Doing Diatoms

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zzffnn · #241 Post by **zzffnn** » Fri Jul 29, 2016 1:36 pm

For Rod and Kurt:

Diatom cleaning and mounting methods:
http://www.microscopy-uk.org.uk/mag/ind ... atoms.html

Manipulation/orientation:
http://www.microscopy-uk.org.uk/mag/ind ... atoms.html

rnabholz · #242 Post by **rnabholz** » Fri Jul 29, 2016 3:20 pm

Thanks zz.

I had seen the first, but the second was new to me. He almost makes it sound like a sane pursuit..... ;^)

KurtM · #243 Post by **KurtM** » Fri Jul 29, 2016 6:51 pm

I had seen both before, but that's not to say I was or am able to entirely understand them. In the cleaning article it says "hydrochloric acid (household quality will do)". So what do I go shopping for if I want hydrochloric acid?

No doubt I could stand to re-read both articles. Still haven't gotten around to experimenting with incineration with a torch.

rnabholz · #244 Post by **rnabholz** » Fri Jul 29, 2016 7:02 pm

You would ask your local Helpful Hardware Man for Muriatic Acid.

KurtM · #245 Post by **KurtM** » Fri Jul 29, 2016 8:28 pm

Then why the thunder don't they just SAY that?! It's frustrating to read about diatom cleaning when you're a bumbling uneducated lout like me.

zzffnn · #246 Post by **zzffnn** » Tue Aug 02, 2016 10:03 pm

I wanted to collect some diatom samples for Rod and Kurt, from our kayak trip today, but did not find enough diatoms to send. Details and sample photos here: viewtopic.php?f=10&t=3559&p=32177#p32177

rnabholz · #247 Post by **rnabholz** » Wed Aug 03, 2016 2:29 am

You know that I have whiffed on some of my attempts. I hope you will try again.

A day paddling is always a good day, diatom scarcity be darned!

Rod

zzffnn · #248 Post by **zzffnn** » Wed Aug 03, 2016 3:59 am

Rod,

If you see golden brown slime in the future, I suggest scrapping off just that layer and put some into a dry zipper bag, without further dilution. You don't need them alive anyway. That may get you more pure concentrated diatoms.

Taking along a field scope will help too. I have this pocket inverted scope (80x-160x) and like to use it with DIY deep well slides:
http://www.ebay.com/itm/Meade-08025-Rea ... ect=mobile

This upright (100x-450x) pocket scope works reasonably well too, though its short working distance at 450x does not allow use of deep well slides (but the 1st inverted pocket scope can go up to 160x with deep well slides):

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

viewtopic.php?f=16&t=2246

Image quality of both is good at lower end and reasonable for higher magnification. Neither has a condenser and thus cannot go up to NA 0.65. Good enough to tell diatoms (and soecific diatom shapes) from other protists though.

rnabholz · #249 Post by **rnabholz** » Fri Aug 05, 2016 9:42 pm

Hey zz,

I ordered one of the Meade Readiview scopes for the vacation trip in a week or so. It will be nice to screen the samples before we leave to be sure I "got the goods".

Thanks for the pointer.

Rod

zzffnn · #250 Post by **zzffnn** » Fri Aug 05, 2016 10:40 pm

Rod is now armed to the teeth and ready to take over the diatom world

rnabholz · #251 Post by **rnabholz** » Sat Aug 06, 2016 1:02 am

zzffnn wrote:Rod is now armed to the teeth and ready to take over the diatom world

Well if $40 bucks was all it took to do that, I should have done it a long time ago. ;^)

zzffnn · #252 Post by **zzffnn** » Sat Aug 06, 2016 3:29 am

The magnetic ring of that scope can be removed to accommodate thick well slides, if necessary. That ring is only there to hold the slide/cover slip.

And 80x and 160x are not parfocal, but adjustment is not difficult.

rnabholz · #253 Post by **rnabholz** » Fri Aug 19, 2016 5:28 pm

Back from a short week of vacation.

We spent our time in Wisconsin at the Kettle Morraine Northern Unit. http://dnr.wi.gov/topic/parks/name/kmn/

The name refers to the the glacial features that are found there, including numerous lakes and ponds. We paddled two of the lakes, Mauthe and Long Lakes.

: The Fleet; LongFleet.JPG (82.21 KiB) Viewed 155840 times

: Sample Location; Long Shore.JPG (93.44 KiB) Viewed 155840 times

I used the opportunity to gather samples from both lakes from my canoe. I use a small garden rake to grab what I want, and a plasic bin to hold it. Here is a shot - please excuse the dirty boat, the process made a bit of a mess.

: Sampling Equipment; LongRig.JPG (113.56 KiB) Viewed 155840 times

The target material was found coating the aquatic plants, a fine gray covering that when disturbed immediately reminded me of the behavior of good diatom material. A bit hard to see here, but it was clearly evident in person

: Target Diatom Material; LongTarget.JPG (134.01 KiB) Viewed 155840 times

I gathered samples from a couple of different spots and soon had plenty to work with.

: Sample bin; LongBin.JPG (98.09 KiB) Viewed 155840 times

rnabholz · #254 Post by **rnabholz** » Fri Aug 19, 2016 5:42 pm

Back at camp I prepared a quick slide and using a field microscope confirmed that diatoms were indeed present in large quantities.

I them proceeded to process the samples to separate them from the plant matter.

Using a 1 gallon zip lock bag, I placed a portion of the plant material in the bag along with some water from the sample. Sealing the bag, the bag was shaken and kneaded until the water showed the cloudiness the suggested that our target had been liberated from the plant matter.

At that point the plant matter was removed and the water carrying the diatoms was collected and saved. It exhibited the usual "clumpy" look of the good stuff. It all looks very promising.

: Long Lake Raw Sample; LongSample.jpg (117.49 KiB) Viewed 155839 times

Upon returning home, another look at the raw sample seems to show a very clean sample, with very little mineral content, no doubt because of the collection from the plants instead of bottom sitting rocks or other material. Because of that, I have decided for this sample to process the first portion of the sample without filtering with the stocking strainer. I did pass the sample through a very large meshed kitchen strainer to catch the loose plant matter, but all diatoms should pass easily.

I have samples from both Long and Mauthe Lake cooking now.

In one other side trip I did collect one other sample.

: Lake Michigan Sample; LakeMichiganSample.jpg (125.68 KiB) Viewed 155839 times

This is from Lake Michigan. I am not sure what I have here, I carried it home just as you see it here. I will be working with it soon and will let you know.

gekko · #255 Post by **gekko** » Fri Aug 19, 2016 10:34 pm

It sounds like you had a wonderful, and very fruitful, vacation. Thanks for the lovely documentary photos, and looking forward to the photomicrographs

.

KurtM · #256 Post by **KurtM** » Fri Aug 19, 2016 11:29 pm

A dirty canoe is a happy canoe - that's what water hoses are for!

Pretty nice looking paddle ya got there!

Glad you all had a good time, can't wait to see what you brought back.

rnabholz · #257 Post by **rnabholz** » Sat Aug 20, 2016 12:32 am

gekko wrote:It sounds like you had a wonderful, and very fruitful, vacation. Thanks for the lovely documentary photos, and looking forward to the photomicrographs .

Thanks Gekko. Coming Soon to a Forum Near You.

rnabholz · #258 Post by **rnabholz** » Sat Aug 20, 2016 12:49 am

KurtM wrote:A dirty canoe is a happy canoe - that's what water hoses are for! Pretty nice looking paddle ya got there!

Glad you all had a good time, can't wait to see what you brought back.

I guess dirt is a sign that she's in use, so that's good, but I think she'll get a good clean up this weekend.

The paddle is a Shaw and Tenney 1897 in stained Ash. My all time favorite. I have had it nearly 20 years and used it for 95% of the paddling I have done. A carved one piece paddle. Just love it.

I have taken some quick looks at the lake samples during the cleaning process, a really excellent variety, some really large ones too. Lots of Epithemia and multiple types which is new for me.

Still seeing lots of very fine deritus. Going to go for another round of HP and see if I can clear it up a bit. If not, it should still work with proper dilution.

rnabholz · #259 Post by **rnabholz** » Mon Aug 22, 2016 3:19 am

Results from the lake samples can be seen here:

viewtopic.php?f=6&t=3661

viewtopic.php?f=6&t=3672

rnabholz · #260 Post by **rnabholz** » Tue Sep 20, 2016 12:09 am

A long overdue update.

The Lake Michigan sample that is seen in the earlier post above in the plastic tray finally got the attention it deserved.

We had returned from vacation and as my schedule went, I had to leave town a few days later. I brought the sample down to my secret lair. There I placed it sitting open, and I placed a fluorescent lamp about 12 inches above the tray, reasoning that the light should keep thing in good shape until my return when I would process it.

About three days later my wife sends me a text message reiterating her love for me, and her support for my various hobbies, but says that she draws the line at having that stinking container of black "seaweed" in the basement and advises that I could find it behind the house about 50 feet away, which in her estimation was still too close. Opps....

Upon my return home it was just where she said it would be and to hear her tell it, smelling even worse, and I have to admit it really was awful.

So I leapt into action, rubber gloves, Vicks Vapor Rub under my nose in order to suppress the gag reflex, I grabbed handful after handful shaking and squeezing the water (and hopefully diatoms) from the nasty black plant matter until I had a tray full of black water. After it had settled I siphoned off the extra water and was left with a great looking diatom bearing material.

From there it was the usual process with Hydrogen Peroxide and Potassium Dichromate. The results were well worth the effort, yielding what I consider to be my best and most diverse sample to date. My first encounter with a huge centric and various other new forms, more of which I am still finding as I continue to scan the slides from the sample. What a treat this turned out to be. Here are some of the threads that I posted with images from the sample and a shot of that incredible large centric Ellerbeckia arenaria.

viewtopic.php?f=6&t=3780

viewtopic.php?f=6&t=3796

viewtopic.php?f=6&t=3803

viewtopic.php?f=6&t=3825

: Ellerbeckia arenaria 60µm; Centric 1373.jpg (106.11 KiB) Viewed 155720 times

: Ellerbeckia arenaria 63µm; Centric 1266.jpg (171.27 KiB) Viewed 155720 times

rnabholz · #261 Post by **rnabholz** » Tue Sep 20, 2016 1:01 am

I was thrilled by a recent offer by our esteemed member zzffnn of some marine samples he had gathered on his recent vacation. Among them was a diatom sample from Armand Bayou that was scraped from a submerged tree.

Kind of funny to think that you would be happy to get this in the mail, but I really was!

: Fans Sample Bag.jpg (109.8 KiB) Viewed 155718 times

Contained therein was some green plant matter that I could immediately showed signs of that characteristic look of suspended diatoms in some of the water.

: Fans Sample Cleaning.jpg (98.21 KiB) Viewed 155718 times

To separate the diatoms from the plant matter I placed it a jar with added water and shook it like a James Bond martini. I then drained the water off by pouring it through a kitchen strainer, and repeated the process twice more.

: FansRinsed.jpg (154.81 KiB) Viewed 155718 times

rnabholz · #262 Post by **rnabholz** » Tue Sep 20, 2016 1:05 am

I took the opportunity to set aside a bit of the strained water with some of the vegetation from the strainer to keep as a live sample. From that sample put together a wet mount to see just what might be in there. I think it looks very promising. Here are a few afocal "snapshots" - not fine art - that I took to document it. All are 40x fields.

: Fans Sample 4625.JPG (108.69 KiB) Viewed 155718 times

: Fans Sample 4626.JPG (142.72 KiB) Viewed 155718 times

: Fans Sample 4629.JPG (128.75 KiB) Viewed 155718 times

: Fans Sample 4631.JPG (123.02 KiB) Viewed 155718 times

So now I will let the collected sample settle overnight, drain off the supernatant and be ready to get started with the cleaning process tomorrow night. Stand by for updates.

zzffnn · #263 Post by **zzffnn** » Tue Sep 20, 2016 2:57 am

Great work, Rod!

I did not see the last (4631) diatom in my first and only squeeze/filtration mount. Most likely because I did not shake the sample hard to separate diatoms from vegetation.

That vegetation material may have some interesting protists there too, if they survived the shipping.

Armand Bayou, Texas has brackish water, I think. Though on the date that I collected the sample (Sep 8), water level was high and salinity is very very low. Kurt can probably tell you more about Armand Bayou.

This is approximately where I collected the sample from submerged (dead borken) tree branch:
29.593190,-95.088084

You can type that in Google or Google map and zoom in all the way to see where it is.

My wife treats my sample jars the same way

Smell wasn't too bad, baby poop or vomit can be a lot worse

KurtM · #264 Post by **KurtM** » Tue Sep 20, 2016 3:49 am

DANG that sample looks interesting! And right there in my own home stomping grounds too. Guess I need to get with the program and pull more local samples this winter.

mrsonchus · #265 Post by **mrsonchus** » Tue Sep 20, 2016 3:52 am

Fantastic! Now that's what I call dedication, by both Husband & Wife!

A really interesting report - almost makes me want to get the vapour-rub on and go fishing & scraping! Some very nice looking specimens in there - you'll have a great deal of fun and learn a lot sifting through and identifying those for certain, let alone the slides to follow. Great work from you both!

Keep these reports coming - I may not be a Diatom-man but I know a great adventure when I see one! Lovely clear pictures and great tale-telling to-boot!

Nicely done old chap!

zzffnn · #266 Post by **zzffnn** » Tue Sep 20, 2016 11:53 am

KurtM wrote:DANG that sample looks interesting! And right there in my own home stomping grounds too. Guess I need to get with the program and pull more local samples this winter.

^ You know what Kurt - I thought that sample was boring (too common) and messy. It was NOT golden brown either, more like greenish brown (it did not even look like prime diatom material to my amateur eyes). I took it while trying out my new kayak the first time (so I did not take my portable scope).

Even when I looked at the sample under scope, I was not impressed either, since I only saw those long and slender common forms.

I sent it to Rod, just because I wanted him to eyeball / guess how difficult it is to clean/mount it, so that next time I know whether or not to send similar-looking sample. I told Rod not to waste reagents and time in cleaning/mounting, if he does not like the sample.

If I were to make a decision myself, I wouldn't send it alone. But I was sending Rod the Pensacola sands anyway, so I thought it wouldn't waste much to ride long.

gekko · #267 Post by **gekko** » Tue Sep 20, 2016 12:28 pm

Seriously serious, no-compromise work! The proof is in the beautiful results.

rnabholz · #268 Post by **rnabholz** » Tue Sep 20, 2016 1:02 pm

zzffnn wrote:Great work, Rod!

I did not see the last (4631) diatom in my first and only squeeze/filtration mount. Most likely because I did not shake the sample hard to separate diatoms from vegetation.

That vegetation material may have some interesting protists there too, if they survived the shipping.

Armand Bayou, Texas has brackish water, I think. Though on the date that I collected the sample (Sep 8), water level was high and salinity is very very low. Kurt can probably tell you more about Armand Bayou.

This is approximately where I collected the sample from submerged (dead borken) tree branch:
29.593190,-95.088084

You can type that in Google or Google map and zoom in all the way to see where it is.

My wife treats my sample jars the same way Smell wasn't too bad, baby poop or vomit can be a lot worse

Thanks again for the sample. It appears as though the fine mineral content will be something to contend with, but there is a nice population of diatoms that will make it worth the effort to clean.

Those colonials are very interesting, especially the large one. Who knows what other interesting things we will find? Should be fun!

rnabholz · #269 Post by **rnabholz** » Tue Sep 20, 2016 1:07 pm

KurtM wrote:DANG that sample looks interesting! And right there in my own home stomping grounds too. Guess I need to get with the program and pull more local samples this winter.

Pulling samples in winter is an activity reserved for you southern folk. I can feel my season starting the turn towards closing. I needed to get busy too so that I have projects for theb long winter nights ahead.

rnabholz · #270 Post by **rnabholz** » Tue Sep 20, 2016 1:17 pm

mrsonchus wrote:Fantastic! Now that's what I call dedication, by both Husband & Wife!

A really interesting report - almost makes me want to get the vapour-rub on and go fishing & scraping! Some very nice looking specimens in there - you'll have a great deal of fun and learn a lot sifting through and identifying those for certain, let alone the slides to follow. Great work from you both!

Keep these reports coming - I may not be a Diatom-man but I know a great adventure when I see one! Lovely clear pictures and great tale-telling to-boot!

Nicely done old chap!

Thanks John.

My long suffering wife indulges my many unusual pursuits, whether it is leaving her alone on a Saturday night while I spend a night with my telescopes, or hosting decaying aquatic plant material, she hasn't kicked me out yet ;^)

I know it is just a matter of time until we suck you into Diatoms..... Come to the Slimy side....

To clarify, the vapor rub was only necessary be cause of the age of the sample, normally there is not an issue. Don't want to scare anybody off.

The story will continue as long as there is interest from the group. Thanks for yours,

Rod

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