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. is also worth a visit.   Both websites will help you as you start your explorations of the hidden worlds of nature.


Fascination in ecology’s dark side …


There is, we are told frequently, too much sex and violence on the television.  Much of it, I am afraid to say, courtesy of natural history documentaries which are too quick to focus on anthropomorphic organisms participating in acts to which humans can relate than on the more prosaic organisms that constitute the bulk of both biomass and diversity in ecosystems.   I’ve written about this subject before (see “The complicated life of simple plants”) but a quick analysis of the index for The Blue Planet – the book which accompanied David Attenborough’s series for the BBC – offers some (semi-) objective evidence.

No surprise, for me at least, to see “phytoplankton” and “diatom” on the right hand side of the graph when I ranked organism groups from the most cited to the least.   It was a desire to promote the “unfashionable end of biodiversity” that prompted me to start this blog, to raise the profile of organisms that are responsible for half the primary production on the planet (see “every second breath …“).  On the other hand, I was pleasantly surprised to see “kelp” in a strong mid-table position.   The Blue Planet book has a beautifully-illustrated chapter on kelp forests, describing the brown seaweeds that live in ocean littoral zones and the organisms that live on and amongst them in detail.


An analysis of index entries in The Blue Planet for major organism groups.   Each category contains all page references to the organism group, along with any sub-categories classified underneath this (so, for example, “dolphin” includes references to “care of young”, “hunting”, “sonar” etc.)

Having set out my argument for anthropomorphism as the driver behind natural history documentary programming, I was surprised to see that sharks came out as top of my list of index entries (which, I assume, roughly correlates to the amount of space that the authors devote to these organisms).   My explanation is simply that interest in sharks reflects human fascination with the dark and macabre: they are the Hannibal Lectors or Walter Whites of the underwater world.

I don’t underestimate the effort and technical skill needed to get good footage of charismatic aquatic vertebrates, whether sharks, whales or penguins.   However, once the footage has been obtained, it is easy to weave stories with which viewers can empathise.   Making documentary programmes about microscopic algae carries its own technical challenges but, even when the footage has been obtained, for how long can you hold the viewer’s attention?   Or, perhaps more to the point, can you persuade a commissioning editor that you can hold the viewer’s attention for long enough to justify the investment?

Whilst musing on the fascination with the dark and the sinister reminded me of press coverage of an upcoming exhibition on the art and influence of Caravaggio at the National Gallery and, from here, to other great artists whose works often have macabre undertones.  Géricault’s Raft of Medusa and Artemesia Gentileschi’s Judith Slaying Holofernes were two works that immediately sprang to my mind but you could include almost every crucifixion scene painted from the Renaissance onwards.   The Dutch Golden Age stands in stark contrast to these, often focusing on the everyday, the mundane.   Every time I look at a Vermeer, I marvel at how he can raise prosaic activities to this higher level, how he can convert a mundane act such as pouring milk from a jug into a transcendent moment (see “A wet afternoon in Berlin“).   The analogy between the existential drama that seems to be a subtext for every natural history documentary and the quietly spinning flywheels of nature that convert solar energy to sugars and, from there, power the processes that drive the ecosystems of which the charismatic organisms beloved of television natural historians, are obvious.

I have a theory that television natural history is a prime recruiting agent for undergraduate ecologists whilst, at the same time, presenting a very distorted view of the reality of ecology.   The reality is that the bulk of the biomass in ecosystems is in the primary producers – the plants – followed by the organisms that eat these and finally by the predators.   The histogram at the top of this article, by contrast, has sharks and whales receiving far greater attention than kelp and phytoplankton (coral reefs are a complication to this argument to which I will return at some point).   Students may be entranced by the images they see on television, but the reality of ecology is very different and, dare I say, involves more mathematics than most biology undergraduates want to contemplate.

The point of my diversion on the art of Vermeer was to offer a suggest that the route to greater public understanding of the unfashionable end of biodiversity lies not in trying to hype this up to be something that it will never be, but to appeal to a quieter, more contemplative side of human nature.   Algae are not for those with short attention spans, looking for instant gratification, but they are perfect objects for meditating on the diversity of life on earth and, indeed, for the myriad of hidden processes that keep life on earth ticking over …


Byatt, A., Fothergill, A. & Holmes, M. (2001).  The Blue Planet: A Natural History of the Oceans.  BBC Publications, London.

Every second breath …

“I am determined”, said Kathy Willis of the Royal Botanic Gardens at Kew in an interview in The Independent on Monday, “to prove botany is not the ‘Cinderella of science’”. How does she plan to do this?   Her platform for this bold endeavour is a new series for Radio 4 entitled “Plants: from Roots to Riches”.   It starts next week and there will be 25 episodes, airing daily just after the World at One.   A quick look at the series website was enough to convince me that this series will not present botany as the ‘Cinderella of science’. Ugly Sister, maybe, but certainly not Cinderella.

Okay: I write a blog about the unfashionable end of biodiversity so you should probably have a rough idea of where this is all heading.   I went to the program website where the subjects for the first two week’s episodes are listed.   I saw one episode on fungi and one on cycads, which are a group of Gymnosperms but otherwise there is a very strong bias towards the flowering plants, the brash, over-dressed near relatives of the algae who, in my version of the pantomime that is natural history broadcasting, are ideally cast for the role of ‘Cinderella’.

Does it matter? It is flowering plants, after all, which provide us with most of our carbohydrate intake, many fibres and pharmaceuticals and clothe our landscapes in myriad different ways. Why should we concern ourselves with a group of organisms that most of us never notice?

Try this exercise: breathe in, breathe out. Don’t breathe in. Hold your breath. Now breathe in again.   And out. Hold your breath again.   Repeat. Keep repeating. Keep skipping every other breath.

That’s why I am bothered.

Half of all the energy that is trapped by the sun and converted to energy comes from algae. In the course of photosynthesis plants and algae produce oxygen. It replaces the oxygen that plants and animals – including us – suck out of the air for our own survival.   Algae, indeed, put a lot of that oxygen into the atmosphere in the first place (see “Every (fifth) breath you take …”). They also represent a large part of our planet’s biodiversity (see “The sum of things …”).   I am forever worried when algae get side-lined in favour of the more visually spectacular elements of the plant and animal worlds though I don’t have an easy solution.

This is not a moan directed at Kathy Willis in particular. Indeed, she is in good company as David Attenborough, too, is a serial offender.   My problem is a broader one about how we can overcome the inevitable bias in natural history programming.   I have been writing a blog about algae for 18 months now. I know the problems. These organisms are not anthropomorphic, they have no courtship rituals, their sex life makes pandas appear horny (see “The perplexing case of the celibate alga” amongst other posts) and their offspring do not have big, yearning eyes.   People usually notice algae only when human activities have disrupted the balance so the algae become a problem. It is hard to convince people of the important role that algae play in the natural world. That’s why I suggest that it is algae that deserve the title of “Cinderella of Science”.   Just remember: every second breath …

Of course, I may be too hard on Kathy Willis. We can only see the first two week’s programs on the website at the moment. Maybe … just maybe … she’s leaving the best until last.


Kirchman, D.L. (2012). Processes in Microbial Ecology. Oxford University Press.

A paper you should all read …

I have tried to use this blog to promote the benefits of a broad interest in natural history over the narrow specialisms encouraged by modern academia. Consequently, I was delighted to see this issue receiving serious consideration in an essay in the latest issue of Bioscience: Natural History’s Place in Science and Society. It is open access, so you can read it even if you don’t have a subscription to Bioscience. No excuses, then. I’ve even given you the link.

The authors start with a definition of natural history as “the observation and description of the natural world, with the study of organisms and their linkages to the environment being central.” Natural history, in other words, is inherently cross-disciplinary and multiscaled. Implied, but never actually stated, is that the decline in natural history is a direct consequence of the growth of biochemical and molecular technologies. The latter may be excellent for answering questions about single organisms (and no-one would dispute the benefits for human health) but one cannot avoid knowing more and more about less and less. We need observation-based approaches if we are to ask the right questions in the first place, especially where more than one organism is involved.

I made my own case for this in a paper in Ecological Indicators last year. I was not arguing that there was no place for specialists, only that the day-to-day management of ecosystems needed people who were familiar with a wide range of organisms and who could make high-level decisions drawing on several complementary strands of evidence. The problem is more acute for the lower organisms, the focus of this blog, which lack the charismatic qualities of larger organisms such as birds.

By noting the decline in ‘natural history’ teaching in universities, the authors of the Bioscience essay are locating the cause of the problem in the supply-side of the equation (to use the language of economists). I have also wondered if there is not an issue in the demand for such courses. With the possible exception of bird watching, there has been a general decline in active participation in natural history in favour of ‘consuming’ nature via the television screen. Students come to university enthusiastic about the idea of natural history but find the opportunities for fieldwork to be limited and the reality of fieldwork less appealing. More so, perhaps, if struggling to name unfamiliar organisms (because of their lack of previous experience) in the vagaries of our climate. And, let us not forget, our flora and fauna are so much drabber than at the exotic locations that David Attenborough’s budget lets him visit.

The beauty of the Bioscience essay is that it not only laments the decline in ‘natural history’, it also presents examples of where broad cross-discipline thinking has led to insights that reductionist approaches alone could never have reached. And it has reclaimed the term ‘natural history’ for serious scientists. This, in my opinion, is more than just a matter of semantics. Anyone who uses science to argue for change needs to make the fullest possible use of the grey area between the jargon-filled papers of academic specialists and the non-technical beneficiaries of their endeavour. I’m proud to be a natural historian.


Kelly, M.G. (2013). Simplicity is the ultimate sophistication: building capacity to meet the challenges of the Water Framework Directive. Ecological Indicators 36: 519-523.

Tewksbury, J.J,, Anderson, J.G.T., Bakker, J.D., Billo, T.J., Dunwiddie, P.W., Groom, M.J. Hampton, Herman, S.G, Levey, D.J., Machnicki, N.J., Martinez del Rio, C., Power, M.E., Rowell, K., Salomon, A.K., Stacey, L., Trombulak, S.C. & Wheeler, T.A. (2014). Natural history’s place in science and society. Bioscience 64: 300-310.