Doing Diatoms

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rnabholz
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Re: Doing Diatoms

#361 Post by rnabholz » Sun Nov 27, 2016 1:11 am

Thanks zz.

I was surprised to find such a dense deposit of them on the dead leaves, especially as they likely had not been there all that long.

Made four slides this afternoon, inverted cure. Not a lot of different forms, but I have just done a cursory scan and a bit of shooting.

Thanks for the interest.

Rod

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Re: Doing Diatoms

#362 Post by rnabholz » Mon Nov 28, 2016 3:48 am

Images from Dutch Creek can be seen here:

viewtopic.php?f=6&t=4204

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Re: Doing Diatoms

#363 Post by zzffnn » Mon Nov 28, 2016 6:25 pm

I checked some Galveston beach samples last weekend. A sea weed sample had many diatoms (with concentration similar to Armand Bayou vegetation), but those diatoms (likely Meridion circulare) were the fragile ones that wouldn't survive cleaning. Also found about 3 big Coscinodiscus diatoms there, which was present in a Galveston sample I took last spring.

The beach foamy sand sample did not have any diatom, though a few forams or micro shells were present.

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Re: Doing Diatoms

#364 Post by rnabholz » Mon Nov 28, 2016 10:42 pm

Good effort.

They are out there somewhere.

My experience this weekend with the relatively small creek has me looking differently at small bodies.

Creeks, business park and other decorative type ponds or lakes, retention ponds, anything has water in it for a period of time.

Last year, looking for Protists, I swept up the only astrionella that I have ever seen in a sample from a corporate pond.

Keep looking!

Rod

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Re: Doing Diatoms

#365 Post by zzffnn » Tue Nov 29, 2016 6:56 pm

Inspired by Rod's tips about looking into tiny ponds and vegetation, we did a 20-minute field collection at a nearby condo complex.

We found a pure culture of Rhopalodia, which looks like this:
https://westerndiatoms.colorado.edu/tax ... odia_gibba
viewtopic.php?f=6&t=3723&hilit=diatom

Amount is good enough for cleaning/mounting. But we did not collect it, since there is only one species present.

The pond is a tiny one. You can tell its size, by comparing it with my backpack located at 8 o'clock position of this photo:
pond.jpg
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The pond vegetation, from which we collected the Rhopalodia diatom, looked like this:
weed2.jpg
weed2.jpg (294.54 KiB) Viewed 6962 times
So diatoms can be there, in any pond. As long as there is sunshine and a little vegetation.

By the way, Rod. If you want to clean/mount that Rhopalodia diatom sample, I can go back and collect/process it for you.

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Re: Doing Diatoms

#366 Post by rnabholz » Tue Nov 29, 2016 8:47 pm

Great example of exactly what I was droning on about.

A very small pond, but still diatoms are found. Cool.

The Amateur Diatomists newsletters have a number of articles about gathering sample from mill ponds.

Rhopalodia is a very pretty form. Were they all the same size?

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Re: Doing Diatoms

#367 Post by zzffnn » Tue Nov 29, 2016 8:58 pm

The Rhopalodia diatoms I saw are of different sizes, some of which are not small.

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Re: Doing Diatoms

#368 Post by rnabholz » Tue Nov 29, 2016 9:17 pm

In that case, if you get a chance I would like to have a sample if you don't mind me sending you on the errand. No rush.

I find them really striking and a sample with multiple sizes would be great fun to explore.

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Re: Doing Diatoms

#369 Post by Dale » Tue Nov 29, 2016 10:00 pm

Is there a good way to extract the diatoms from the slimy strands?
Dale
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Re: Doing Diatoms

#370 Post by rnabholz » Tue Nov 29, 2016 11:52 pm

Dale wrote:Is there a good way to extract the diatoms from the slimy strands?
Dale
I just put them in a jar with some of the habitat's water, maybe a third to half full. Close the lid, and gently shake. Quit when the water gets "dirty".

Then just drain the water out and save it. You can repeat the same procedure as many times as you still see production.

Hope that helps.

Rod

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Re: Doing Diatoms

#371 Post by Dale » Wed Nov 30, 2016 1:46 am

Yes indeed, thank you sir.
Dale
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Re: Doing Diatoms

#372 Post by zzffnn » Wed Nov 30, 2016 2:47 am

Rod is a gentleman. I squeeze vegetation like mad, if I am in a rush :mrgreen:

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Re: Doing Diatoms

#373 Post by Dale » Fri Dec 02, 2016 10:48 pm

Two questions:
1. I have 2 vcrs headed for the dump, but I could salvage the drums
for any slide ringer wannabe's.
2. Fan, how did you ship the ziplock to Rod? I'm still looking for the cheapest way to
ship sand.
2.1 For the first gross filtration I'm looking at putting a round mesh screen into
a Buchner funnel. I have not yet tried cutting the mesh cause I fear it may unravel.
Dale
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Re: Doing Diatoms

#374 Post by zzffnn » Sat Dec 03, 2016 12:06 am

Dale,

I will take one VCR drum, if it is still available. You can send it later on, together with other things or samples to Rod or to me, say next year. No rush at all. Thank you.

I usually mail sand or raw samples in $6.8 USPS Priority Small Flat Rate Box, only because it is convenient. Sending it in First Class box requires you to weight and size the box, but may be slightly cheaper. Or for small amount, sample can be sent in tape-enforced large envelope, which may be the cheapest way. But then, you want to make sure there is enough sand to make slides and it is not easy to tell - better send more than not sending enough?

I will cover shipping cost of your next Hawaii sand sample to Rod, so don't worry about it.

I don't cut the steel sieve - I simply lay it over a wide mouth container. Yes, it may it may unravel.

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Re: Doing Diatoms

#375 Post by rnabholz » Sat Dec 03, 2016 1:12 am

Organizing things a bit tonight.

Here is a season's efforts, samples I have gathered and others sent to me by friends here. 35 vials of samples and 2 more yet to be "bottled". Since each one of the vials would literally produce hundreds of slides there is a lot of potential here.

Thanks to all who have contributed to the effort!
Rack End.jpg
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Rack Side.jpg
Rack Side.jpg (137.04 KiB) Viewed 6904 times
Rack End Labels.jpg
Rack End Labels.jpg (122.9 KiB) Viewed 6904 times

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Re: Doing Diatoms

#376 Post by Dale » Sat Dec 03, 2016 2:01 am

ZZ, glad you are not in a hurry, as I have to pick one of 3 machines to transfer a ton
of vhs tapes. Not wanting to waste the Pensacola sand I have been trying to filter
other stuff, with messy results. Now I am at Ocean Shores, and will bring home
a bucket of real sand. With my lab packed I am quite limited in what I can do. I
have been busy writing down almost every word in this awesome thread.
Dale
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Re: Doing Diatoms

#377 Post by zzffnn » Sat Dec 03, 2016 2:38 pm

Dale wrote:ZZ, glad you are not in a hurry, as I have to pick one of 3 machines to transfer a ton
of vhs tapes. Not wanting to waste the Pensacola sand I have been trying to filter
other stuff, with messy results. Now I am at Ocean Shores, and will bring home
a bucket of real sand. With my lab packed I am quite limited in what I can do. I
have been busy writing down almost every word in this awesome thread.
Dale
Thank you Dale,

Ocean Shores sounds like a good place for diatom hunting. May I suggest taking sand samples from different beaches, say some 30 min driving away from each other?

That was how I found my one and only one diatom spot in Pensacola (I sampled 6 locations).

A 100x scope (10x objective + 10x eyepiece) is enough for scanning samples, in the field or at home. Condenser is not required at that magnification for that purpose, though it will help enhance contrast under oblique or DIY darkfield. A battery powered LED or mirror+LED flashlight/headlight will work as light source.

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Re: Doing Diatoms

#378 Post by zzffnn » Sat Dec 03, 2016 2:44 pm

Rod,

I like how organized you are! I cannot say I was as organized, when I was a scientist. If you want to be a perfectionist, I suggest a lab book registering all GPS coordinates of your collection sites :mrgreen:

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Re: Doing Diatoms

#379 Post by Dale » Sat Dec 03, 2016 10:47 pm

ZZ, my intention for the sand was only to have material to practise filtering methods, to evaluate
mesh and etc., learn some lab skills. I hope you did not think I took a scope or any lab equipment
to the ocean, almost everything I own has been packed in moving boxes for the big move.

Is there any reason I could not buy a cheap 10X obj and eyepiece, and fasten them into a
rigid tube? I don't have the knowledge to know what would or would not work. A short
barrel would be nice. What optical characteristic would be most tolerant to misalignment?

Do you want any of this Ocean Shore sand?, I could use it as packing for the vcr drums!
Dale
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Re: Doing Diatoms

#380 Post by zzffnn » Sun Dec 04, 2016 12:19 am

Dale,

I made a DIY portable scope like that before (and it works), but did not like it as ergonomics is not great. For diatoms, you would appreciate an integrated transmitted light and good focus adjustment at 100x total magnification. That makes DIY not convenient to make or use.

I have the following two portable scopes and they are both cheap and cheerful:

http://www.ebay.com/itm/332047365464
Rod bought and uses this one in the field.

I prefer the ergonomics and magnification of this one over the Meade:

http://www.ebay.com/itm/micro-microscop ... 1830741617

viewtopic.php?f=16&t=2246

But it may not be as durable - I have broken mine once and repaired it myself.

I only want the Ocean Shores sand (and will cover shipping), if it has good amounts of diatoms. If you are not sure, then don't ship it alone (please ship it together with your next Hawaii sand and the VCR drum). Thank you.

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Re: Doing Diatoms

#381 Post by rnabholz » Sun Dec 04, 2016 12:26 am

zzffnn wrote:Rod,

I like how organized you are! I cannot say I was as organized, when I was a scientist. If you want to be a perfectionist, I suggest a lab book registering all GPS coordinates of your collection sites :mrgreen:
Well, I had a bunch of these vials laying around so I had to do something. The next step is to find an appropriate storage box for the rack, add numbers to the top of the vials, and a reference card to the box lid cross referencing the numbers to the location.

You idea for GPS coordinates is a good one. I will work on it.

Thanks

Rod

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Re: Doing Diatoms

#382 Post by exmarine » Sun Dec 04, 2016 7:33 am

Hi Guys,
I am sorry to see you are in a bit of a pickle when it comes to sending stuff to each other, (lucky people) I mean if you each send a sample to different members then what a brilliant collection you would all have ,
and please give a thought for your buddies across the pond, who as yet are lagging way behind on this score. Its too far and probably too expensive to send samples to the UK.
Keep sending each other the samples as its a way of members seeing the same diatoms and getting a different reaction to them, brilliant way to open a field of what each of you see and decide what species it might be.
From a little old diatom collector in the UK. :mrgreen: :mrgreen:

All the best members keep on sending the samples. Sounds positively rude.

Mo The exmarine
Thank you :shock:
Best regards
exmarine :x

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uses Watson Stereo 1960 ish.

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Re: Doing Diatoms

#383 Post by rnabholz » Mon Dec 05, 2016 12:11 am

Didn't mean to leave anybody out!

I for one would be approachable on doing an exchange with European members. Perhaps it makes more sense to exchange either cleaned diatoms or slides rather than damp sand or wet samples from the standpoint of minimizing shipping costs.

To take it one more step, perhaps we can both gather materials from multiple members and share it among a similar group on the other side, mailing only one package each?

Thoughts everyone?

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Re: Doing Diatoms

#384 Post by zzffnn » Mon Dec 05, 2016 12:23 am

rnabholz wrote:Didn't mean to leave anybody out!

I for one would be approachable on doing an exchange with European members. Perhaps it makes more sense to exchange either cleaned diatoms or slides rather than damp sand or wet samples from the standpoint of minimizing shipping costs.

To take it one more step, perhaps we can both gather materials from multiple members and share it among a similar group on the other side, mailing only one package each?

Thoughts everyone?
Aye!

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Re: Doing Diatoms

#385 Post by rnabholz » Tue Dec 06, 2016 2:48 am

Today is a good day - Diatoms in the mail!

Thanks to our forum mate Lorez, who so kindly sent me a sample that he collected locally, I have a project tonight.

In an envelope ingeniously made from what appears to be a manila folder and packing tape, I found a sand sample double bagged in zip lock baggies.
Leisire Lake Sample.jpg
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Written on the side of the bag were the GPS Coordinates for the sample site, which according to Google places it at Leisure Lake just outside of Fremont, Nebraska. (Lorez, please correct me if I have it wrong.)
Leisure Lake Cleaning.JPG
Leisure Lake Cleaning.JPG (143.08 KiB) Viewed 6815 times
To separate the diatoms from the sand I will place a portion of the sample in a jar, along with some distilled water and gently shake and swirl it, hopefully rinsing the diatoms free.

After just couple of minutes it is easy to see that something has rinsed free.
Leisure Lake Suspension.JPG
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After pouring off the clouded water into beaker for safe keeping, I repeat the same process, and continue until the sample doesn't produce the clouded water we are after. Then we replace the clean sand with fresh sample and repeat
Leisure Lake Complete Clean.JPG
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After processing the entire sample with this technique we have a nice beaker full of cloudy water full of what we hope are diatoms.

Once the collection beaker has settled, it looks very promising indeed.
Leisure Lake Settle.JPG
Leisure Lake Settle.JPG (94.58 KiB) Viewed 6815 times
Now a quick test slide to see if we indeed have collected diatoms in this material confirms that we have what we are seeking. I am struck by what appears to be a very nice populations of centric colonial forms along with Navicula, Pinnularia, and others. Looks very promising.

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Re: Doing Diatoms

#386 Post by rnabholz » Tue Dec 06, 2016 2:59 am

Now to condense our beaker full of water and diatoms into a manageable size sample to clean.

Transferred the beaker contents into sixteen 15ml tubes.
Leisure Lake Ready To Spin.JPG
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Eight tubes at a time will fit into my centrifuge. I will spin them at around 400rpm for 10 minutes.
Leisure Lake Spin Loaded.JPG
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Leisure Lake Spinning.JPG
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Each tube yields a bit of the good stuff.
Leisure Lake Spin Down.JPG
Leisure Lake Spin Down.JPG (93.78 KiB) Viewed 6813 times
After pouring off the supernatant, I use a pipette to gather the material at the bottom of the tube and consolidate it into a single tube.

Then one last spin of the gathering tube with a tube full of water as a counterweight to keep the centrufuge balanced and we have a tube full of some great looking material that is ready for cleaning chemicals.
Leisure Lake FInal.JPG
Leisure Lake FInal.JPG (89.69 KiB) Viewed 6813 times
To be continued....

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Re: Doing Diatoms

#387 Post by zzffnn » Tue Dec 06, 2016 3:13 am

Looks great, Rod.

400 rpm is a good speed. Higher speed of over 800 rpm may damage diatoms. People in the "diatom forum" Yahoo group seem to agree that centrigue may damage diatoms - some even spin at 100 rpm.

I am running a cleaning experiment with 31.45% muriatic acid bought for $11 from pool chemicals section of Home Depot. I wrote down some comments there in the Diatom Forum, bascially I would like to avoid boiling strong acid (cold fume is ok with my outside balcony)
https://groups.yahoo.com/neo/groups/dia ... opics/3668

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Re: Doing Diatoms

#388 Post by rnabholz » Tue Dec 06, 2016 5:19 am

Thanks zz

I suppose I could slow things down even more, I will give that a try.

I did see your posting to the Yahoo Group. Your reluctance is much like mine.

I am interested in your acid results. I actually bought some Muriatic Acid a couple months ago, but I believe it is a weaker formulation. I haven't had the courage to use it yet.

Watching and learning...

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Re: Doing Diatoms

#389 Post by KurtM » Tue Dec 06, 2016 3:54 pm

I looked at the label on my muriatic acid and see 19.27% ... dang! Looks like a trip to Home Depot is in order for a 30% jug.

Muriatic acid/hydrochloric acid/HCI has always been a bit of a mystery to me. First, all three of those names I just used mean the same thing and are interchangeable. Secondly, I have been made to understand that HCI pre-treatment is pretty much necessary in marine samples, otherwise salts will react with other chemicals used to clean diatoms and mess up your slides. But I've done many a marine sample before ever trying HCI and never had a problem. I'm only wanting to get some because everyone says I need it, not because I've encountered any real need for it.

But I just can't shake that nagging feeling that I'm missing something here...

In other news, how does one determine the RPM's of his centrifuge? My new electric one goes pretty slow, and so far it's the only speed I have used, outside of testing. It appears to be roughly the same speed as a casual cadence hand cranking my manual centrifuge.
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Re: Doing Diatoms

#390 Post by Charles » Tue Dec 06, 2016 4:10 pm

Looks like some good stuff Rod! Why use distilled water and not just tap water for the initial suspension and cleaning and then use the DW on the final 3 rinses after it has all been cleaned and rinsed 3 times in tap water first?

I've given up on the centrifuge. I just let it settle by gravity for about 2 hours, I then siphon the top water off to another container which I let stand even longer in case there are diatoms still floating around. May take longer but I know the forms won't be damaged.

Keep up the good work!

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