Doing Diatoms

[zzffnn]

Good work, Rod! That is what I call dedication.
The centric form is especially beautiful!

[KurtM]

The first two are cracking good - wow! Don't worry Rod, you and Fan aren't the only interested parties still about, not by a long shot! I haven't had time to do squat with microscopy, and have been operating vicariously through you and others on this forum (thanks!). You'll be seeing lots more participation out of me later this month when I finally return home on the 14th or so.

Yes, I brought along a couple microscopes, just too darn busy to use 'em. I have managed to collect a few samples for future reference. Gonna be tough to beat those you have been showing, though.

[rnabholz]

Good work, Rod! That is what I call dedication.
The centric form is especially beautiful!

Thanks zz.

Not sure it is dedication, probably more like a child waiting to open up a birthday present.... ;^)

[rnabholz]

The first two are cracking good - wow! Don't worry Rod, you and Fan aren't the only interested parties still about, not by a long shot! I haven't had time to do squat with microscopy, and have been operating vicariously through you and others on this forum (thanks!). You'll be seeing lots more participation out of me later this month when I finally return home on the 14th or so.

Yes, I brought along a couple microscopes, just too darn busy to use 'em. I have managed to collect a few samples for future reference. Gonna be tough to beat those you have been showing, though.

Hey Kurt

Glad to hear you are still out there somewhere, hope you are enjoying your excursion.

Thanks for the comment. That centric could probably benefit from a stack, I may have to circle back to it.

Look forward to seeing what you dragged out of the river.

[zzffnn]

I have managed to collect a few samples for future reference.

Kurt,

I suggest going back to your previous favorite locations/spots/rocks, when you collect diatom samples again. I did that and got some nice diatoms last week, from Mooday Gardens' shore (Offatts Bayou, 29.276251,-94.852624).

Sadly, the Galveston rock slime sample, while full of beautiful live diatoms, did not survive a gentle water boiling (which was necessary to reduce its smell).

Two major forms dominanted the Galveston sample, Meridian Circulare and the first form in the first picture of this thread: http://www.photomacrography.net/forum/v ... +heine+col.

After boiling, MC totally disappeared, while the unnamed form looked empty and boring. I am guessing that the MC there were immature and lacked thick silica backbone to survive boiling. Rod and I decided not to clean/mount this sample.

I am going back to the same spot, between March-August next year though. I clearly remember a nice big centric form used to be abundant in a March sample (but not present in quantity in this latest October sample).

I also sampled surf side beach sand at 3 other Galveston locations (San Louis Pass/under bridge, about 8-10 miles east of San Louis Pass, and East Beach jetty), but came up empty handed. Galveston sand this time have many diatom-sized mineral particles (that are much smaller than Pensacola Langdon sand), which would be a pain to clean/mount even if there are good diatoms in it.

[Dale]

Wow, 335 posts, after a lot of pm's I still have a few questions. Are the HP and PD really available
at grocery stores? Just how little is little when adding PD, and how often should sample be checked?
The flat well slides you all mention, are they all home made?
Thanks for mentioning safety while collecting. Next year I will collect from Lumahai Beach, one of
the most dangerous, but samples will not be from the surf!
Dale

[rnabholz]

Hi Dale

You are looking for Hydrogen Peroxide in 35% concentration. The drug store variety is around 3%

The good news is you may find it at local health food stores or of course online. Here is what I use:

Pure Health Discounts Certified Food Grade 35% 8 oz Hydrogen Peroxide with 1oz Bottle Dropper https://www.amazon.com/dp/B01AKIGJXI/re ... hyb0C6G5KC

The Potassium Dichromate is also available online. Here's an ebay item number: 121841814299

PD does require care in handling and in use. Avoid contact with skin and inhalation of fumes. HP at 35 can cause tingling in contact with skin and will temporarily turn skin white (20 minutes), so careful handling is warranted.

As you may have read in the thread, combined the reaction is energetic and unpredictable. I have taken to using a 500ml beaker to hold 50ml of HP and diatoms when doing the PD reaction. Always have plenty of room for the reaction to expand

I also place that breaker on a tray or in a stainless bowl to catch any overflow.

To that 50ml sample, I add about the equivalent of a half baby aspirin of PD - No More, then wait. Many times the reaction will not be immediate. Just let it set, it will happen. The reaction will continue and ultimately turn orange and stop bubbling. It is then complete.

zz will have to jump in on the side question, as he is the one that uses them.

[Dale]

Thanks Rod, just what I needed. Just checked my new neighborhood in Sequim
for streams, and there are many. Not sure about lakes.
Dale

[zzffnn]

Dale,

Most credit cards are 0.8-1.2mm thick. So I cut expired ones into 4 thin strips as slide edges. The use silicone glue (aquarium grade) to glue them onto a common microscopw slide. Do NOT use super glue as it is not water proof.

Those DIY slides hold a lot more water than regular slides. They can be moved around with regular slide holder and won't be thick enough (unlike petri dish) to obstruct other high power objectives.

Due to surface tension (water can attach to credit card edges to become flat surface - as long as you don't add too much water), such flat surface introduces minimal optical distortion and requires minimal focus adjustment at edges (much less than a spherical water droplet). You may also be able to fine tune water thickness, in such a DIY slid, than in a petri dish (which requires much more water, is usually not flat in bottom and scratches easily/has poorer optical quality).

Petri dishes still hold more water though.

For portable field use at 10x objective or less, petri dish may work better. Because petri dish is more durable and can withstand higher wind speed (if you attach fridge Saran wrap to petri dish with a rubber band).

[rnabholz]

A development in my mounting process to pass along.

I had heard a while back that some folks used an unconventional approach of curing their diatom slides. They position the slides on the hotplate with the coverslip DOWN.

The reasoning is that this approach means that diatoms remain as close as possible to the underside of the slip, which promotes sharpness and contrast.

I posted a question on the Yahoo Diatom board and got a response highly in favor of the approach.

Tonight I have it a try. As per the guidance that I was given, I placed two stacks of two slides on the hot plate. I then prepared the slide as usual, then carefully placed it across the stacked slides with the slip down.

Slip Down Set Up.JPG (111.96 KiB) Viewed 181418 times

I then increased the heat slowly, and was relieved to see the Pleurax bubble but not knock the coverslip off the slide. Cool.

After the cook and cooling, I placed the slide on the scope. My distinct impression is that there IS an improvement in resolution and contrast. I do see more details is some difficult to resolve forms. I am also finding that more of the forms are presented more squarely making them focused all the way across the face.

Again, that is my first impression, and I will explore more with the camera in the coming days, but I am excited about the possibilities.

[Dale]

Were the bubbles gone when you were done?

[rnabholz]

Were the bubbles gone when you were done?

Yes, as it cures the bubbling ends and the slip is evenly covered

[Dale]

Cool. I'm awaiting some lab stuff to try all this, and have yet to order the cleaning
chemicals. The link you gave me for the HP is for 8oz, would you suggest a larger
quantity? 16oz for $12 ?
Dale

[rnabholz]

Cool. I'm awaiting some lab stuff to try all this, and have yet to order the cleaning
chemicals. The link you gave me for the HP is for 8oz, would you suggest a larger
quantity? 16oz for $12 ?
Dale

Yes if you think you will use it reasonably soon. The incremental cost not that great as you point out. It does have a slightly limited shelf life after opening. Refrigeration can slow that down.

[Dale]

I think the sand/mineral particles are heavier (more dense) than diatoms and should sink to the very bottom of centrifuge tubes. Diatoms layer should stay above sands, if you spin fast enough. At least, that would happen in research lab centrifuges.
What designates a 'research lab centrifuge'?
Dale

[Dale]

"I think the sand/mineral particles are heavier (more dense) than diatoms and should sink to the very bottom of centrifuge tubes. Diatoms layer should stay above sands, if you spin fast enough. At least, that would happen in research lab centrifuges."

What designates a 'research lab centrifuge'?
Dale

[zzffnn]

What designates a 'research lab centrifuge'?

Those are huge, heavy and expensive. We don't need one. Their motors/rotors can spin at over 10k and is usually self-cooled and precisely machined/matched. Programming, such as gradual acceleration or deceleration is possible.

[Yvan]

Nice.

[zzffnn]

It depends on how big the mineral particles are.

For Pensacola FL sand (and for capturing most protists from vegetation), I don't even need a centrifuge. Shake, gravity and 300 micron filtration is enough.

For Galveston TX sand, which has lots of diatom-sized minerals, size and density difference between diatoms and sand is quite little.

When density difference is enough, one can try to let gravity work for a few seconds to sink the minerals and quickly pour/suck out diatoms that are still in suspension. Loss of yield may happen that way. But you will get some diatoms that way, if there are enough in raw material.

Research centrifuge and density gradient solution can separate small amounts of particles with minute density difference, but it is usually not accessible to hobbyists.

[rnabholz]

The Fox River sample cleaned up nicely and shows a nice variety of forms. Most are mid sized and fairly common, but feature some nice colonial chains and a few Craticula scattered about.

You can have a look at some of them here:

viewtopic.php?f=6&t=4112

The Mecan River sample seemed a bit less diverse than the Fox, and the diatoms were generally smaller. Still lots to explore and take in. A few images from the sample are here:

viewtopic.php?f=6&t=4102

viewtopic.php?f=6&t=4134

viewtopic.php?f=6&t=4119

viewtopic.php?f=6&t=4175

[rnabholz]

Couldn't help but notice the resemblance between this story and my "Poleclaw/Clawpole" invention. Glad to see the I am only a step or two behind chimps.....

http://www.dailymail.co.uk/sciencetech/ ... -wild.html

[zzffnn]

Couldn't help but notice the resemblance between this story and my "Polehook/Hookpole" invention. Glad to see the I am only a step or two behind chimps.....

http://www.dailymail.co.uk/sciencetech/ ... -wild.html

Rod, you are tooooo humble.

Inspired by you, I went to my local Home Depot and bought this rake:

http://m.homedepot.com/p/True-Temper-Su ... /202804437

I like it since its tine have enough strength to pick up small-medium sized rocks. Not just scooping rocks over, but picking up them. I have tested it. Sizee and weight is perfect for a kayak and price is cheap as well. Note most rakes at Home Depot do not have tines that are stiff enough to pick up rocks - it is best to go in person and check them out.

[rnabholz]

Zz

Not sure I could possibly be humble enough after discovering monkeys have long been using a method to gather algae that just occurred me a week ago.... Now I wonder if they have a fast, fool proof, non-acid cleaning protocol?

Your tool looks great for the job. Should give you access to more locations which of course should mean better diversity.

Good hunting!

[rnabholz]

Just for fun, a shot of the bench with last of the recent Wisconsin slides with the remaining cleaned diatoms in the front tubes, and the diluted samples for mounting in the rear. Hours of fun to produce and years of enjoyment ahead. :^)

Wisconsin Oct 2016 Samples

Wisconsin Oct 16 Samples.jpg (125.72 KiB) Viewed 181314 times

[rnabholz]

Time for me to gather samples is running out for the year, so I am trying to take advantage of all the remaining good weather.

Today is a beautiful sunny day, so I headed out to the river to round up a sample. The river level is down a bit, making for muddy and treacherous shorelines, so this was a job for "The Claw"

Claw Attached.jpg (182.98 KiB) Viewed 181305 times

Here you can see the material that I was after, the diatom laden algae. Here I am standing about as close as I can safely get. The bank of the river is elevated about 3 feet over the water level.

Claw Target.jpg (230.44 KiB) Viewed 181305 times

Extended the pole is about 12 feet long or so.

Claw Extended.jpg (146.23 KiB) Viewed 181305 times

To gather the material I just reach out, snag the material, twist the pole to snare it on the hook, pull the pole back in and place the good stuff in a waiting bucket. Clean, Safe and High and Dry.

Claw Loaded.jpg (195.5 KiB) Viewed 181305 times

It is really working out very well.

[zzffnn]

Very nice 12 feet reach, Rod.

Your sampling site looks very promising. I like that clear water and reachable algae.

Most of my sampling sites do not have both factors. Most of the time, water is greenish and visibility is low (Houston TX is a bit polluted). I have only been to a garden pond that looked as promising, but it was October and diatoms there were too small and not diverse enough.

[rnabholz]

Very nice 12 feet reach, Rod.

Your sampling site looks very promising. I like that clear water and reachable algae.

Most of my sampling sites do not have both factors. Most of the time, water is greenish and visibility is low (Houston TX is a bit polluted). I have only been to a garden pond that looked as promising, but it was October and diatoms there were too small and not diverse enough.

The algae is loaded. Take a look at the cloud in the water in the shot with the material on the claw. That is all escaping diatoms!

The water in this river generally is a bit less clear. The lower water levels in Fall, due to the typically lower precipitation means less run off from fields which makes a nice difference.

The sample is cooking now.

[rnabholz]

Up a few entries you saw my experiments with inverted curing of slides. I have made it part of my regular process, but the process of placing and flipping the slides on the stacked slide jig while hot was a bit difficult and nerve-racking to say the least. I thought there had to be a way to make it easier.

The first thought was to get rid of the stacked slides, they were always moving as I placed slides, and they took up valuable space on the hot plate. The other component was finding a way to handle the slides safely.

After thinking about it for a few days, I had an idea. Cheap, simple and readily available.

Here is the kit:

Invert Kit.jpg (113.39 KiB) Viewed 181242 times

The key component is "micro" sized binder clips. To that we add a paper clip bent to serve as a lifter - that is it. Above are 4 slides with Pleurax and slips ready to go on the hot plate.

To make this work it is very simple, just attach a binder clip to each end of the slide. The binder clips grip with enough security to lift the slide by the clip. If I fold the clip handle down, the slide is suspended about 2mm above the surface of the hot plate, easily close enough to heat up. With the clip folded up, the spacing changes to about 6mm, which is perfect for the final curing portion of the process.

So with the clips attached and handles positioned one up and one down on each clip, it is on to the hot plate in low mode.

Invert Low Above.jpg (94.53 KiB) Viewed 181242 times

Invert Low.jpg (68.31 KiB) Viewed 181242 times

When the main curing is done and it is time to flip the slide, simply take the Paper Clip Lifter, slide it through the space in the jaws of the clip, slowly lift and invert the slide, and remove the clip. Easy Peasy, no fumbling, dropping or burns.

Invert High Above.jpg (99.57 KiB) Viewed 181242 times

Invert High.jpg (72.15 KiB) Viewed 181242 times

When the cure is complete, just use the lifter to remove from the plate to cool.

This really makes this process a lot simpler and safer.

[rnabholz]

Another family outing, another chance to gather a sample.

I was not sure what success I might have this late in the season, but hauling the sample kit isn't much trouble and the time invested small so why not?

This trip was to Wapsipinicon State Park in Anamosa, Iowa. The Wapsipinicon river that you have heard me mention in this thread regularly as it flows through my home town makes it way south and runs through this pretty park featuring some really interesting geography, limestone bluffs, caves and most importantly for my interest, Dutch Creek.

Dutch Creek Drive.jpg (223.04 KiB) Viewed 181207 times

A tribuitary to the Wapsi, I was interested to see just what it might hold versus what I have found in all of the Wapsi samples I have gathered.

Dutch Creek.jpg (296.09 KiB) Viewed 181207 times

With the trusty PoleClaw in hand I made my way down to the creekside. No signs of the algae streamers that I had found in my last outing, but there were lots of submerged leaves. Using the pole to disturb a bit of them showed an immediate release of a fine cloud of particles, the kind that experience tells me hold diatoms.

Dutch Creek Leaves.jpg (209.45 KiB) Viewed 181207 times

So I used the pole to gather a good batch of those leaves in my bucket. I sat at a nearby picnic table and placed a batch of the leaves in a jar added some of the creek water and shook it. Sure enough the water rinsed the material off of the leaves and I had a batch of that familiar diatom holding material.

Returning home later, I made a wet slide to confirm what I was pretty sure was a good sample and this is what I saw.



Lots and lots of diatoms everywhere. Not a great diversity, but this was by no means a comprehensive look at the entire sample, which usually means that there will be pleasant surprises in the cleaned sample.

Speaking of pleasant surprises, this fellow waddled across my view. The cherry on top of a great outing.

[zzffnn]

Nice work, Rod. Thank you for sharing.

I saw at least 5 forms there in the video.

I have not found a river/bayou with sunken leaves like that around me, but will pay more attention next time.