The complexities of measuring mass…


Once upon a time, measuring the quantity of algae growing on the beds of streams and rivers was a painstaking, slow process that invariably revealed large amounts of spatial and temporal variation that, very often, obscured the ecological signals you were looking for. That has changed in the last decade thanks to the availability of field fluorimeters such as the BenthoTorch.  This makes it much quicker and easier to measure chlorophyll concentrations, the usual proxy for algal quantity.  Thanks to devices such as this it is now much easier to discover that your ecological signal is masked by spatial and temporal variation.

We’ve generated a lot of data about the fluxes of algae in the River Ehen using a BenthoTorch over the past five years and are in a position where we can start to make some generalisations about how the quantity of algae vary over the course of a year.  In broad terms, the results I showed in “The River Ehen in January” back in 2014 have not varied greatly over subsequent years, with peak biomass in mid-winter and low biomass in the summer (due, we presume, to intense grazing by invertebrates).  Curiously, we see a much less distinctive seasonal pattern in the nearby Croasdale Beck, but that is a story for another day….

The BenthoTorch uses an algorithm to partition the fluorescence signal between three major algal groups and, though this is not without issues (see below), I thought it might be interesting to see how these groups varied with biomass trends, and consider how this links to ecological theory.  The first group I’m considering are the green algae which, in this river, are mainly filamentous forms.   The general pattern, seen in the graph below, is for a gradual increase in the proportion of green algae, which fits with the current understanding of thicker biofilms having greater structural complexity with filamentous algae out-competing attached single celled algae to create a “canopy” of algae that are more effective at capturing light and other resources.  The relationship is, however, strongly wedge-shaped so, whilst many of the thickest biofilms have a lot of green algae, there are also thick biofilms where green algae are scarce or even non-existent.  Croasdale Beck shows a similar, but less pronounced, trend.


Relationship between the proportion of green algae and the total quantity of benthic algae (expressed as chlorophyll concentration) in the River Ehen (a.) and Croasdale Beck (b.).   The blue lines show quantile regression fits at p = 0.8, 0.5 and 0.2.   The image at the top of the post shows Ben Surridge using a BenthoTorch to measure algal biomass beside Croasdale Beck in Cumbria.

The second graph shows that this pattern of a gradual increase in proportion is also the case for diatoms and, once again, there is a broad wedge of points with an upward trend.  But, once again, there are also samples where biomass is high but diatoms are present in very low numbers or are even absent.   What is going on?

The problem is clear I think, if one looks at the final image in “The only way is up …” where the very patchy nature of algal communities in the River Ehen (and, indeed, many other rivers).   There are plenty of algae on this boulder, but not organised in a homogeneous manner: some zones on the boulder are almost pure diatom whilst others are almost pure green algae (and there are also zones that are almost pure Lemanea– I’ll come to that in a future post).   We try to sample the stones as randomly as possible so you can see the potential for getting very different numbers depending on where, on a stone, we point the BenthoTorch’s sensor.


Relationship between the proportion of diatoms and the total quantity of benthic algae (expressed as chlorophyll concentration) in the River Ehen (c.) and Croasdale Beck (d.).   The blue lines show quantile regression fits at p = 0.8, 0.5 and 0.2.  

With experience, you can make an educated guess about the types of algae present in a biofilm.  I’ve tried to capture this with my watercolours, using washes of raw sienna for the diatoms and a grass-green for the green algae, which roughly matches the colour of their respective growths in the photo in my earlier post.   The two groups of algae a are relatively distinct on that particular boulder.   The top row roughly matches the upper “edge” of the graph showing variation in diatoms, whilst the bottom row emulates the upper “edge” of the graph showing variation in green algae.  These are the two extreme situations; however, we also often see darker brown growths in the field, which can be recreated by mixing the raw sienna and grass-green together.  When I peer through a microscope I often see green algae smothered in diatoms: genera such as Oedogoniumare particularly prone as they have less mucilage than some of the others we find in the Ehen. Their filaments often host clusters of Fragilariacells as well as Achnanthidium minutissimum, whilst stalked Gomphonemaand chains of Tabellaria flocculosaoften grow through the tangle of green filaments.   The dark brown colour is deepened yet further by the colour of the underlying rock, so my effort on white watercolour paper is a little misleading.


A colour chart showing how different proportions of green algae and diatoms influence the colour of biofilms.

The final graph shows how, as the average biomass increases in the River Ehen, so the variability in biomass also increases.   The River Ehen is one of the cleanest rivers I know but I suspect that this pattern in benthic algal quantity could be reproduced in just about any river in the country. What I would not expect to see in any but the purest and most natural ecosystems is quite so much variation in the types of algae present.   Once there is a little enrichment, so I would expect the algae to become more of a monoculture of a dominant filamentous alga plus associated epiphytes.  Like much that happens in the microscopic world of rivers, it is easier to describe than it is to measure.

That, however, is only part of the story but I’ll come back to explain the patterns in the other main groups of algae in the Ehen and Croasdale Beck in my next post.


The relationship between mean chlorophyll density and the standard deviation (based on measurements from five separate stones) for samples from the River Ehen and Croasdale Beck. 



Croasdale Beck in February


My latest trip to the west Cumbria coincided with the period of freakily warm weather that marked the end of February (in marked contrast to a year previously when we were in the midst of the “Beast from the East”).   It felt like spring had come early although the skeletal outlines of leafless trees were incongruous against the backdrop of blue skies and, despite feeling the warmth of the sun on our faces as we worked, the water still had a wintery chill when the time came to plunge in my arm.

There were thick growths of algae on the bed of Croasdale Beck: a quick check with my microscope later showed this to be mostly Odontidium mesodonand Gomphonema parvulumand this piqued my curiosity to see how different species responded to the fluctuations in biomass that we observe in the streams in this region. I’ve talked about this before (see “A tale of two diatoms …”), suggesting that Platessa oblongellatended to dominate when biofilms were thin whilst Odontidium mesodon preferred thicker biofilms.  That was almost two years ago and I now have more data with which to test that hypothesis, and also to see if any other common taxa had an equally strong preference for particular states.


A cobble from the bed of Croasdale Beck in February 2019 showing a brown biofilm (approx. 1.7 micrograms per square centimetre) dominated by Gomphonema parvulumand Odontidium mesodon.   The photograph at the top of the post shows Ennerdale Water photographed on the same day.

I should also be clear that, in Croasdale Beck especially, diatoms are the main algal component of the biofilm, so they are not so much responding to a particular state of the biofilm as actively contributing biomass to create that state.  The other photosynthetic organism that is obvious to the naked eye in this part of Croasdale Beck is the cyanobacterium Chamaesiphon fuscus (see “A bigger splash …”) but this forms crusts on stone surfaces rather than contributing to the superstructure of the biofilm itself. We do find other filamentous algae, but intermittently and in smaller quantities.

We’ll look at Platessa oblongellafirst, bearing in mind that this was shown to be a mixture of two species about halfway through our study (see “Small details in the big picture …”).   The graph below, therefore, does not differentiate between these two species although, from my own observations, I have no reason to believe that they behave differently.   What I have done in these graphs is to divide the biomass measurements and the percent representation of these taxa in each sample into three categories: low, middle and high.   In each case, “low” represents the bottom 25 per cent of measurements, “high” represents the top 25 per cent of measurements and “middle” represents all the rest. The left-hand graph shows biomass (as chlorophyll a concentration) as a function of the relative abundance of the diatom whilst the right-hand graph shows the opposite: the relative abundance of the diatom as a function of the biomass.  These graphs bear out what I suggested in my earlier post: that Platessa oblongella(and P. saxonica) are species whose highest relative abundances occur when the biofilm is thin.  So far, so good.


Relationship between relative abundance of Platessa oblongella (including P. saxonica) and biomass in Croasdale Beck, Cumbria.  a. shows biomass (as chlorophyll a) as a function of the relative abundance of the two species (Kruskal-Wallis test, p = 0.047) whilst b. shows the relative abundance as a function of biomass (p = 0.057).

My second prediction in my earlier post was that Odontidium mesodonpreferred moderate or thick biofilms; however, whilst there is a clear trend in the data, differences between low, middle and high values of neither biomass nor relative abundance are significant.   The explanation may lay in the strong seasonality that O. mesodondisplays, thriving in spring but less common at other times of year (see “More about Platessa oblongella and Odontidium mesodon”).  However, there are no strong seasonal patterns in biomass in Croasdale Beck, and this disjunction introduces enough noise into the relationship to render it not significant.


Relationship between relative abundance of Odontidium mesodon and biomass in Croasdale Beck, Cumbria.  a. shows biomass (as chlorophyll a) as a function of the relative abundance of O. mesodon (Kruskal-Wallis test, p = 0.568) whilst b. shows the relative abundance as a function of biomass (p = 0.060).

I then tried looking at the relationship between relative abundance and biomass for a few other common taxa but with mixed results.   None of Achnanthidium minutissimum, Gomphonema parvulum complex or Fragilaria pectinalis showed any clear relationship; however, when I looked at Fragilaria gracilis, a different pattern emerged, with a significant relationship between the quantity of biomass and the proportion of this species in the sample.  That, too, is not a great surprise as I often see clusters of Fragilaria gracilis cells growing epiphytically on filamentous algae within the biofilm.  Whilst Platessa oblongella, which sits flat on the stone surface, seems to be a species that thrives when the biofilm is thin, so Fragilaira gracilisis favoured by a more complex three-dimensional structure, where it can piggy-back on other algae to exploit the light.   I suspect, however, that in a stream such as Croasdale Beck, where the substratum is very mobile, Fragilaira gracilis will also be one of the first casualties of a scouring spate which will, in turn, open up the canopy allowing Platessa oblongella back.   Even though my results for Odontidium mesodonare not significant, I still think it plays a part in this sequence, occupying the intermediate condition when some biomass has accumulated.  It looks to me as if it also likes cooler conditions which then complicates interpretation of my results.

Indeed, I am being rather selective in the results that I have included here.  Three of the six species I investigated showed no response and one of the three that I did include showed a trend rather than a statistically-convincing effect.  I suspect that the situation will rarely be as simple as I have shown for Platessa oblongella and Fragilaira gracilis.  Nonetheless, there is enough here to make me want to scratch a little more and try to understand this topic better.


Relationship between relative abundance of Fragilaria gracilis and biomass in Croasdale Beck, Cumbria.  a. shows biomass (as chlorophyll a) as a function of the relative abundance of F.gracilis (Kruskal-Wallis test, p = 0.010) whilst b. shows the relative abundance as a function of biomass (p = 0.036).


Croasdale Beck, photographed in February 2019. 

How Craticula got its name

Here is a puzzle for anyone who is learning to identify diatoms: how many species are shown in the plate below?   All share the same size and outline but they are very different in other respects, including several that we would normally regard as important for separating different species.   The left-hand image is an isolated girdle band, so let’s leave that to one side for the moment.  What about the two middle valves?   Both have a raphe in two parts, that runs along the midline, but the arrangement of their striae is very different.   And how do these relate to the pair on the right, which seem to have stout silica bars which traverse the cell?

The answer is that all belong to the same species: Craticula cuspidata.   Image b. is the way that it is most often seen (although it is not a particularly common species in the UK).   You should be able to see the raphe and fine striae which are more-or-less parallel to one another and perpendicular to the midline of the valve.   If you look with a scanning electron microscope, you’ll see that each of the striae is composed of a series of round or elliptical pores, equidistantly spaced so that the striae may appear to be running longitudinally as well as across the valve.


Craticula cuspidatafrom Pitsford Water, January 2019.   a. isolated girdle band; b.  “normal” valve; c. valve at “heribaudii stage”; d., e.: valves at “craticulae” stage. Scale bar: 10 micrometres (= 1/100thof a millimetre).  Photos: Chris Carter.

Although the genus Craticula was described in the 19thcentury by Grunow, it was considered to be part of the genus Naviculafor most of the 20thcentury.  We now regard the strictly parallel striae as one of the characteristics of Craticula but, if you think of it within in the broader realm of “Navicula” (basically, boat-shaped diatoms with a central raphe), many of which have radiate striae, then you might be happy to consider valve c. as being related to valve b.   In this case, it would have been called “Navicula cuspidata var. heribaudii”.   However, in 1979 Anne-Marie Schmid of the University of Salzburg, grew cultures of “normal” Craticula cuspidata in increasing salt concentrations and was able to show this (and the structures seen in images d. and e.) were responses to the stresses that this caused.

Under certain conditions, it seems, the normal process of cell division breaks down so that, rather than producing two daughter cells, each composed of two silica valves, just one “internal valve” is produced so that there are, in effect, three valves for two cells.  One of the cells then degenerates leaving a single functional cell albeit with one extra valve.   This phenomenon is not confined to Craticula but seems to be better understood for this genus than for others for reasons that I will come to shortly.   In this particular case, the internal valve has a similar outline to the parent, but a different arrangement of striae

Images d. and e. show another aspect of the same phenomenon: the formation of a “craticula” (from the Latin for “grid-iron”).  Schmid showed that this stage actually happens at lower salt concentrations than the “heribaudii” stage but that it, too, is related to the formation of these “internal valves”.   There is a thickening of silica along the central rib, after which transverse “buttresses” grow out and, finally, a silica band is laid down around the edges of the valve.  Schmid suggested that the resulting structures were resting stages, noting that she had found such structures in ponds in the Namib Desert that were only wetted for short periods every other year or so.  When they dried up, salinity increased very rapidly and these “resting spores” lay in the bottom muds protected by layers of “jelly” (i.e. extracellular polysaccharides).  About 11 days after she re-suspended them in distilled water, she observed viable cells gliding around again.

In the early 1990s, it became clear for other reasons that members of this genus were quite different from Naviculaso the original name was resurrected.  That leaves us with the unusual situation of a genus that is named after rarely-seen monstrosities.   It would be akin to naming Fragilaria “twisty diatoms” because, as we saw in “A twist in the tale …” a different form of stress causes a characteristic reaction in members of that genus.    Because Craticula is not a particularly common genus, and because “craticulae” valves are a relatively rare phenomenon within that genus, it is likely that most people have never seen the structure after which it was named.


Mann, D.G. & Stickle, A.J. (1991).  The genus Craticula. Diatom Research6: 79-107.

Schmid, A.-M. (1979).  Influence of environmental factors on the development of the valve in diatoms.  Protoplasma99: 99-115.

Life out of water …

Last time I wrote, I mentioned that those diatom genera that did not have to be permanently submerged in order to thrive (so-called “aerophilous diatoms”) often appeared together in samples.   Having seen some Luticola muticaearly in my analysis of the sample from Castle Eden Burn, it was no surprise to find Diadesmisand Simonsenialater in the same analysis.   If anything, the biggest surprise was that I did not also find Hantzschia amphioxys, another habitué of the damp fringes of diatom society.

A quick analysis of my database puts these thoughts into context.   There are 6500 samples in my database, so we can see, from the total number of records of each of the aerophilous genera that these are relatively scarce in the samples I encounter.  That is largely because my sampling approaches are biased against the habitats where these thrive (more about this below).   Aerophilous diatoms are more common than you might think; it is scientists with a yearning to learn more about them that is in short supply.

Hantzschiaand Simonseniaare both less frequent and less abundant than the other two genera, never occurring in numbers exceeding ten per cent of the total but, when they form more than one per cent of the total, there is a very high chance that you will also find other aerophilous taxa in the sample.   Humidophilaand Luticolaare sometimes found in higher numbers, and when this is the case, then the proportion of other aerophilous taxa is also often high: 75 per cent of samples where Humidophilais abundant, for example, have at least one other aerophilous taxon present at one per cent or more.

Frequency of other aerophilous genera in samples with Hantzschia, Humidophila, Luticolaand Simonsenia.    Each genus is represented by two rows: records where it formed 10 per cent or more of the total number of valves and records where it formed more than one per cent.   Similarly, records for other aerophilous genera are also stratified into those where they comprise more than 10 per cent of the total and those where they comprise more than one per cent.  

Genus number of records   other aerophilous genera
>10% >1%
Hantzschia 147 >10% n/a n/a
>1% 0.50 0.70
Humidophila 248 >10% 0.25 0.75
>1% 0.09 0.29
Luticola 630 >10% 0.09 0.35
>1% 0.05 0.16
Simonsenia 61 >10% n/a n/a
>1% 0.50 1.00

Over the years, I have come to use this information informally as a way of knowing whether the results of an analysis are likely to be giving me useful insights into ecological condition.   Many of the samples I analyse are collected by other people and sent to me.   These samplers should have been working to protocols that ensure that they check that the stones they choose were fully submerged for some time prior to their visit.  However, the person collecting the sample may have to make a judgement about river and lake level fluctuations in the period before their visit.  Finding lots of cells of aerophilous taxa in a sample is a good hint that something is awry.

The German method for ecological status assessment actually uses the proportion of aerophilous taxa as a check on the reliability of an assessment.    I suspect that they are not the only ones, but They have a list of 46 species that they regard as aerophilous taxa, and use a threshold of five per cent in a sample as a threshold.   The genera I’ve discussed all feature prominently, along with representatives of 19 other genera. Most of these are represented by only one or two species, although there are seven species of Nitzschia, five of Pinnulariaand six of Stauroneis.   I suspect that some species on this list are more tolerant of desiccation than others. We do not know enough of the physiological mechanisms behind this tolerance but it would seem that a few genera (Hantzschia, Humidophila, Luticiola) have definitely got this hard-wired into their genotypes, whilst other genera have members which are mostly aquatic in their habit but with a few exceptions able to survive out of water for some time.   I, personally, would trust the five per cent threshold if it was restricted to the hardcore aerophilous genera, with other taxa on the list providing supporting evidence. I would also add the proviso that there should be more than one aerophilous taxon contributing to that five per cent.  I would be happier, too, if there were a few experimental studies behind these lists and thresholds but, as ever with the world of diatoms, taxonomists are several steps ahead of the physiologists and so we are heavily dependent on anecdotal information when interpreting results.

List of taxa regarded as aerophilous in the German system for assessing ecological status in rivers. 

Name Authority
Achnanthes coarctata (Brébisson) Grunow in Cleve & Grunow 1880
Chamaepinnularia parsura (Hustedt) C.E.Wetzel & Ector in Wetzel et al. 2013
Cosmioneis incognita (Krasske) Lange-Bertalot in Werum & Lange-Bertalot 2004
Denticula creticola (Østrup) Lange-Bertalot & Krammer 1993
Diploneis minuta Petersen 1928
Eolimna subadnata  (Hustedt) G. Moser, Lange-Bertalot & Metzeltin 1998
Fallacia egregia (Hustedt) D.G. Mann 1990
Fallacia insociabilis (Krasske) D.G. Mann 1990
Fistulifera pelliculosa (Brébisson ex Kützing) Lange-Bertalot 1997
Halamphora montana (Krasske) Levkov 2009
Halamphora normanii (Rabenhorst) Levkov 2009
Hantzschia abundans Lange-Bertalot 1993
Hantzschia amphioxys (Ehrenberg) Grunow 1880
Hantzschia elongata (Hantzsch) Grunow 1877
Hantzschia graciosa Lange-Bertalot 1993
Hantzschia subrupestris Lange-Bertalot 1993
Hantzschia vivacior Lange-Bertalot 1993
Humidophila aerophila (Krasske) Lowe, Kociolek, Johansen, Van de Vijver, Lange-Bertalot & Kopalová, 2014
Humidophila brekkaensis (J.B.Petersen) D. Lowe, Kociolek, Johansen, Van de Vijver, Lange-Bertalot & Kopalová, 2014
Humidophila contenta (Grunow) Lowe, Kociolek, Johansen, Van de Vijver, Lange-Bertalot & Kopalová, 2014
Humidophila perpusilla (Grunow) Lowe, Kociolek, Johansen, Van de Vijver, Lange-Bertalot & Kopalová, 2014
Luticola cohnii (Hilse) D.G. Mann 1990
Luticola dismutica (Hustedt) D.G.Mann1990
Luticola mutica (Kützing) D.G. Mann 1990
Luticola nivalis (Ehrenberg) D.G. Mann 1990
Luticola nivaloides (W.Bock) J.Y.Li & Y.Z.Qi 2018
Luticola paramutica (W. Bock) D.G. Mann 1990
Luticola pseudonivalis (W.Bock) Levkov, Metzeltin & A.Pavlov 2013
Luticola saxophila (W.Bock ex Hustedt) D.G.Mann 1990
Mayamaea nolensoides (W. Bock) Lange-Bertalot 2001
Melosira dickiei (Thwaites) Kützing 1849
Muelleria gibbula (Cleve) Spaulding & Stoermer 1997
Neidium minutissimum Krasske 1932
Nitzschia aerophila Hustedt 1942
Nitzschia bacillarieformis Hustedt 1922
Nitzschia disputata J.R. Carater 1971
Nitzschia harderi Husedt 1949
Nitzschia modesta Hustedt 1950
Nitzschia terrestris (J.B. Petersen) Hustedt 1934
Nitzschia valdestriata Aleem & Hustedt 1951
Orthoseira dendroteres (Ehrenberg) Genkal & Kulikovskiy in Kulikovskiy et al. 2010
Orthoseira roseana (Rabenhorst) Pfitzer 1871
Pinnularia borealis Ehrenberg 1843
Pinnularia frauenbergiana E. Reichardt 1985
Pinnularia krookii (Grunow) Hustedt 1942
Pinnularia largerstedtii (Cleve) Cleve-Euler 1934
Pinnularia obscura Krasske 1932
Simonsenia delognei (Grunow) Lange-Bertalot 1979
Stauroneis agrestis J.B. Petersen 1915
Stauroneis borrichii (J.B.Petersen) J.W.G.Lund 1946
Stauroneis gracillima Hustedt 1943
Stauroneis lundii Hustedt 1959
Stauroneis muriella J.W.G. Lund 1946
Stauroneis obtusa Lagerstedt 1873
Surrirella terricola Lange-Bertalot & Alles 1996
Tryblionella debilis Arnott ex O’Meara 1873


Schaumburg, J., Schranz, C., Steizer, D., Hofmann, G., Gutowski, A. & Forester, J. (2006).  Instruction protocol for the ecological assessment of running waters for implementation of the EC Water Framework Directive: macrophytes and phytobenthos.  Bavarian Environment Agency

Return to the Serra da Estrela


Back in October I wrote about the algae and other plants that I had found in a small stream draining the Serra da Estrela mountains in Portugal (see “Notes from the Serra da Estrela”).  I’ve now had a chance to look more closely at the diatoms that I found there, and can offer a few thoughts on the ecology of the stream.

I collected two samples from the stream: one by brushing the top surface of the granite stones with a toothbrush and the other from the darker patches that I described in the earlier post.   These were a mix of algae and mosses, with the former dominated by cyanobacterial filaments and diatoms.   I merged the two samples prior to digesting them, but the biofilm on the submerged rocks was very thin so it is the diatoms from the dark patches that dominate the slide that I prepared from this stream.   As my preliminary observations suggested, motile diatoms were very abundant in this sample, with Surirella roba, Navicula angustaand N. exilis all common, along with some Pinnularia and Nitzschia.   I do not often find motile diatoms to be quite so abundant in fast-flowing upland streams, but I suspect that this is because I look in the wrong places.   Our standard sampling method involves scrubbing the tops of submerged stones which, in this type of stream at least, are not situations where motile diatoms thrive.  By contrast, the tangle of cyanobacterial filaments and dead organic matter creates a very different environment, where an ability to adjust position in order to move away from densely-shaded areas and, perhaps, from situations where bacteria and fungi had used up all the available oxygen, was an advantage.


Surirella robafrom the stream at Unhais de Serra, September 2018; a. – f.: valve views; g. – i.: girdle views. Scale bar: 10 micrometres (= 1/100thof a millimetre). The photo at the top of the post shows the view along the valley of the Rio Zêzere towards Mantiegas in the Serra da Estrela.


Miscellaneous diatoms from the stream at Unhais de Serra, September 2018: a. – d.: Cocconeis placentula, complete frustule, rapheless valve and two raphe valves; e. – g.: Navicula exilis; h. N. angusta; i. – k.: Pinnularia subcapitata, two valve views and a girdle view.  Scale bar: 10 micrometres (= 1/100thof a millimetre). 

A chain-forming species of Fragilariawas abundant in the original sample although, by the time I had prepared a slide, the chain had disintegrated into individuals or pairs of cells.  These all belonged to a member of the Fragilaria capucinacomplex, though I am not sure which one. There were also a few cells of the free-living (i.e. non-chain-forming) Fragilaria gracilis.    Eunotia minoror a close relative was also present, sometimes also forming short chains and, finally, I found a number of cells of Cocconeis placentula(possibly var. klinoraphis).

These are all diatoms that I would expect to find in a stream draining a hard rock such as granite in an area that is remote from any industrial or mining influences that might lead to artificial acidification.   There are mines in the area, but these are further south.  These do have a measurable effect on the biology of local streams, as the references at the end of this post attest.   However, this particular stream appears to be in rude health.

A curious side-effect of the years that I have spent looking at diatoms is that a sample such as this can evoke the environments from which it came: an assemblage of soft-water circumneutral diatoms conjures, in my mind, a particular landscape.   The label on the slide, of course, takes me straight back to our time in the Serra da Estrela but, in a more general sense, the diatoms capture an essence that transcends any one particular time or place.   Analysing diatom slides can become an escape from the humdrum and a chance to remember warmer days …


Fragilaria species from the stream at Unhais de Serra, September 2018: a. – g.: chain-forming member of Fragilaria capucina complex (a.-c.: valve views; d.-g.: girdle views); h.-j.Fragilaria gracilis.  Scale bar: 10 micrometres (= 1/100th of a millimetre).


Eunotiacf. minorfrom the stream at Unhais de Serra, September 2018: j. – n.: valve views; o. valve view of a related species; p. girdle views. Scale bar: 10 micrometres (= 1/100thof a millimetre). 


Luis, A.T., Teixeira, P., Almeida, S.F.P., Matos, J.X. & Silva, E.F. (2004).  Environmental impact of mining activities in the Lousal area (Portugal): Chemical and diatom characterization of metal-contaminated stream sediments and surface water of Corona stream.  Science of the Total Environment409: 4312-4325.

Silva E.F., Almeida, S.F.P., Nunes, M.L. & Fredrik, A.T.L. (2009). Heavy metal pollution downstream the abandoned Coval da Mó mine (Portugal) and associated effects on epilithic diatom communities.  Science of the Total Environment407: 5620-5636.

A year in the life of the River Wear …

After six bimonthly visits to the River Wear at Wolsingham during 2018, I can now step back and have a look at the complete dataset to see what patterns emerge.   Over the course of the year, I have visited the site six times and recorded a total of 107 species: 5 Cyanobacteria, 32 green algae, 69 diatoms and one red alga.  The true figure is probably higher than this, as the green algae include a number of “LRGT” (see “Little round green things …”) and certainly did not receive the same level of attention as the diatoms.

This crude enumeration of species, however, disguises some interesting seasonal patterns with, as I described in “Summertime Blues” and “Talking about the weather …”, abundant growths of green algae during the heatwave and associated low flow periods.  This can be seen clearly in the bar chart showing the seasonal changes in the river: diatoms predominate in the early part of the year whilst green algae are very scarce.  The bloom of the green filamentous alga Ulothrix zonata that I expected to see in March was missing due, I suspected, to the hard weather we experienced in late Feburary (see “The mystery of the alga that wasn’t there …”) but, by the summer, the river had taken on a very different complexion and was dominated by small green algae.   The last sample of the year, collected in November, showed a return to diatom dominance with a late autumn showing of Ulothrix zonata(see “The River Wear in November …”).


Relative proportions (by approximate biovolume) of the main groups of algae found in the River Wear at Wolsingham during 2018.  

Looking back at records of a similar exercise in 2009, I see that the beginning and end of the year were quite similar, with thick biofilms dominated by diatoms; however, the algae in the summer of 2009 were very different to those I found in 2018.  My 2009 exercise involved visits every month rather than every other month and I see that I recorded more Cyanobacteria in June and July 2009 than I found in Summer 2018.  These were mostly filaments of Phormidium retziiand tufts of Homoeothrix varians, which I assumed to be a consequence of intense grazing (there is evidence that invertebrates find Cyanobacteria to be less palatable than other algae).  By July, Cyanobacteria comprised over half the total biovolume of algae; however, there was a major spate soon after my visit.  I was surprised to find, when I visited in August, a noticeably thicker biofilm smothering the rocks and, when I looked closely, this was dominated by the small motile diatom Nitzschia archibaldii.   The Cyanobacteria had disappeared almost completely.   I attributed this change to the invertebrate grazers being washed away by the spate, allowing the algae to grow unhindered.  As the biofilm grew in thickness, so the algal cells start to shade each other, and a diatom that can glide through the biofilm has an advantage over any that are stuck to one place.  Diatoms remained dominant for the remainder of the year, although my November sample came just after another storm and the stones I sampled were completely bare.


Relative proportions (by approximate biovolume) of the main groups of algae found in the River Wear at Wolsingham during 2009.   A sample was collected in November but no living algae were recorded from it.

Overall, however, the similarities between the years outweighed the differences in the summer assemblages, whilst the composition of communities between late autumn and late spring was remarkably similar across the two years.   The changes in summer 2018 extended beyond just a shift in the balance of algae in favour of greens: there were also changes in the composition of diatoms too.  In fact, the changes in diatoms proved to be quite powerful mirrors of the changes in the community as a whole.  I have demonstrated this in datasets spanning a number of sites in the past but it is reassuring to see that they are also reflecting patterns within one site.   On the other hand, if I only had examined the diatoms, I would have missed some of the most interesting changes in the river over the course of the year.

Another observation is that no single sample from 2018 contained more than a quarter of the total algal diversity that I recorded over the course of the year.  Every month saw some new arrivals and some departures (or, more likely in some cases, a few taxa that were present had dropped below my analytical detection limit).  Some of these were expected (the seasonal dynamics of Ulothirx zonata, for example); others not (e.g. dominance by Keratococcus bicaudatusin the summer).  I discussed this in “A brief history of time-wasting …” and, in honour of that post, am not going to repeat myself here. In an age when our environmental regulators are cutting back on the amount of data that they gather, I shall go into 2019 reflecting on Yuval Noah Harari’s comment that “the greatest scientific discovery was the discovery of ignorance”.

A day out in Wasdale


A few days after my trip to Weardale I found myself beside the River Irt, a few hundred metres below the point where it flows out of Wastwater, in the western part of the Lake District.   Whereas the River Wear drains a catchment underlain by Carboniferous rocks, including a high proportion of limestone (see “Co. Durham’s secret Karst landscape”), the Irt’s catchment is largely underlain by ancient volcanic rocks, resulting in much softer water.   I was curious to see how different the algae were here compared to those in the Wear.

The river bed at this point is dominated by boulders of granite, which host a patchwork of mosses, filamentous algae and discrete growths of diatoms (visible on the right-hand side of the figure below).  Between these there were areas of pebbles and gravels, suggesting good habitat for freshwater mussels.   The patches of filamentous algae (mostly no more than a couple of centimetres in length) were a mixture of Mougeotiaand Zygnema, similar to the forms that I find in the River Ehen, a 30 minute drive to the north.   These two species differ in the form of their chloroplasts (Mougeotiahas a flat plate whilst Zygnemahas two star-shaped chloroplasts, attached by thin cytoplasmic strands to resemble an animal skin stretched on a frame) but are closely-related, both belonging to the family Zygnemtaceae.


An underwater photograph of the substratum of the River Irt in November 2018 showing patches of filamentous green algae, mosses and (on the right-hand side) diatoms growing on granite boulders.


Filamentous green algae from the River Irt, November 2018.   The upper photograph shows cells from a filament of Mougeotiawhilst the lower image shows two filaments of Zygnema. Scale bar: 20 micrometres (= 1/50thof a millimetre).

In between the tufts of filamentous algae were apparently bare patches of rock (they almost certainly had a very thin biofilm that would be hard to sample in isolation from the lusher algal growths that shared their habitat) and some conspicuous orange-brown growths of colonial diatoms.  These turned out to be almost pure growths ofGomphonema hebridense, or a close relative (I can’t give a definitive answer until I have examined cleaned material), growing on long mucilaginous, sometimes branched, stalks to create a veritable “bush” of diatoms.  There were a few other species of diatom growing within this bush, most notably some cells of Achnanthidium (cf.) caledonicumthat seemed to be growing on short stalks attached to the Gomphonemastalks, but also a few cells of Gomphonema capitatum(which also grows on long stalks) and some chains of Tabellaria flocculosa.

Gomphonema hebridenseis a diatom that I have written about several times before, as it is also common in the River Ehen, and also presents a number of interesting challenges to taxonomists (see “Diatoms and dinosaurs”). Whatever future studies reveal, however, the presence of colonies of this (or these) species that are visible with the naked eye is something I associate with only the cleanest rivers in the country during the cooler times of year.  It should not have been a great surprise to me to find it flowing out of one of the most pristine lakes in England (see “The Power of Rock …”).


A close up of cells within a colony of Gomphonemacf hebridense.  Several mucilaginous stalks are also visible as well as (top left) a cell of Achnanthidiumcf caledonicum.   Scale bar: 10 micrometres (= 100th of a millimetre).

The predominance of boulders over smaller, more easily moved stones, suggests a river that has more energy than the River Ehen, one of my regular Lake District haunts.   Both flow out of lakes whose catchments include some of the wildest and most mountainous terrain in the country.   Lakes tend to act as shock absorbers in catchments, slowing down the water that pours off the fells after heavy rain.   Streams in this part of the world that have no such impediments to flow tend to have rocky, mobile beds and relatively sparse algal communities.   By contrast, the Irt and Ehen just below their respective lakes have relatively lush growths of algae.   The substrates of the two rivers, however, are very different: the Ehen having very few boulders in comparison to the Irt, due to the presence of a weir at the outfall. This allows Ennerdale Water to be used as a water supply for the towns of north west Cumbria but, at the same time, turns the lake into an even more effective hydrological shock absorber.  Yet more of the energy that should be washing smaller stones down the river is no longer available except after the most exceptional storms.

That’s my working hypothesis, then: the Irt is a river that is subject to just enough high energy events to move the rocky substrates around yet no so many that rich algal communities cannot develop between these.  The Ehen, by contrast, has fewer events, leading to fewer opportunities for the algae to be scoured away, whilst unregulated streams such as Croasdale Beck (see “What a difference a storm makes …”) have such regular scouring spates that the algal communities are usually sparse.   I might be wrong, of course and I might be back in a years time with a better hypothesis.  Until then …