Getting started with microscopy

I talked about algae last week at an event organised by Durham Wildlife Trust (part of the publicity for The Natural History of Upper Teesdale) and I promised them a post about how to get started in microscopy and, more specifically, to start discovering more about algae.  I have illustrated the post with some of Chris Carter’s spectacular images of algae to whet your appetites for exploring the world of freshwater algae …

Broadly speaking, the natural historian wants a microscope for one of two tasks: to make small things bigger or to make invisible things visible.   There is not really a sharp dividing line between these two categories, as the illustrations of Cladophora filaments in “Summertime blues …” show.   You might start out looking at a handful of green slime pulled from your garden pond, but then you might see smaller algae growing on those filaments that you want to examine too.   The good news is that you should be able to get hold of a reasonable microscope with the capacity to magnify up to 400 times for about the same outlay as a digital SLR camera.   That should let you see all but the smallest algae.   If you are sure that your interests lie mainly in “making small things bigger” then you should consider a low power dissecting microscope (these are probably the best way of introducing children to microscopy, as there is a smooth transition between the tangible but small object that has piqued their interest and the larger, more detailed image that they see when they peer through the microscope’s eyepieces).

However, even though a basic microscope need not cost a fortune, good microscopes are expensive so my advice to a beginner is to search out a rerfurbished second hand microscope.  In north east England, I can recommend JB Microscopes but Google should help you find dealers elsewhere in the country.   A reasonably local supplier is necessary because you should really try out a microscope before you buy.   There are reputable mail order suppliers (e.g. Brunel Microscopes) but I would not want to spend a large sum on a piece of equipment that I had not had a chance to use first.

A colony of the diatom Meridion circulare.  The image at the top of the post shows desmids from the genus Micrasterias.   Both photographs by Chris Carter. 

If you are on a limited budget, I suggest you go for a good basic microscope with the option to fit a camera at a later stage.  It is possible to take a reasonable photograph by pointing a digital camera (or even a smartphone) down the microscope’s eyepiece and it is better to put up with the shortcomings of these images than to sacrifice the quality of the microscope itself.

Once you have your microscope, you will also need slides, coverslips, forceps, some plastic Pasteur pipettes, a couple of needles, a scalpel and some collecting tubes.  You can buy all of these from Brunel Microscopes and NHBS, both of whom cater for both the amateur and professional markets.   They also sell boxes of prepared slides, which are a good way to get some experience at using a microscope.

The microscopic world generally lacks the type of user-friendly well-illustrated identification guides that help us identify wild flowers, birds, butterflies and so on.   Most books are aimed at the academic market and are, consequently, expensive.   If you want to get started with freshwater algae, one useful resource is this guide to the larger algae found in rivers: RAPPER_manual_version1.7_May2016.  It was produced to accompany a method for rapid assessment of streams and rivers and, as the journey towards formal publication has stalled, I am happy to make it available here.

Hydrodictyon reticulatum, the water-net, photographed by Chris Carter.  500 mm (micrometres) is half a millimetre.

Useful websites include AlgaeVision and the Diatom Flora of Britain and Ireland.  As most freshwater algal genera are found throughout the world, Diatoms of North America is also a useful resource.

The Freshwater Biological Association have affordable booklets on the identification of desmids and diatoms and there is an AIDGAP key, too, for freshwater diatoms.   The latter is badly in need of updating but, people assure me, is still useful for beginners.

There are plenty of other online resources, but l would recommend visiting the website of the Quekett Microscopical Club, a long-established group of enthusiasts whose interests span the whole realm of natural history and optics.   www.microscopy-uk.org.uk is also worth a visit.   Both websites will help you as you start your explorations of the hidden worlds of nature.

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How to win the Hilda Canter-Lund competition (4)

Daniella Schatz’ image of the coccolithophore Emiliania huxleyi is one of a relatively small number of electron micrographs to have made it to the shortlist of the Hilda Canter-Lund prize and, though not an outright winner, it offers some useful lessons to anyone considering submitting an image in next year’s competition.

The first point to note is that Daniella has not submitted a single image, but a montage of two separate images. The competition rules state that “basic image enhancement (i.e. cropping, adjustment of contrast, colour balance etc) is permitted, along with focus stacking and stitching. However, excessive image manipulation is not acceptable.”   “Excessive image manipulation” is not easy to define; however, Daniella’s montage worked for the judges because the two elements together tell a story about the life of this alga.  The left- and right-hand images are the “before” and “after” cases of a major factor controlling the ecology of Emiliania huxleyi.  Daniella wanted to tell the story of the decline and fall of E. huxleyi blooms in the oceans; in the process she also evoked a long tradition of memento mori – artworks that remind viewers of their own mortality, and of the fragility of all life on earth. Another montage, this time by Alizée Mauffey, made it to the short list in 2017; again, the images were not selected and placed for aesthetic reasons, but to illustrate the range of functional traits within intertidal macroalgae.

Daniella piles on a little more “image manipulation” by using false colour to highlight the tiny EhV201 virus cells that are scattered across the right hand cell and which are responsible for its sorry state.  A couple of SEMs that have been enhanced by false colour are submitted each year but the artificiality of the medium rarely results in a major improvement to the image.  The stark monochrome of SEMs places them in a long and noble tradition of black and white photography that should not need this type of enhancement.   She, however, challenges this by using false colour very sparingly and to draw attention to an important element of her story.

And so to the “story”: we now ask all entries to the competition to be accompanied by a legend of about 100 words explaining a little more about the picture.   Most experienced phycologists will recognise the left hand image as a coccolithophore but many viewers will see these as abstract geometric shapes. The legend is important to help the viewer decode these shapes and place them into a broader context; in this case, by emphasising their role in global carbon cycling.  Having said that, most of the shortlisting takes place without reference to the legend with initial screening based primarily on the quality of the images.  I do remember, however, that Daniella’s image was one where we did need the legend in order to understand what she was trying to say.

A detail from Daniella Schatz’ Scanning Electron Micrograph (SEM) of the coccolithophore Emiliania huxleyi showing the large dsDNA Emiliania huxleyi virus (EhV201, coloured orange). EhV is a large dsDNA virus that is responsible for the demise of vast oceanic blooms of E. huxleyi. During viral infection the cells undergo programmed cell death and shed their coccoliths, important components of the carbon cycle.  The individual viruses are each about 100 nanometres (1/10000th of a millimetre) in diameter.

We also encourage photographers, particularly those submitting microscopic images, to include a measure of scale in the legend, particularly for microscopic images.  This is important, as lay audiences will have little idea about the size of the objects that are being portrayed.   When images are used as illustrations, then a scale bar is appropriate (see “The stresses of summertime …” for a recent example); however, a scale bar is likely to be an unwelcome intrusion in an otherwise balanced composition so a sentence in the legend is usually more appropriate.   Remember that the term “micrometre” might not be easily understood by many viewers, and it is a good idea to explain dimensions in millimetres as well.

When the votes were counted in 2015, Daniella’s image lost out to Günter Forsterra’s stunning view of the Beagle Channel off the coast of Chile.  However, it stands as a fine example of conceptual approach to the Hilda Canter-Lund competition – with several different elements combining to convey an idea that is more than the sum of its parts.   The photographer of the microscopic world rarely has the luxury of the “decisive moment” and, instead, the quality of the final image often lies as much in post-production as it does in image capture.

Return to Croft Kettle

It has been over three weeks since I last wrote about Croft Kettle. However, with the diversions to Milan and Trento behind me, I can now settle down and continue to sort out the images I had taken from the samples I collected back in May.   I’ve also dug out some other slides from previous visits in order to show the full range of diversity that we’ve encountered over the years.

One of the most abundant diatoms gliding through the mass of Cymbella stalks surrounding the Chara stems was Navicula radiosa, illustrated below. The name derives from this diatom’s strongly radiate striae, which are not visible in the live specimens that I photographed.   What you can see clearly are the two long, narrow plastids (chloroplasts), one on either side of the valve.   Another Navicula species which I have seen in this habitat at Croft Kettle, but which was not obvious in the samples I collected in May is illustrated in the next illustration: Navicula oblonga.   This is enormous by diatom standards: the largest individual I found in a sample I collected in May 1999 was just over a fifth of a millimetre long. It is hard to fit an entire valve of N. oblonga into a field of view to photograph at 1000x magnification, so the images below were all taken at 400x. N. oblonga is a relatively rare diatom in the UK in my experience, with an apparent preference for hard waters, extending into slightly brackish conditions.

Croft_Kettle_150529_#2

More diatoms associated with Chara hispida stems in Croft Kettle, May 2015: a, b., c.: Navicula radiosa; d. Amphipleura pellucida.   Scale bar: 10 micrometres (= 1/100th of a millimetre).

My return to Croft Kettle was prompted, you may remember, by a talk about a fossil lake in the Sahara which had a similar diatom flora (see “The desert shall rejoice and bloom …”). Both Cymbella cymbiformis and Navicula oblonga featured in the assemblages that Nassouma Yahiaoui found there, along with representatives of Epithemia and Mastogloia, both of which I found in my May 2015 samples, though neither presented themselves in particularly photogenic poses.   I did include some photographs of another species of Epithemia in my description of Cassop Pond, which is also associated with the Permian limestone.

Navicula_oblonga_Croft_May1

Navicula oblonga associated with Chara stems in Croft Kettle, May 1999. Scale bar: 25 micrometres (= 1/40th of a millimetre).

One other interesting species that I found at Croft Kettle, though it was not present in Nassouma’s Guern Toil profile, was Amphipleura pellucida. This is a long, delicately-featured diatom with a small, H-shaped plastid in the centre.   A silica rib runs along the centre of the valve; this splits as it approaches the poles to contain a short raphe slit. The combination of silica rib and raphe resembles the end of a sewing needle. Microscopists have long been interested in Amphipleura pellucida because the striae are extremely-closely spaced (37-40 in 10 micrometres).   This means that they can only be resolved by the very best optics and, consequently, slides containing A. pellucida are used as test objects. The slide I used to photograph the specimens below was given to me by John Carter (see “Remembering John Carter”) and was made from material collected in 1872 by “Firth”. Some hunting on the internet suggests that this was William Allott Firth, who was a Quaker from Yorkshire. Croft Kettle is less than a kilometre from the Yorkshire – Durham county boundary and Darlington, the nearest town, has strong Quaker connections too.

It is a good idea to have a test slide with Amphipleura pellucida to hand when you are buying a microscope.   The sales reps whose job it was to demonstrate new microscopes used to breeze into our lab in shiny suits reeking of cheap aftershave and talk the talk about how wonderful their product was.   We would then hand them our test slide and say “resolve that”.   After twenty minutes fiddling with the microscope set-up they would usually make some excuse and retreat with their tails between their legs.   I got a certain sadistic pleasure from watching these fast-talking laboratory sales representatives being defeated by a handful of gunk collected by a Victorian amateur natural historian.

Amphipleura_pellucida_Croft

Ampipleura pellucida from a sample collected from Hell Kettles in 1872 by Robert Issac Frith. Scale bar: 10 micrometres (= 1/100th of a millimetre). Bottom right: the slide from which the specimens were photographed.