Tuesday, 12 September 2017

Fungal Identification Skills Workshop

I took myself off to Barnsley last weekend for a Fungal Identification Skills Workshop organised by the British Mycological Society (BMS). I must say, I wasn't expecting Northern College to be quite so grand. It's a super venue for a residential course.

The workshop was led by Carol Hobart, a very experienced mycologist and active member of the BMS, and was designed to focus on developing microscopic identification skills just what I needed!

For a residential course spread over three days, it was also incredibly good value as the accommodation costs were subsidised by the BMS, and Carol our tutor was very generously volunteering her time.

The course began on Friday evening and (no thanks to the traffic on the M25 and M1) I made it just in time for Carol's introductory talk.

Looking back, Carol packed so much information into this talk, and the rest of the weekend, that it's impossible for me to try and summarise it here. But I thought I'd jot down a few of the key learning points for me... before I forget them!

Using spore colour to get to genera

OK, so I knew that spore colour is an important feature in identifying mushrooms and assiduous readers of this blog (if there are any) will know that this has, on occasion, been a cause of both frustration and elation.

What I didn't realise is the extent to which, traditionally, spore colour has been used to group and order different genera. So, if you pick up a book like Roger Phillips 'Mushrooms', you'll find that the mushrooms that give a white spore print at are the beginning and the mushrooms that give a dark spore print are at the end. Neat!

DNA analysis is now reeking havoc with the traditional ordering of fungi, by providing deeper insights into how fungi have evolved and their 'real' related-ness (which I got some insights into on my trip to Kew). Nevertheless, spore colour remains a good initial clue to genera. I should pay more attention to it.

My microscope is fine

I have, for some time, been inclined to think that there is something wrong with my microscope. I've looked at other people's micrographs on the internet and at the illustrations in books which show what microscopic features are supposed to look like, and despaired that what I see down my microscope usually looks rather obscure and featureless.

Yes, my Dad's old microscope is pretty basic (it's an old version of Brunel Microscopes 'Wedmore SP03', currently retailing for £106.67 + VAT). But once Carol had kindly cleaned a load of dust off it for me and shown me how to optimally focus the light we established it's actually fine.

Of course, at that price bracket you don't get the depth of field and focus-stacking that other, more expensive, microscopes can provide. But, used properly, my microscope should be good enough to see most microscopic features. This is very reassuring to know!

Don't be scared of using dried material!

I think I'd somehow got the impression that one has to be a terribly serious mycologist to use dried material and it must be fiendishly difficult to work with. This is not true at all!

Carol had brought a selection of dried material to the workshop literally, dried out mushrooms – and explained that dried material will usually exhibit all the same microscopic features as fresh material (at least for basidiomycetes, I'm not sure if this is the case for ascomycetes). So they're ideal to work on when identifying fungi from their microscopic features, as is necessary with many genera. Carol advised mounting dried material in ammonia, as it rehydrates the material more readily than water.

You can dry specimens either on top of a radiator, or using a standard food dehydrator. Stored in a (labelled) bag or envelope the material will keep indefinitely and can easily be sent off in the post, if the collection turns out to be of interest to another mycologist or herbarium. Which it may well do, if you happen to find anything rare or unusual.

But you do need to make as comprehensive notes as possible of the fresh specimen, as mushrooms can look (and smell) completely different when dried.

I think using dried material may be the answer to my biggest mycological problem. No more mouldy mushrooms in the fridge! And now I have something to keep me occupied during all those boring months when there are no mushrooms around: work on my dried material.

You have to cut things into TEENY TINY pieces

Another revelation on this weekend's microscopy course is that the reason the stuff I've been looking at under the microscope usually looks obscure and featureless is not because there's anything wrong with my microscope it's because I've been whacking great slabs of mushroom onto my slides.

I might have thought I was putting a small piece of mushroom onto the slide, before popping a cover slip on teetering on top of it. But watching Carol prepare a 'gill squash' (literally, a piece of gill squashed onto a slide) has given me a whole new understanding of the word 'small'.

Carol showed us how she uses a dissecting microscope to cut an absolutely miniscule slice of mushroom, using very fine tweezers and some pointy things which she makes herself out of a sewing needle super-glued onto the tip of an old propelling pencil. And she showed us different ways to cut your section, depending on which part of the mushroom you need to look at.

Now, Carol made this look very easy. But it was soon revealed to me that it takes a lot of skill.

Still, with a whole weekend to practise, I did eventually manage to prepare a reasonable 'gill trama' squash particularly tricky as it requires taking a very thin cross section through the gill.


I was pleased with it any way.

Stains stain things

Working with stains is a leap I haven't had the courage to make on my own, but Carol gave us a very helpful overview of the commonly used stains, and what they're used for.

Over the weekend I got some practise working with Congo Red. We were shown how with some care – you can deposit a small dab on your slide and draw it under the coverslip to make key features in your squash more visible, by staining the cell walls. Congo Red is very red though (and reportedly carcinogenic), so you have to be careful it doesn't stain you, or anything else.

Other stains are also available and used for looking at different features. PlaqSearch has also been recommended as a good general purpose stain which is entirely safe to use, so I plan to give that a try.

Reagents react with things

In her introductory talk, Carol explained that Melzers reagent can cause what's called an 'amyloid' reaction in some tissues and spores, in which the material turns blue-black.

This can be particularly spectacular in Russula spores, where Melzers reagent changes the colour of the spores and allows you to see their intricate ornamentation, as illustrated here:

Capturing the unforgettable moment when I first saw an amyloid reaction. You probably had to be there.


MycoKey is awesome! 

Over the course of the weekend, Carol also introduced us to the MycoKey software (available on a 14 day free trial and then it costs 40 € + VAT for a licence) which looks like a fantastic resource for beginners as well as experienced mycologists. It contains synoptic (multi-access) keys to genera, which means you can tell it a range of features you've observed and the software will give you a list genera to which your specimen could belong. You can then flick through an extensive photo library, showing different species from a particular genus. I think this will be incredibly helpful for me, as I still often get stuck trying to figure out what family I'm in. 

The software also gives you access to all the keys from Funga Nordica in .pdf format (which are unlocked when you purchase the licence), so you can press onwards towards a species identification. (But, be warned! As I've commented before, the keys in Funga Nordica can be a bit daunting.)

Compared to the price of many fungus identification books, this seems like a very cost-effective and convenient way to get access to a wealth of identification resources.

It's good to meet other mycologists

Although I learned a lot over the course of the weekend, probably the main thing I learned was that microscopic examination takes considerable skill. And that skill can only be built with practise, which takes time (more than a weekend). Several people on the course commented that you can't really learn these skills from a book because the tecniques are so very manual and precise. You need to see someone do it.

So I'm extremely grateful to Carol Hobart for giving her time to show us how she does what she does, and introduce us to the basics of microscopic examination.
There were several occasions, over the course of the weekend, when I found working with the material rather frustrating. Preparing a squash, doing the right thing with the chemicals, getting it under the microscope, and finding the features you're looking for (if they are indeed there, which they might not be) can be very hard. It can make you feel like a bit of a dunce when it doesn't go how you wanted it to. In a weird way, being on the course gave me some reassurance that mycology just is hard. But you don't need to struggle on your own there are other people out there who are on the same journey, and we can help each other.

As John F. Kennedy once (almost) said:
"We choose to do mycology ... not because it is easy, but because it is hard." 


  1. Excellent blog! I'm lucky enough to have watched Carol do those squashes quite a number of times now. It's a steep learning curve, but very rewarding when you get something special to see. My next challenge is knowing what the hell I'm looking at, then what is the significance of that particular feature. Oh well, onward and upward! Incidentally, you might be interested in focus stacking software. There are several out there. You can use Photoshop, but I found it nigh on impossible. I use Helicon Focus. Not cheap but pretty good and very easy to use and it works on mac. There's a free one which is supposed to be pretty good - Combine ZP, but no good to me as a mac user. https://www.blipfoto.com/entry/2247060353756169253 One of my early successes.
    Lovely to meet you Clare. Hope our paths cross again! Chris (The one huddled in the front corner)

    1. So nice to see this comment, Chris - glad you liked the blog! I'm itching to have a go at some more microscopy now. Thanks again for the tip about micro-science.co.uk by the way, I put my order in on Sunday night for a few basic chemicals to get me started, and then bethought myself afterwards that it would be good to get some KOH as well. John was so helpful in amending my order - he chucked in the bottle of KOH for free.

      I've always assumed you need to have a camera attached to your microscope and rigged up to the computer to use focus stacking software - is that right? I've been taking photos down the microscope with my smartphone - don't think it's got a facility to attach a camera. Maybe when I get the hang of gill squashes, I'll think about investing in a fancier microscope...

      I'm sure we'll meet again! Have a great season. Clare

    2. Glad you had a good experience with micro-science.
      To stack, you just need a series of photos with the focus adjusted from front to back (or vice-versa ) of your subject. To be honest, most of the stacking I've done has been with macro photography, adjusting the camera focus, but no reason it shouldn't be done by adjusting the focus on your microscope. Would be easier with you camera fixed (maybe a tripod) though so you have a hand free to adjust the focus. If I have time, I might have a go at that. My microscope camera is pretty rubbish, so I might try it with my phone. I'll let you know!