Diatom ID Please

Have problems identifying an organism? Ask for help here.
Post Reply
Message
Author
User avatar
mrsonchus
Posts: 4175
Joined: Tue Feb 03, 2015 9:42 pm
Location: Cumbria, UK

Diatom ID Please

#1 Post by mrsonchus » Tue Nov 24, 2020 4:12 pm

Hi, I was rummaging through some old slides and took this diatom image. I'd like to know exactly which species it is if possible. This is in no-way my area but I'd like to find the species and an SEM image to let me see just how the BF image has represented it....
measured punctae.jpeg
measured punctae.jpeg (66.41 KiB) Viewed 5602 times

I tentatively suggest that it's a type of pleurosigma, but species? This ID is beyond me I'm afraid, any help appreciated.
John B

User avatar
75RR
Posts: 8207
Joined: Sun Oct 12, 2014 2:34 am
Location: Estepona, Spain

Re: Diatom ID Please

#2 Post by 75RR » Tue Nov 24, 2020 5:42 pm

It is a Gyrosigma. One can distinguish it from pleurosigma because the stria are in a cross pattern, i.e. at 90 degrees

The Pleurosigma has stria that are diagonal to the transapical rows. See links below

https://diatoms.org/genera/pleurosigma/guide

+ possible candidate: https://diatoms.org/species/gyrosigma_acuminatum

Glossary: https://diatoms.org/glossary/transapical_axis


Stria are usually measured in 10µm
Zeiss Standard WL (somewhat fashion challenged) & Wild M8
Olympus E-P2 (Micro Four Thirds Camera)

MichaelG.
Posts: 3976
Joined: Mon Apr 10, 2017 8:24 am
Location: North Wales

Re: Diatom ID Please

#3 Post by MichaelG. » Tue Nov 24, 2020 6:41 pm

75RR wrote:
Tue Nov 24, 2020 5:42 pm
It is a Gyrosigma. […]


Stria are usually measured in 10µm
.

Making John’s approximately 14 per 10µm

... is that, in itself, sufficient for species identification ?
... I have no idea.

MichaelG.
Too many 'projects'

User avatar
75RR
Posts: 8207
Joined: Sun Oct 12, 2014 2:34 am
Location: Estepona, Spain

Re: Diatom ID Please

#4 Post by 75RR » Tue Nov 24, 2020 6:58 pm

.
MichaelG. wrote:
Tue Nov 24, 2020 6:41 pm
75RR wrote:
Tue Nov 24, 2020 5:42 pm
It is a Gyrosigma. […]


Stria are usually measured in 10µm
.

Making John’s approximately 14 per 10µm

... is that, in itself, sufficient for species identification ?
... I have no idea.

MichaelG.
On my screen the horizontal bar is 17mm, so if 17 = 70% then 100% = 24mm which gives me 18/19 stria in 10µm
Zeiss Standard WL (somewhat fashion challenged) & Wild M8
Olympus E-P2 (Micro Four Thirds Camera)

User avatar
mrsonchus
Posts: 4175
Joined: Tue Feb 03, 2015 9:42 pm
Location: Cumbria, UK

Re: Diatom ID Please

#5 Post by mrsonchus » Tue Nov 24, 2020 7:53 pm

I'll just re-measure the 10µ puncta count...

Looks like 14-15 puncta per 10µ measured along axis.

Image
John B

MichaelG.
Posts: 3976
Joined: Mon Apr 10, 2017 8:24 am
Location: North Wales

Re: Diatom ID Please

#6 Post by MichaelG. » Tue Nov 24, 2020 9:22 pm

75RR wrote:
Tue Nov 24, 2020 6:58 pm
.
MichaelG. wrote:
Tue Nov 24, 2020 6:41 pm
75RR wrote:
Tue Nov 24, 2020 5:42 pm
It is a Gyrosigma. […]


Stria are usually measured in 10µm
.

Making John’s approximately 14 per 10µm

... is that, in itself, sufficient for species identification ?
... I have no idea.

MichaelG.
On my screen the horizontal bar is 17mm, so if 17 = 70% then 100% = 24mm which gives me 18/19 stria in 10µm
.

Sorry, I was going by John’s numbers
10 divided by 0.71 =

MichaelG.
Too many 'projects'

User avatar
75RR
Posts: 8207
Joined: Sun Oct 12, 2014 2:34 am
Location: Estepona, Spain

Re: Diatom ID Please

#7 Post by 75RR » Tue Nov 24, 2020 9:31 pm

.
Here is a enlargement of the first measurement which I read as 7.1µm = 14 stria

if that should read 10µm then it is not Gyrosigma acuminatum.
.
Attachments
7.1µm.png
7.1µm.png (20.79 KiB) Viewed 5525 times
Zeiss Standard WL (somewhat fashion challenged) & Wild M8
Olympus E-P2 (Micro Four Thirds Camera)

User avatar
mrsonchus
Posts: 4175
Joined: Tue Feb 03, 2015 9:42 pm
Location: Cumbria, UK

Re: Diatom ID Please

#8 Post by mrsonchus » Tue Nov 24, 2020 9:48 pm

Hmm, according to 75's link to G.acuminatum seems to have too many puncta at 18-22/10µ....

My first image with 2 measurements makes the puncta about 0.71µ apart using the parallel-line measurement tool giving of course 10/0.71=14 or 15 per 10µ depending upon just how the puncta are counted and the line is drawn.

My second image with the 10µ line seems to agree with this. Perhaps then not enough puncta for G.acuminatum....

What is the 'std method' - are the ends of the line placed upon a punctum's central-axis for example - is the line drawn to ensure no pinta are touched by either line-end? Perhaps the 1 per 10µ difference possible is not significant anyway at the LM level?
John B

MichaelG.
Posts: 3976
Joined: Mon Apr 10, 2017 8:24 am
Location: North Wales

Re: Diatom ID Please

#9 Post by MichaelG. » Tue Nov 24, 2020 9:56 pm

75RR wrote:
Tue Nov 24, 2020 9:31 pm
.
Here is a enlargement of the first measurement which I read as 7.1µm = 14 stria
.
.
Strange ... I read it as the distance between the two parallel lines being 0.71µm

MichaelG.
Too many 'projects'

MichaelG.
Posts: 3976
Joined: Mon Apr 10, 2017 8:24 am
Location: North Wales

Re: Diatom ID Please

#10 Post by MichaelG. » Tue Nov 24, 2020 10:04 pm

mrsonchus wrote:
Tue Nov 24, 2020 9:48 pm

What is the 'std method' - are the ends of the line placed upon a punctum's central-axis for example -
.

It shouldn’t matter where you count from ... You are simply counting ‘cycles’
... Just like measuring the pitch of a screw thread
... Always remember to count from Zero
[you need to count ‘fence panels’ not ‘fence posts’ ... if you see what I mean]

MichaelG.
Too many 'projects'

User avatar
75RR
Posts: 8207
Joined: Sun Oct 12, 2014 2:34 am
Location: Estepona, Spain

Re: Diatom ID Please

#11 Post by 75RR » Tue Nov 24, 2020 10:31 pm

MichaelG. wrote:
Tue Nov 24, 2020 9:56 pm
75RR wrote:
Tue Nov 24, 2020 9:31 pm
.
Here is a enlargement of the first measurement which I read as 7.1µm = 14 stria
.
.
Strange ... I read it as the distance between the two parallel lines being 0.71µm

MichaelG.
I read lines as length of 7.1µm :) Did not occur to me that it might be period µm stria

Given mrsonchus second image then it would seem that length was 10µm after all

So Gyrosigma sp.
Zeiss Standard WL (somewhat fashion challenged) & Wild M8
Olympus E-P2 (Micro Four Thirds Camera)

User avatar
mrsonchus
Posts: 4175
Joined: Tue Feb 03, 2015 9:42 pm
Location: Cumbria, UK

Re: Diatom ID Please

#12 Post by mrsonchus » Tue Nov 24, 2020 11:34 pm

Hi folks - you won't believe this - as I was putting the slide away I dropped it then stood on it! I lost the slide - which is now in a million pieces in the bin... Sometimes these things happen I know - but I still haven't stopped muttering about it... :(

It's a shame because I really quite enjoyed exploring it. :cry:

I might even buy a few online - goodness it's been a while since I bought a slide!
John B

User avatar
75RR
Posts: 8207
Joined: Sun Oct 12, 2014 2:34 am
Location: Estepona, Spain

Re: Diatom ID Please

#13 Post by 75RR » Wed Nov 25, 2020 8:15 am

mrsonchus wrote:
Tue Nov 24, 2020 11:34 pm
Hi folks - you won't believe this - as I was putting the slide away I dropped it then stood on it! I lost the slide - which is now in a million pieces in the bin... Sometimes these things happen I know - but I still haven't stopped muttering about it... :(
That is a pity!

Mrsonchus did not mention provenance, but I am thinking that I should have started searching nearer to home, rather than go to Diatoms of North America. https://diatoms.org/about

I did so because they have a nice explanation vis-à-vis Plurosigma/Gyrosigma.

Then there was the stria miscount ...


K.D. Kemp uses Gyrosigma balticum in his 8 Form Test Slides. These are some of the stats:

"Gyrosigma balticum (Ehrenberg) Rabenhorst (1853), p. 47, pl. 5, fig. 6
BASIONYM: Navicula baltica Ehrenberg (1830); p. 114
SYNONYM: Pleurosigma balticum (Ehrenberg) Wm. Smith (1852), p. 8 pL. 2, fig. 1.
TYPE LOCALITY: Baltic Sea. Marine
NEOTYPE: BM 81615 designated by Sterrenburg (1995) Valves vaulted, sigmoid,
with parallel margins in the central half of the valve and tapering to obtuse apices (Fig.45).
Length 210–430μm, width 25–35μm. Longitudinal and transverse striae 10–15 in 10 μm."
...

Plus link: https://www.researchgate.net/publicatio ... ew_species
Zeiss Standard WL (somewhat fashion challenged) & Wild M8
Olympus E-P2 (Micro Four Thirds Camera)

MichaelG.
Posts: 3976
Joined: Mon Apr 10, 2017 8:24 am
Location: North Wales

Re: Diatom ID Please

#14 Post by MichaelG. » Wed Nov 25, 2020 8:30 am

mrsonchus wrote:
Tue Nov 24, 2020 11:34 pm
Hi folks - you won't believe this - as I was putting the slide away I dropped it then stood on it! I lost the slide - which is now in a million pieces in the bin... Sometimes these things happen I know - but I still haven't stopped muttering about it... :(
You could have ‘endless hours of fun’ searching for a definitive small shard :shock:
75RR wrote:
Wed Nov 25, 2020 8:15 am

Plus link: https://www.researchgate.net/publicatio ... ew_species
That’s a great link, thanks !
... Serves nicely to demonstrate how much there is to learn.

MichaelG.
Too many 'projects'

User avatar
mrsonchus
Posts: 4175
Joined: Tue Feb 03, 2015 9:42 pm
Location: Cumbria, UK

Diatoms Reborn!

#15 Post by mrsonchus » Wed Nov 25, 2020 5:36 pm

Update!
Managed to remove pieces of coverslip from shards of broken original slide!
A good number of diatoms and pieces were salvageable after a short application of 'Histoclear II'....

I re-mounted them in 'Histomount' with coverslip of course.
The originals were mounted I think in a higher RI mountant which may be why they were visible with BF.
The Histomount re-mounted were invisible in BF so I switched to phase, but only at 40x and with fully-open
aperture diaphragm which presumably lowered the n.a. somewhat...

The puncta frequency did however measure again at 14 per 10µ so I may presume the shard measured is from the same Genus of diatom?

An interesting exercise came from the breakage.
I may well buy some old (cheap...) diatom slides broken or in poor condition and re-mount (perhaps even arrange or sort them?)
them - in a high RI mountant as practiced with diatoms - should be a great way of acquiring different species and slide-selections - recycling!

Here are a couple of images from the re-mount - mountant still liquid I'm afraid - images may well improve significantly as the mountant firms-up a little....

This is the 14 puncta per 10µ piece of (Gyrosigma.sp) diatom,
Image

Another diatom that was in the original now annihilated slide....
Image
Who'd have thought - from a disaster into perhaps a way for me to make a few slides without any processing/cleaning of diatoms! Worth a try for sure....
Last edited by mrsonchus on Wed Nov 25, 2020 8:31 pm, edited 4 times in total.
John B

MichaelG.
Posts: 3976
Joined: Mon Apr 10, 2017 8:24 am
Location: North Wales

Re: Diatom ID Please

#16 Post by MichaelG. » Wed Nov 25, 2020 6:21 pm

Splendid stuff, John
... Well done, Sir

‘though I can’t currently see the images

MichaelG.
Too many 'projects'

User avatar
75RR
Posts: 8207
Joined: Sun Oct 12, 2014 2:34 am
Location: Estepona, Spain

Re: Diatom ID Please

#17 Post by 75RR » Wed Nov 25, 2020 6:29 pm

.
I can't either at the moment but I could before.

Wanted to ask what you used to manipulate them?
Zeiss Standard WL (somewhat fashion challenged) & Wild M8
Olympus E-P2 (Micro Four Thirds Camera)

User avatar
mrsonchus
Posts: 4175
Joined: Tue Feb 03, 2015 9:42 pm
Location: Cumbria, UK

Re: Diatom ID Please

#18 Post by mrsonchus » Wed Nov 25, 2020 6:41 pm

Fixing-it now chaps!

How's that now?
John B

Hobbyst46
Posts: 4277
Joined: Mon Aug 21, 2017 9:02 pm

Re: Diatom ID Please

#19 Post by Hobbyst46 » Wed Nov 25, 2020 7:32 pm

Great accomplishment John B.
Please give more details - HOW did you manage to salvage them from the (broken?) coverslip fragments ?

User avatar
mrsonchus
Posts: 4175
Joined: Tue Feb 03, 2015 9:42 pm
Location: Cumbria, UK

Re: Diatom ID Please

#20 Post by mrsonchus » Wed Nov 25, 2020 8:29 pm

75RR wrote:
Wed Nov 25, 2020 6:29 pm
.
I can't either at the moment but I could before.

Wanted to ask what you used to manipulate them?
Hi 75' - all I did was pick them up as it were with a very-fine paintbrush - which could of course easily be refined but was O.K. for this 'proof of concept' if you like. (something I habitually do before investing time, effort and maybe funds into a project or workflow).
The solvent used was Histoclear II - a limones-based replacement for xylene, although I use Histoclear I for my Botanical slides and had H2 to spare for this possibly futile effort.

The coverslip and slide pieces from the chaos (diatoms mounted between of course) I simply immersed for about an hour, which was enough for a microtome-blade to slip between the round coverslip+sealant and slide (the classic black-ringed diatom slide of old).
The diatoms, formerly visible as mounted, immediately became invisible with the influx of Histoclear II, as expected - but I had no trouble seeing them when I placed the pieces on a slide under my stereo 'scope with my Heath-Robinson black-card darkfield stop beneath.

Some had remained on the slide, more had remained on the underside of the coverslip. As the solvent completely immersed the diatoms they were easily retrieved and placed into a tiny drop of waiting Histomount on an 18mm square coverslip.
From there, with diatoms on coverslip, in mountant, and a clean slide previously dipped into solvent (H-clear II) I simply mounted the coverslip as I routinely would with a section mounted onto a slide - controlling any 'creep' away from starting position on one side by using a dissecting point to prevent slippage, whilst lowering the other end to engage mountant (with diatoms therein) with slide's surface. Lowering very gently indeed in a necessarily-controlled manner to complete the mount.

NOTE: The drop of mountant is allowed to become a little viscous before lowering the coverslip. If just right it will settle nicely, without air-bubbles etc, and only occupying about 25% (in terms of area) of the space under the coverslip - keeping the diatoms together. It's then a simple enough matter to add tiny drops of mountant at the edges of the coverslip to enable them to fill this space and make a completely mounted coverslip - any excess may be removed later, but I have a lot of experience mounting (and re-mounting/staining in fact) very thin botanical sections and was lucky enough to get this just right.

This was just a test to see if it was feasible or perhaps possible, which it has turned-out to be. A very crude method which has many obvious opportunities to both refine and modify/adapt for perhaps re-mounting broken or compromised diatom slides - or as I may prefer, the 'opening' of old slides to use the diatoms for my own selection and arrangement onto new slides - basically using old diatom slides for the raw-material - the diatoms they contain!

If you try it be aware that invisibility will be the first event as solvent (not mountant e.g. Naphrax, which wouldn't have this effect given a suitably high/different RI)
engulfs diatoms - have darkfield ready to hand on a stereo 'scope! If simply re-coverslipping then I'd suggest drawing around the 'main body' of diatoms on the underside of the slide with a permanent marker such as a sharpie, as I use in my teeny lab. This will help you to keep your bearings!

Far easier than it sounds - honestly, with a stereo 'scope and a steady hand it's entirely possible.
John B

Hobbyst46
Posts: 4277
Joined: Mon Aug 21, 2017 9:02 pm

Re: Diatom ID Please

#21 Post by Hobbyst46 » Wed Nov 25, 2020 8:41 pm

Thanks for the details John B. Impressive !
I am practicing diatom selection, and the only messy case that I dared to challenge so far was to finish the mounting of a diatoms on a coverslip, when the coverslip suddenly flipped and fell on a carpet and, according to the Buttered Toast Free Fall theorem, it was lying upside down...diatoms on the bottom...

MichaelG.
Posts: 3976
Joined: Mon Apr 10, 2017 8:24 am
Location: North Wales

Re: Diatom ID Please

#22 Post by MichaelG. » Wed Nov 25, 2020 9:53 pm

mrsonchus wrote:
Wed Nov 25, 2020 6:41 pm
Fixing-it now chaps!

How's that now?
Lovely ... thanks !

MichaelG.
Too many 'projects'

User avatar
mrsonchus
Posts: 4175
Joined: Tue Feb 03, 2015 9:42 pm
Location: Cumbria, UK

Re: Diatom ID Please

#23 Post by mrsonchus » Wed Nov 25, 2020 10:39 pm

Hi again.
The mount is definitely improving, the diatoms are now just visible with 'normal' BF!
Here are a few images just taken I used both an IF550 filter and a slight touch of oblique to give a little relief - which I think has added detail. Also I was able to use my 60x (which I only have in BF version - no phase yet) 0.90 n.a. planapochromat which may have helped.

A few new BF/DF + slight oblique images from the slightly firmer slide....
Image

Closer-in crop,
Image

Image

Again cropped - seem to be 'anchor-shaped' ends to the central 'lines' whatever they are....
Image

Image

Image

Here's a link to my shared G-Photo album with a few more to peruse if you like...
John B

User avatar
mrsonchus
Posts: 4175
Joined: Tue Feb 03, 2015 9:42 pm
Location: Cumbria, UK

Re: Diatom ID Please

#24 Post by mrsonchus » Wed Nov 25, 2020 10:42 pm

Hobbyst46 wrote:
Wed Nov 25, 2020 8:41 pm
Thanks for the details John B. Impressive !
I am practicing diatom selection, and the only messy case that I dared to challenge so far was to finish the mounting of a diatoms on a coverslip, when the coverslip suddenly flipped and fell on a carpet and, according to the Buttered Toast Free Fall theorem, it was lying upside down...diatoms on the bottom...
Arrrgghhh - we've all done it! One of my favourite tricks is to snap a slide in half while I'm cleaning the bottom of it and holding it by the label-end.... ;)
John B

User avatar
mrsonchus
Posts: 4175
Joined: Tue Feb 03, 2015 9:42 pm
Location: Cumbria, UK

Re: Diatom ID Please

#25 Post by mrsonchus » Thu Nov 26, 2020 12:06 am

Almost forgot, a stack and a crop of it,

Image

Cropped,
Image

I wonder if the even tinier 'struts' within the 'holes' are real or an artifact?
John B

Post Reply