More from the River Wear

As well as the green patches at the margins of the river, there were also a huge number of small, brown patches floating on the surface, ranging in size from about a two pence coin to a medium-sized leaf.  There seemed to be an almost constant procession of these floating down the river, and they piqued my interest.

I had seen similar mats elsewhere and had a fair idea of what to expect when I put a small part of one under the microscope.  What I saw was a tangle of blue-green filaments, each about 15 micrometres wide, some of which, if I watched closely, glided slowly across the field of view.  These filaments belong to a genus called Oscillatoria, a close relative of Phormidium, which we have met in earlier posts.  Several Oscillatoria species live in the plankton, but this one, probably O. limosa, often forms mats of this type.


Mats of Oscillatoria limosa and other algae photographed as they floated down the River Wear in July 2013.   The patch on the right is about five centimetres across.  Inset: a single filament of O. limosa.  Scale bar: 10 micrometres (1/100th of a millimetre).

As well as the Oscilllatoria filaments there were also several other algae, including Spirogyra and a number of diatoms.   The tangle of filaments creates a good habitat for motile diatoms.  Indeed, motility confers a competitive advantage as it allows organisms to adjust their position within the mat in order to increase their rate of photosynthesis.  One of the most distinctive diatoms in this sample was the needle-shaped cells of Nitzschia acicularis slowly weaving their way around the filaments and other particles on the slide.


A filament of Spiroygra from the mat collected from the Wear in July 2013 with (inset) a cell of the diatom Nitzschia acicularis.  Scale bar: 50 micrometres (1/20th of a millimetre).

My guess is that these mats were formed on the bottom of slower-flowing sections of the river and sheared away from the silty surfaces as the oxygen produced by photosynthesis made them more buoyant during the day.  This, combined with the constant drag of the water over the mats growing on the unstable silty substrates eventually leads to the mats shearing away from the bottom and floating to the surface.

On the evening after I collected these samples, however, there was a heavy downpour and the next morning the river was in spate, with turbid brown water swirling through the arches of the bridges and over the weirs.   All but the more firmly-anchored aquatic plants were dislodged by this, and on my next visit I could see almost none of the floating algae that I have written about here.  Like the grass of the field, they are here today yet tomorrow are gone…


The River Wear in summer

The long period of warm, dry weather has had a pronounced effect on our rivers.  Whilst out rowing on the River Wear last week, I noticed bright green patches at several points along the edges and many small brown leaf-sized mats floating down the channel.  The Wear at Durham is held back by a series of weirs, built originally to serve mills, so the current here is slower than in most parts of the river, which may have helped these to proliferate here.


The River Wear at Durham, showing the weir impounding the river beside the Old Fulling Mill.  July 2013.

The green patches were either free-floating or entangled amongst other vegetation at the side of the river and had a rough feel when I rubbed a portion between my fingers.  I could just make out, with my naked eye, individual unbranched filaments.   Under the microscope, these were revealed to belong to the genus Oedogonium.  As is the case for several other green algae that we have met, identification of species within this genus requires reproductive organs, yet these are rarely seen in natural populations.   The filaments of this particular population were about 45 micrometres wide, with individual cells between one or two times as long as broad.  There appear to be many small chloroplasts though, in fact, these are all part of a single “reticulate” (net-like) chloroplast which is spread around the cell’s perimeter.  One other diagnostic property of Oedogonium is the presence of “cap cells” (arrowed in the diagram below).  About one in ten cells have a series of rings at one end.  These are “scar tissue” arising from when the cell has divided.


a. Floating mats of Oedogonium in the River Wear, July 2013 (collected close to the left foreground in the picture above); b. low magnification view of the tangle of filaments; c. single filament of Oedogonium showing the “caps” (arrowed).   Scale bar: 50 micrometres (1/20th of a millimetre).

Oedogonium was not the only green alga floating in the Wear at this time.  I also found some growths of an alga whose tubular growth form bore a superficial resemblance to a sausage skin.  This alga used to be called Enteromorpha – a comment on the superficial resemblance to an intestine.  However, it has recently been reclassified into a genus called Ulva.   Ulva is very common in estuaries and in the marine intertidal zone but a couple of forms are also found in freshwaters too   They can be found attached to surfaces, via tiny rhizoids, but, in rivers at least, they are more commonly found free-floating or trapped amongst other vegetation.  The hollow tubes act as a buoyancy aid by trapping the oxygen produced from photosynthesis.

Neither Oedogonium nor Ulva flexuosa are new records for the River Wear but it is unusual to find quite so much here in Durham.   The weather is the most likely explanation, but they serve as a useful reminder of how rivers subtly change their character as the year progresses.


Ulva flexuosa growing in the River Wear at Durham, July 2013.  

Epiphytes with epiphytes …

The most abundant algae in the intertdal zone at Whitburn were the kelps and wracks (mostly Fucus and Laminaria species).   We visited at low tide, so saw them as a thick layer strewn across the rocky platform.  However, once the tide comes in, the buoyant stems and leaves lift up and the seabed is transformed into a forest of fronds, gently swaying in the current.   Dirk Schories’ image in this year’s Hilda Canter-Lund award shortlist gives a good idea of what such a “kelp forest” looks like from underwater.

Just as the trees in a terrestrial forest provide a structure within and around which many other organisms live, so the kelp is itself a “foundation species”, providing both habitat and resource for many other members of the intertidal community.   And just as ivy uses forest trees as a support, enabling it to climb higher in the canopy, so we find smaller algae growing on the stems (technically “stipes”) of Fucus and Laminaria.   A tuft of brown filaments, just a couple of centimetres in length, caught my eye.  Even with the naked eye I could tell from the brown “cloud” around these filaments, that these, too, had their own epiphytes.

Being amongst so many seaweed experts mean that the filaments were quickly named for me as Pilayella littoralis.   The individual filaments were about 30 micrometres wide, with occasional branches.   The filaments were divided into cells, each containing many brown-coloured chloroplasts lining the edges.   Scattered along the surface of the filaments were club-shaped cells of a diatom called Licmophora, which were attached to the Pilayella filament by a mucilage pad at the narrow end.   These, too, were filled with many small, brown chloroplasts, making it hard, at times, to distinguish between the two organisms amidst the muddle of filaments.   Just occasionally, the Licmophora formed much longer stalks, with a series of diatom cells budding off, indicating the points when the original cell had divided.


a. a filament of Pilayella littoralis from Whitburn, Tyne and Wear, with epiphytic Licmophora cells.   b. a stalk of Licmophora cells from the same site.  Both images are composites built from “stacks” of individual images using Helicon Focus software.  Scale bar: 25 micrometres (1/40th of a millimetre).

The similarity in colour between the Pilayella filaments and Licmophora cells is due to the two organisms sharing a number of pigments, most notably a carotenoid called fucoxanthin.  This, in turn, suggests a common evolutionary origin.  Pilayella belongs to the same group of algae as Fucus and Laminaria, the Phaeophyceae, or brown algae.   I was about to sketch out a rough evolutionary history of these in relation to the diatoms, linking them both via a common phylum, the heterokontophyta.   However, as I was checking some facts using the very useful website, I found that this uses an alternative classification.   In this, diatoms and brown algae are found in separate phyla, the Bacillariophyta and Ochrophyta respectively.   Diatoms and brown algae do share a common origin, but the story may have changed since I last had to teach this and I need to go and do some more homework.  The better part of valour, said Falstaff, is discretion, and rather than incur the wrath of taxonomists (any ten of whom will venture at least eleven opinions on high level classifications), I will stop at this point.

Microscopic monsters in mud …

As I spend most of my life studying freshwaters, I thought it would be good to dip my toes into some saline water for a change, and so joined a group of colleagues on an excursion to explore the seaweed flora of the north east coast.   I met them at a rocky shore on a glorious sunny day at Whitburn, just north of Sunderland surrounded by tonnes (literally) of kelps and wracks.  After a little time, these gradually resolved into a rich assemblage of red, brown and green seaweeds, some crusts on rocks, some tufts of filaments and others branched fronds, some of which were as tall as a person.

Amongst all this profusion and diversity of algae, however, I saw a few chocolate-brown patches on the finer sediments and, when I looked closely, I could see oxygen bubbles on these, indicating that these, too, were busy photosynthesising.  Under the microscope, these patches prove to be composed almost entirely of diatoms, in particular, “S”-shaped cells belonging to a genus called Pleurosigma.   There are about four genera of diatoms which have this “sigmoid” outline, but I have no idea why this has arisen.   It is not, as far as I know, a property found in any other groups of algae either.   In this case, the Pleurosigma was existing alongside smaller “straight” diatoms (Navicula and Nitzschia spp.).


Diatoms growing on fine sediments (“mud”) at Whitburn, Tyne and Wear, July 2013.   Note the chocolate-brown patches on the grey-brown mud and note, too, the lighter speckles, which are tiny oxygen bubbles.  The red-lidded bottle is seven centimetres tall.


Pleurosigma sp. (and a cell of Navicula) from the chocolate-brown patches on the surface of intertidal mud at Whitburn, July 2013.  The scale bar is 25 micrometres (1/40th of a millimetre) long.

One property that all the diatoms had in common was that they were moving.   The video shows them moving on surface of the glass slide and cover slip that I was using to view them under my microscope but, in their natural habitat they would be moving over and around the sediment particles and each other.

A video showing cells of Pleurosigma from intertidal sediments at Whitburn, Tyne and Wear, moving around the glass slide.  The cells are approximately 75 micrometres long.

Being able to constantly adjust position offers a clear advantage to diatoms such as Pleurosigma which live in unstable habitats such as intertidal sediments.  Each tidal cycle brings fresh sediment which could be deposited on top of the cells, burying them and cutting out the light they need for photosynthesis.  Their ability to move around the sediment means that they can relocate to more favourable conditions when this does happen. However, the incoming tide also brings other problems, in the shape of grazing animals and, consequently, the diatoms have evolved endogenous rhythms which mean that they move downwards in the sediment as the tide comes in, then back to the surface as it retreats.  It is tempting to regard microscopic organisms as “simpler” than the larger organisms with which they share their habitat.  The reality is that they are just as sophisticated (having had as long, or longer, to evolve), but all their complexity has to be packed into a single cell.


Stigonema in 3D

My experiments with stacking remind me just how “flat” the world that microscopists live in can become.   Had I paid more attention in school physics lessons, I might be able to explain why this is so.  I never think of the microscopic world as flat when I am using my microscope because, like other microscopists, I can use the fine focus controls to move through the image and create, in effect, a mental “stack” of images which allows me to imagine the third dimension.   It is only when I look at photographs with blurry out-of-focus sections, that the reality is drilled home.  Software packages that allow us to make composite “stacked” images really do represent a major step forward in this respect.

As I mentioned in a post back in May (Phworrrrhhh … algal sex in 3D!), it is also possible to go a step further and produce three-dimensional images and, always ready to test Chris Carter’s mettle, I put a small portion of the Stigonema that I had collected in Norway into an envelope and posted it off to Northampton.  Results came back a few days later and a couple of the images are reproduced below.  Once again, you’ll need 3D glasses to view these properly.  You can buy these online (try or go to your local newsagents and see if there are any magazines with a free pair stuck on the front.


Stigonema mamillosum from the River Atma, Norway, an anaglyph (three-dimensional image) by Chris Carter.


Stigonema mamillosum from the River Atma, Norway, a higher magnification image of the same population as the previous image,.  Photographed by Chris Carter.

There is a serious point here: it is too easy to forget just how artificial the world that we look at through our microscopes really is.  We flatten perspective and view objects at light intensities much greater than anything they encounter in nature, yet we claim to be students of the natural world.  Perching a pair of cardboard 3D glasses on the end of your nose may not add much to your aura as a serious scientist, but it does allow a small insight into the natural forms of the organisms that we study that is not normally available.

Now … with added depth of field …

My images of Stigonema highlight one of the biggest problems in photomicroscopy: the very shallow depth of field that is inevitable at high magnifications means that any object that is distinctly three-dimensional will only ever be partly in focus.  In this case, I managed to get the main branch in crisp focus but the side branches are blurry and out-of-focus.  After I had taken those photographs, however, I made my first experiments with a technique called “stacking”.


One “slice” of the “stack” of images of Stigonema mamillosum, collected from the Atma River in July 2013.  Note how parts of the image are out of focus whilst others are crisply focussed.

The idea is that you take a series of photographs of the same object, adjusting the focus slightly each time so you end up with a series of images, each showing a different “level” of the object in crisp focus.   I then downloaded a software package called Helicon Focus that takes this “stack” of images and selects the sharply-focused parts of each which it then combines into a single composite image that appears to have much greater depth of field than any of the originals.


The composite image of Stigonema mamillosum produced from a “stack” of seven images, including the earlier image in this post.  Note how the depth of field now appears to be much deeper in the composite image.  Scale bar: 50 micrometres (1/20th millimetre).

Helicon Focus is not the cheapest of the packages that create composite stacked images, but a quick trawl of the internet (in particular, the Quekett Microscopical Club’s useful web pages) suggested that this was the easiest and most intuitive to use.   And it did prove fairly straightforward: probably no more than thirty minutes elapsed between downloading the software and producing my first “stacked” image from a batch I had taken the day before.  I’ll be trying this again before too long…

Subsidiarity in action

Back in June, I collected a sample from the edge of Lago di Maggiore in Italy and performed an impromptu analysis to see if the outcome, based on my experience of British lakes, was in any way comparable with that of my Italian colleagues (see post of 17 June 2013).  This is necessary if the EU’s environmental legislation is to provide a level playing field for all Member States and has occupied much of my professional life over the past eight years or so.   Standing beside the Atma River, I decided to conduct a similar experiment, once again scraping some of the slippery film from the submerged rocks into a small bottle that I could slip past airport security in my hand luggage.


A chain of three cells of Tabellaria flocculosa from the Atma River in Norway, July 2013.  The scale bar is 10 micrometres (1/100th of a millimetre) long.

The most abundant diatom in the sample, by far, was Tabellaria flocculosa, comprising well over 90% of all the diatoms that I saw.   This forms long chains, each cell attached to the next by a pad of mucilage at one corner, which tangle in and around the other algae (in this case, mostly green alga such as Mougeotia).   There were a few diatoms that I could not identify in this sample, because of the ad hoc method of analysis, but there were enough that were identifiable for me to be able to run the results through the calculations which we use in the UK to evaluate the status of rivers.

Had I performed this analysis on a UK river, I would have concluded that it was at “high status” (i.e. very close to its natural state), exhibiting no signs of enrichment by nutrients or of acidification.   The good news is that this is what Susi concludes, based on her own analyses, which use the algae other than diatoms.  So this informal exercise gives me double confidence:  that standards in Norway and the UK are similar, and that we can reach the same conclusions using two different groups of algae.

The most surprising aspect, for me, is that I still had a good mobile signal whilst sampling this site.  I usually associate “high status” with remote locations where the mobile signal is non-existent.