could very well be just the strains from Angkor that can do it - but I can’t help wondering - how widespread is autotrophy in the genus Mycobacterium? What about these ones we can’t grow? What about M. leprae? I’d be willing to bet money on the fact that no one has tried these “obligate” pathogens on substrates such as sulfur or ammonium for autotrophic growth or even on things like methanol and things other than complex medical-microbiology broths. 

The human body is an environment like any other and yet medically-related organisms are usually treated and handled differently to how an “environmental” microbiologist would work. I think there’s probably a lot to gain by doing a bit of swapping of strains and trying some of these organisms that have “no sink in the environment” and are “obligate” pathogens or have to have a host on some of the less mainstream substrate combinations to see if they will grow at all. I’d be willing to bet that out of 154 species of Mycobacterium, more than two exhibit some degree of lithotrophy.

——

Boden et al., 2008. Environ. Microbiol. 10, 3225-3236.

Cooksey et al., 2004. Int. J. Syst. Evol. Microbiol. 54: 2385-2391.

Hennessee et al., 2009. Int. J. Syst. Evol. Microbiol. 59: 378-387.

Hormisch et al., 2006. Syst. Appl. Microbiol. 27, 653-660.

Kasumi et al., 2011. Frontiers Microbiol. Physiol. 2, 104. 

Lukins & Foster, 1963. Z. Allg. Mikrobiol. 3, 251–264.

The Blackleg Miner - Part 2

In yesterday’s post about biomining, I mentioned I was involved in a second type of mining and that’s the subject of today’s post: genome mining.

Last week I submitted a manuscript that I had written to a journal for consideration for publication concerning the genome sequence of a strain of Methylomonas methanica. The manuscript has 27 authors based at 8 institutions in 5 different countries and is the biggest project in terms of number of authors that I have been involved in and, of those 27 authors, I’m at the front, because I pulled most of it together in the end, though I started out about 5th and gradually moved forwards, particularly as I ended up writing the manuscript itself - that wasn’t planned originally but that’s how it ended up. This is the second genome sequence that I have worked on - the first being that of Methylophaga thiooxydans, which I published earlier this year with a much smaller team. 

Both of these organisms are Bacteria found in the marine environment and, since they both have “Methylo-” generic names, they evidently have a lot in common. Members of the genus Methylomonas are methanotrophic, which means that they can grow on methane as a source of carbon. There is an apparent peculiarity amongst a lot of Bacteria that can grow on methane in that they seem to depend upon it - they’ve lost the ability to grow on pretty much anything else. Personally, I don’t think this makes evolutionary sense and I’m sure they can use other things though refuse to do so in the lab. Members of the genus Methylophaga are still fussy eaters but far less so - they can’t grow on methane but they can grow on methanol, methylated amines, dimethylsulfide and a lot of other “one-carbon” or “C1” compounds, in addition to fructose and a few other multicarbon compounds - they are methylotrophic. These C1 compounds are prevalent in seawater (yes, even methane) and it makes sense, therefore, that there is something out there eating them. After decades of C1 research around the world, we now know which enzymes and genes are responsible for the metabolism of a lot of these compounds but we’re still struggling with some of the details - which is why the genome sequences are so useful.

The Blackleg Miner - Part 1

Ok - this has nothing to do with the NACODS during the NUM strike or 19th century folk songs - no, this is about a different kind of mining.

Father and son, we’re both miners. My Father mined coal until the mid-1980s but me? I’m a different kind of miner - in fact, I’m TWO different kinds of miner, thinking about it. Firstly, I’m a biominer - I worked for a while mining copper using Bacteria. You might think that a bit far-fetched but, would you believe that gold, copper and uranium are often mined in this way? Amazing though it may seem, over 25% of all the copper mined in the world is mined by Bacteria (well, Archaea too but but let’s keep it simple!). It’s not even a new process either - the Romans discovered it around 2,000 years ago!