Diatom Collecting & Cleaning For Beginners


Kurt Maurer
 

Greetings, All:

I am a retired, self-educated, enthusiast who has been dabbling in astronomy and microscopy among other things as hobbies for some years. In microscopy, I struggle to learn general laboratory methods and techniques such as sample collection, preparation, and the handling of wee things.

I wish to poll this group for advice, suggestions, tips, etc., for how to get an untrained ape to handle diatoms. Specifically, I'd like to be able to collect, clean, and make my own strew slides. I understand there may be a lot to it, and eclipsing Mr. Kemp with my newfound skill is unlikely anytime soon. I have some Pleurax and Cytoseal, plus slides, coverslips, and an iron to use for a hot plate. I purchased the Pleurax along with a cleaned diatom sample from Michel Haak to get started, and have been corresponding with him. Now I want to obtain my own samples.

I have Googled the terms "how to collect diatoms" and "how to clean" diatoms many times and scoured the various web sites, but most suggest expensive equipment and/or employing lab techniques and/or materials (like dangerous acids, yikes) that are rather beyond my reach. In short, I would like to keep this as simple, basic, and inexpensive as possible ... if possible. Thank you.

Cheers,
Kurt Maurer
League City, Texas


Mike Andrews
 

There are some really fine YouTube videos from Japan, in a number of languages, that show how to do this. Look for stuff from "diatomp".

Mike Andrews, W5EGO
WWME Oklahoma area executive team

On Feb 16, 2014, at 10:06 AM, <NGC704@...> wrote:

 

Greetings, All:


I am a retired, self-educated, enthusiast who has been dabbling in astronomy and microscopy among other things as hobbies for some years. In microscopy, I struggle to learn general laboratory methods and techniques such as sample collection, preparation, and the handling of wee things.

I wish to poll this group for advice, suggestions, tips, etc., for how to get an untrained ape to handle diatoms. Specifically, I'd like to be able to collect, clean, and make my own strew slides. I understand there may be a lot to it, and eclipsing Mr. Kemp with my newfound skill is unlikely anytime soon. I have some Pleurax and Cytoseal, plus slides, coverslips, and an iron to use for a hot plate. I purchased the Pleurax along with a cleaned diatom sample from Michel Haak to get started, and have been corresponding with him. Now I want to obtain my own samples.

I have Googled the terms "how to collect diatoms" and "how to clean" diatoms many times and scoured the various web sites, but most suggest expensive equipment and/or employing lab techniques and/or materials (like dangerous acids, yikes) that are rather beyond my reach. In short, I would like to keep this as simple, basic, and inexpensive as possible ... if possible. Thank you.

Cheers,
Kurt Maurer
League City, Texas


Charles Suslavage
 

Hello Kurt,

Welcome to the group. You should download 'An Introduction to the Microscopical Study of Diatoms' by the late Robert B McLaughlin. It is available as a free download from Modern Microscopy, http://www.modernmicroscopy.com/main.asp?article=105

A very informative work! Should get you pointed in the right direction.

Charles


Andy Robins <andy.robins@...>
 

The location for the start of the three part series on collecting and cleaning diatoms is

http://www.youtube.com/watch?v=NrhSqu8YCBo

The chemical used in the cleaning process is ordinary household drain cleaner!

Still nasty stuff, to be treated with care but much easier to get hold of these days than
the traditional strong acids.

I must admit I would never have thought of this but it makes good sense when you think about it.

Like you I am just starting to look into the fascinating subject of diatoms.

Let us all know how you get on.

Regards

Andy R


Stephen S. Nagy
 

There are a number of articles here about cleaning and collecting diatoms:  


 Best wishes,

Stephen Nagy
Helena, MT



Annie
 

Hello all,

I read in the article of Zhang et al. 2010 that he followed Norman-Boudreau's technique in extraction of diatoms from guts of abalone.  but he preserved his diatom samples in distilled water instead of fixing it in slides w/ high refractive media for enumeration of the diatoms.  Can anybody react to this?  Anybody done this procedure?  Will the samples stay preserved in distilled water?  for how long?

Annie


On Mon, Feb 24, 2014 at 11:24 AM, Stephen S. Nagy <snagymd@...> wrote:
 

There are a number of articles here about cleaning and collecting diatoms:  


 Best wishes,

Stephen Nagy
Helena, MT




Charles Suslavage
 

Hello Annie,
With respect to cleaned diatom samples storing them in distilled water is the normal procedure.
The diatom frustule is made of silica and as far as you and I are concerned will last forever when stored in distilled water.
Charles 

From: "Franco, Annie V." <avfranco@...>
To: diatom_forum@...
Sent: Thursday, February 27, 2014 6:00 PM
Subject: Re: [diatom_forum] Re: Diatom Collecting & Cleaning For Beginners
 
Hello all,

I read in the article of Zhang et al. 2010 that he followed Norman-Boudreau's technique in extraction of diatoms from guts of abalone.  but he preserved his diatom samples in distilled water instead of fixing it in slides w/ high refractive media for enumeration of the diatoms.  Can anybody react to this?  Anybody done this procedure?  Will the samples stay preserved in distilled water?  for how long?

Annie
On Mon, Feb 24, 2014 at 11:24 AM, Stephen S. Nagy <snagymd@...> wrote:

 
There are a number of articles here about cleaning and collecting diatoms:  

http://www.diatomsireland.com/diatom-cleaning/?mobile=1

 Best wishes,

Stephen Nagy
Helena, MT


Zlatko Levkov
 

Dear Charles
There is a problem with preservation of diatoms in distillate water. According to my experience, after a week or two, the diatoms start to dissolute and some valve are highly corroded. Such sample cannot be used for SEM at all, but also the slides made from older cleaned sample are with very low quality. I learned from the Hustedt collection in Bremerhaven (Hustedt kept only cleaned samples) that one possible solution is to keep the samples in glycerine. After cleaning the samples and several washing with water, we are discharging the water and a small amount of glycerine is added to the sediment (diatoms). Such conserved sample can be used for several years (at least). However, according to my experience the best way is to keep the original sample (not clean).
Hope this will help you to keep the samples little bit longer
Zlatko


--------------------------------------------

On Fri, 2/28/14, charles suslavage <suslavage@...> wrote:

Subject: Re: [diatom_forum] Re: Diatom Collecting & Cleaning For Beginners
To: "diatom_forum@..." <diatom_forum@...>
Date: Friday, February 28, 2014, 12:23 AM
















 









Hello
Annie,With respect to cleaned diatom samples
storing them in distilled water is the normal
procedure.The diatom frustule is made of silica
and as far as you and I are concerned will last forever when
stored in distilled
water.Charles 
From: "Franco,
Annie V."
<avfranco@...>
To:
diatom_forum@...
Sent:
Thursday, February 27, 2014 6:00 PM
Subject: Re:
[diatom_forum] Re: Diatom Collecting & Cleaning For
Beginners
















 






Hello all,
I read in the article of Zhang et al. 2010 that
he followed Norman-Boudreau's technique in extraction of
diatoms from guts of abalone.  but he preserved his
diatom samples in distilled water instead of fixing it in
slides w/ high refractive media for enumeration of the
diatoms.  Can anybody react to this?  Anybody done
this procedure?  Will the samples stay preserved in
distilled water?  for how long?

AnnieOn Mon, Feb 24, 2014 at
11:24 AM, Stephen S. Nagy <snagymd@...>
wrote:















 









There are a number of articles here about
cleaning and collecting diatoms:  
http://www.diatomsireland.com/diatom-cleaning/?mobile=1

 Best
wishes,
Stephen
NagyHelena, MT

Sent from my
iPhone


Klaus Kemp <klaus.kemp@...>
 

Hello Annie,
    I will probably get hate mail after my posting, but be aware of what has happened to some of my samples. Firstly I have four major collections and frequently find samples that have clearly not been preserved and the tube is full of fungal hyphae, which has then to be recleaned, however the other thing I find frustrating is the sample which is preserved in Formaldehyde, this as has been explained to me by a chemist creates paraformaldehyde and causes any strew to create spurious images when mounted up and also sticks them down on the slide and prevents me picking them up. I am aware that Formaldehyde has now been kicked out of laboratories, however the best solution I have found to prevent fungus developement is a weak solution of Phenol which I know is also banned ( I can remember as a youth being told to gargle in a weak solution if I had a sore throat, fortunately I have survived this to a reasonable old age without any after effects)
    As to Diatom deterioation of samples stored in liquid, I have never found any damage to the finer structures or the alveoli of Mastogloia of which I have several hundred if not over a thousand SEM images, my question is why would an organism that thrives in a water environment choose to do so with a structure that disolves in that environment?
    If you follow the advice of no preservative, would you be kind enough to put a posting back to the group if your samples develop a fungal growth.
Regards
Klaus

----- Original Message -----
Sent: Friday, February 28, 2014 2:00 AM
Subject: Re: [diatom_forum] Re: Diatom Collecting & Cleaning For Beginners

 

Hello all,

I read in the article of Zhang et al. 2010 that he followed Norman-Boudreau's technique in extraction of diatoms from guts of abalone.  but he preserved his diatom samples in distilled water instead of fixing it in slides w/ high refractive media for enumeration of the diatoms.  Can anybody react to this?  Anybody done this procedure?  Will the samples stay preserved in distilled water?  for how long?

Annie


On Mon, Feb 24, 2014 at 11:24 AM, Stephen S. Nagy <snagymd@...> wrote:
 

There are a number of articles here about cleaning and collecting diatoms:  


 Best wishes,

Stephen Nagy
Helena, MT






This email is free from viruses and malware because avast! Antivirus protection is active.



Charles Suslavage
 

Hello Zlatko,
Thank you, very interesting.
I store my samples in distilled water plus alcohol and I have samples from another source that have been stored similarly and have not noted any problems. But I and my friend are only working with the light microscope.
I normally make three slides of any sample I acquire and if it is very interesting or rich with diversity I'll make six so I do not often return to my samples. My oldest sample is just five years old of Cocconeis. I'll make a new slide from this sample and compare it to the original slides, should be interesting.
Charles
From: Zlatko Levkov
To: diatom_forum@...
Sent: Friday, February 28, 2014 1:27 AM
Subject: Re: [diatom_forum] Re: Diatom Collecting & Cleaning For Beginners
 
Dear Charles
There is a problem with preservation of diatoms in distillate water. According to my experience, after a week or two, the diatoms start to dissolute and some valve are highly corroded. Such sample cannot be used for SEM at all, but also the slides made from older cleaned sample are with very low quality. I learned from the Hustedt collection in Bremerhaven (Hustedt kept only cleaned samples) that one possible solution is to keep the samples in glycerine. After cleaning the samples and several washing with water, we are discharging the water and a small amount of glycerine is added to the sediment (diatoms). Such conserved sample can be used for several years (at least). However, according to my experience the best way is to keep the original sample (not clean).
Hope this will help you to keep the samples little bit longer
Zlatko

--------------------------------------------
On Fri, 2/28/14, charles suslavage wrote:

Subject: Re: [diatom_forum] Re: Diatom Collecting & Cleaning For Beginners
To: "diatom_forum@..."
Date: Friday, February 28, 2014, 12:23 AM
















 









Hello
Annie,With respect to cleaned diatom samples
storing them in distilled water is the normal
procedure.The diatom frustule is made of silica
and as far as you and I are concerned will last forever when
stored in distilled
water.Charles 
From: "Franco,
Annie V."

To:
diatom_forum@...
Sent:
Thursday, February 27, 2014 6:00 PM
Subject: Re:
[diatom_forum] Re: Diatom Collecting & Cleaning For
Beginners
















 






Hello all,
I read in the article of Zhang et al. 2010 that
he followed Norman-Boudreau's technique in extraction of
diatoms from guts of abalone.  but he preserved his
diatom samples in distilled water instead of fixing it in
slides w/ high refractive media for enumeration of the
diatoms.  Can anybody react to this?  Anybody done
this procedure?  Will the samples stay preserved in
distilled water?  for how long?

AnnieOn Mon, Feb 24, 2014 at
11:24 AM, Stephen S. Nagy
wrote:















 









There are a number of articles here about
cleaning and collecting diatoms:  
http://www.diatomsireland.com/diatom-cleaning/?mobile=1

 Best
wishes,
Stephen
NagyHelena, MT

Sent from my
iPhone

























































Annie
 

Charles, Stephen and Zlatko:

Thanks so much for the info re distilled water use.  My intention is just to enumerate the diatoms i extracted from the guts. I'm trying to skip the slide fixation part. I got a full time job and got to sink my thesis work after.   I checked the samples and they are still readable after a month.  I hope to keep about 150 samples stored in distilled water (1mL) in 1.5mL vials for three months. That's enough time for me to do check them after working hours. 

I'd really love to do the slide fixation. Get new samples later.  Really amazed by diatom structures. hopefully I can do that after I graduate.

Annie F.



  


On Fri, Feb 28, 2014 at 4:23 PM, charles suslavage <suslavage@...> wrote:
 

Hello Annie,
With respect to cleaned diatom samples storing them in distilled water is the normal procedure.
The diatom frustule is made of silica and as far as you and I are concerned will last forever when stored in distilled water.
Charles 

From: "Franco, Annie V." <avfranco@...>
To: diatom_forum@...
Sent: Thursday, February 27, 2014 6:00 PM
Subject: Re: [diatom_forum] Re: Diatom Collecting & Cleaning For Beginners
 
Hello all,

I read in the article of Zhang et al. 2010 that he followed Norman-Boudreau's technique in extraction of diatoms from guts of abalone.  but he preserved his diatom samples in distilled water instead of fixing it in slides w/ high refractive media for enumeration of the diatoms.  Can anybody react to this?  Anybody done this procedure?  Will the samples stay preserved in distilled water?  for how long?

Annie
On Mon, Feb 24, 2014 at 11:24 AM, Stephen S. Nagy <snagymd@...> wrote:
 
There are a number of articles here about cleaning and collecting diatoms:  


 Best wishes,

Stephen Nagy
Helena, MT



Annie
 

Klaus,

 I will share my samples from preservation using distilled water alone... say after 6 months of preservation?  Only you guys could evaluate it as good material for fixation.

Thank you.

Annie F.  


On Fri, Feb 28, 2014 at 6:05 PM, Klaus Kemp <klaus.kemp@...> wrote:
 

Hello Annie,
    I will probably get hate mail after my posting, but be aware of what has happened to some of my samples. Firstly I have four major collections and frequently find samples that have clearly not been preserved and the tube is full of fungal hyphae, which has then to be recleaned, however the other thing I find frustrating is the sample which is preserved in Formaldehyde, this as has been explained to me by a chemist creates paraformaldehyde and causes any strew to create spurious images when mounted up and also sticks them down on the slide and prevents me picking them up. I am aware that Formaldehyde has now been kicked out of laboratories, however the best solution I have found to prevent fungus developement is a weak solution of Phenol which I know is also banned ( I can remember as a youth being told to gargle in a weak solution if I had a sore throat, fortunately I have survived this to a reasonable old age without any after effects)
    As to Diatom deterioation of samples stored in liquid, I have never found any damage to the finer structures or the alveoli of Mastogloia of which I have several hundred if not over a thousand SEM images, my question is why would an organism that thrives in a water environment choose to do so with a structure that disolves in that environment?
    If you follow the advice of no preservative, would you be kind enough to put a posting back to the group if your samples develop a fungal growth.
Regards
Klaus
----- Original Message -----
Sent: Friday, February 28, 2014 2:00 AM
Subject: Re: [diatom_forum] Re: Diatom Collecting & Cleaning For Beginners

 

Hello all,

I read in the article of Zhang et al. 2010 that he followed Norman-Boudreau's technique in extraction of diatoms from guts of abalone.  but he preserved his diatom samples in distilled water instead of fixing it in slides w/ high refractive media for enumeration of the diatoms.  Can anybody react to this?  Anybody done this procedure?  Will the samples stay preserved in distilled water?  for how long?

Annie


On Mon, Feb 24, 2014 at 11:24 AM, Stephen S. Nagy <snagymd@...> wrote:
 

There are a number of articles here about cleaning and collecting diatoms:  


 Best wishes,

Stephen Nagy
Helena, MT






This email is free from viruses and malware because avast! Antivirus protection is active.