Microscopy Thread

[EnterName]

This thread inspired me to buy a microscope. Just got it yesterday and here is a sample from a random spot of GHA.

It can be a very useful tool, but also simply an interesting way to observe our tanks from a different perspective. Sometimes you will see a lot of change in the microbiology while not noticing much going on on the macroscopic level in the tank, so it can help to pass some time when you have the feeling the tank is stalling a little bit

I'm seeing diatoms, a rotifer, and what I assume to be Prorocentrum sp. dinoflagellates. Do you happen to have a tank that's only a few months or so old?

 

[ScaredGoat]

I have had the tank since 1993, or so, and have always ran it FOWLR. It had a small leak that made me drain and reseal. I finally got around to doing that and got it going in mid March. Used all the old live rock that was dried out and new sand. I did a bleach soak on the old rock, etc. So to finally answer your question, yup I am smack dab in the "Ugly Phase".

 

[EnterName]

I have had the tank since 1993, or so, and have always ran it FOWLR. It had a small leak that made me drain and reseal. I finally got around to doing that and got it going in mid March. Used all the old live rock that was dried out and new sand. I did a bleach soak on the old rock, etc. So to finally answer your question, yup I am smack dab in the "Ugly Phase".

That explains what you were looking at quite well, so nothing to worry about then and no treatment required

 

[sixty_reefer]

Amoeboid
(Class: Tubulinea?)

Note: If you are using the app you might need to switch to a web browser to be able to see the video(s).​

Just recently I found a very small amoeboid organism in a sample from the back wall of my tank. Similar to the Heliozoa I posted the other day, amoeboids aren't a single taxonomic group, which makes classifying them a bit harder. This gets confusing because "Amoeba" is a general term for a group of organisms with no phylogenetic relation, but "Amoeba" is also a genus, which would already be a pretty precise classification.
Either way, I think I found a few hints to narrow it down to class level, but I haven't seen any reports of harmful amoeboids in reef tanks so far, so it probably doesn't matter too much anyway.

(Amoeboid moving on the microscope slide)​

Common Name	Amoeba
Classification	Class: Tubulinea?
Verdict	Harmless (no reported issues in reef tanks)
Size	2μm - 5mm (0.2")
Found	Detritus
Rarity	Medium (in every tank, but not abundant)

Amoebas move by extending so-called pseudopods ("false feet"), of which there are different types. In this case we have a "slug-like" movement with a smooth flow of endoplasm (the small "bubbles" inside the organism) and ectoplasm (the tiny particles at the edge of the organism). This movement, along with the fact that we don't see large branching pseudopods but rather small advancing blobs, is the first hint we need for classification. We can also see a "blob" (possibly a uroid) at the posterior end that stays fairly consistent in shape and looks like it's being dragged behind, which is another clue. From what I've read so far, these signs should put this amoeba in the Tubulinea class, but I haven't spent much time working through a taxonomic key yet, so I'm still cautious about that assessment.

Interesting. Given our recent discussion about observations versus claims, I’m curious about the evidentiary standard being applied here.

“Class: Tubulinea?” is an interpretation based on morphology and movement, which seems perfectly reasonable as a working hypothesis. But “Harmless (no reported issues in reef tanks)”, “Rarity: Medium” and particularly “in every tank” seem to go considerably further than the observation itself.

What evidence supports the claim that these organisms are present in every reef tank or that an unidentified amoeboid organism can be classified as harmless?

I’m not saying those conclusions are necessarily wrong. I’m asking what evidence supports them. Given the standards you’ve been asking me to apply to my own observations, I assume the same standard applies here.

 

[Reefering1]

Interesting. Given our recent discussion about observations versus claims, I’m curious about the evidentiary standard being applied here.

“Class: Tubulinea?” is an interpretation based on morphology and movement, which seems perfectly reasonable as a working hypothesis. But “Harmless (no reported issues in reef tanks)”, “Rarity: Medium” and particularly “in every tank” seem to go considerably further than the observation itself.

What evidence supports the claim that these organisms are present in every reef tank or that an unidentified amoeboid organism can be classified as harmless?

I’m not saying those conclusions are necessarily wrong. I’m asking what evidence supports them. Given the standards you’ve been asking me to apply to my own observations, I assume the same standard applies here.

Did you actually read the post you quoted?

 

[EnterName]

Interesting. Given our recent discussion about observations versus claims, I’m curious about the evidentiary standard being applied here.

“Class: Tubulinea?” is an interpretation based on morphology and movement, which seems perfectly reasonable as a working hypothesis. But “Harmless (no reported issues in reef tanks)”, “Rarity: Medium” and particularly “in every tank” seem to go considerably further than the observation itself.

What evidence supports the claim that these organisms are present in every reef tank or that an unidentified amoeboid organism can be classified as harmless?

I’m not saying those conclusions are necessarily wrong. I’m asking what evidence supports them. Given the standards you’ve been asking me to apply to my own observations, I assume the same standard applies here.

As you can see the taxonomic class is marked with a question mark. This is what I do when I'm uncertain about a classification, but if you read the text of the post you will see that I have explained what kind of morphological hints I used to come to this "conclusion" (movement, pseudopod shape, the shape at the end). These are rather "hints" than fixed rules, especially if only a few hints are used in combination, so I'm still careful until I find an appropriate taxonomic key that gives me reasonable certainty. It's very likely that this will never happen if it turns out that even DIC and staining techniques are insufficient for proper class-level identification which I could imagine.

You will see the question mark ? very often throughout this thread, especially for organisms that cannot be classified with light microscopy alone or are not that common in reef tanks (or rarely reported). Sometimes you will see a "cf." (Latin "confer" = "compare") instead, which is used when the organism looks like the given order/genus/species/whatever, but it hasn't been verified. This is a common practice but I have not gotten to upgrading all posts yet and people that are not familiar with the notation might understand the question mark better.

The presence in all reef tanks refers to amoeboids (the post's title). They are basically unavoidable, similar to Ciliates and Nematodes, regardless of freshwater, brackish water, or saltwater. You can find scientific sources if you are interested that explain how amoeboids are considered cosmopolitan microorganisms that are ubiquitous (see links below). I'm sure a biology book from middle school will tell you the same. It's certainly possible to set up a tank and not have any amoeba in there yet, but sooner or later they will be introduced. I assume you would have to take certain labor-intensive measures to avoid them.

• "Free-living amoebae (FLA) are cosmopolitan microorganisms [...]" https://pubmed.ncbi.nlm.nih.gov/36040629/ (even swimming pools seem to have amoeba from time to time)
• https://academic.oup.com/femsre/article/43/4/415/5484839

The "harmless" verdict refers to reported issues (that's why I added the part in parenthesis). I was not able to find anything about amoeboids in general or of that class to be causing issues in reef tanks, but will gladly change the verdict if you can provide new information. Obviously you don't want to ingest this specimen in any way, and the specimen itself could theoretically eat beneficial bacteria, zooxanthellae or be a parasite, but I can't know that without knowing the species so the verdict applies to amoeboids in general and/or of the class in general (hence the post title).

If you find something that is wrong according to your judgement and where I have not sufficiently supported a "claim", I will be happy to add sources or fix my mistake. If however you just come here for "revenge" because your thread got locked up after MULTIPLE people tried to warn you about your interpretations rather than ID attempts, I would kindly ask you to leave.

For the sake of this thread I won't engage in discussions in bad-faith and/or the recently locked down thread and will instead simply fix or provide sources for whatever you might dig up in your attempts to find something. This was all that what was asked of you and this is a standard I will live up to as good as I can. I could imagine I have forgotten a question mark somewhere or adjusted a classification but not the descriptive text, so just dig deep enough and you will certainly find something. Having someone check would greatly improve the quality of this thread, so I'm happy if someone helps me out a bit.

 

[sixty_reefer]

As you can see the taxonomic class is marked with a question mark. This is what I do when I'm uncertain about a classification, but if you read the text of the post you will see that I have explained what kind of morphological hints I used to come to this "conclusion" (movement, pseudopod shape, the shape at the end). These are rather "hints" than fixed rules, especially if only a few hints are used in combination, so I'm still careful until I find an appropriate taxonomic key that gives me reasonable certainty. It's very likely that this will never happen if it turns out that even DIC and staining techniques are insufficient for proper class-level identification which I could imagine.

You will see the question mark ? very often throughout this thread, especially for organisms that cannot be classified with light microscopy alone or are not that common in reef tanks (or rarely reported). Sometimes you will see a "cf." (Latin "confer" = "compare") instead, which is used when the organism looks like the given order/genus/species/whatever, but it hasn't been verified. This is a common practice but I have not gotten to upgrading all posts yet and people that are not familiar with the notation might understand the question mark better.

The presence in all reef tanks refers to amoeboids (the post's title). They are basically unavoidable, similar to Ciliates and Nematodes, regardless of freshwater, brackish water, or saltwater. You can find scientific sources if you are interested that explain how amoeboids are considered cosmopolitan microorganisms that are ubiquitous (see links below). I'm sure a biology book from middle school will tell you the same. It's certainly possible to set up a tank and not have any amoeba in there yet, but sooner or later they will be introduced. I assume you would have to take certain labor-intensive measures to avoid them.

• "Free-living amoebae (FLA) are cosmopolitan microorganisms [...]" https://pubmed.ncbi.nlm.nih.gov/36040629/ (even swimming pools seem to have amoeba from time to time)
• https://academic.oup.com/femsre/article/43/4/415/5484839

The "harmless" verdict refers to reported issues (that's why I added the part in parenthesis). I was not able to find anything about amoeboids in general or of that class to be causing issues in reef tanks, but will gladly change the verdict if you can provide new information. Obviously you don't want to ingest this specimen in any way, and the specimen itself could theoretically eat beneficial bacteria, zooxanthellae or be a parasite, but I can't know that without knowing the species so the verdict applies to amoeboids in general and/or of the class in general (hence the post title).

If you find something that is wrong according to your judgement and where I have not sufficiently supported a "claim", I will be happy to add sources or fix my mistake. If however you just come here for "revenge" because your thread got locked up after MULTIPLE people tried to warn you about your interpretations rather than ID attempts, I would kindly ask you to leave.

For the sake of this thread I won't engage in discussions in bad-faith and/or the recently locked down thread and will instead simply fix or provide sources for whatever you might dig up in your attempts to find something. This was all that what was asked of you and this is a standard I will live up to as good as I can. I could imagine I have forgotten a question mark somewhere or adjusted a classification but not the descriptive text, so just dig deep enough and you will certainly find something. Having someone check would greatly improve the quality of this thread, so I'm happy if someone helps me out a bit.

Thanks for clarifying. I’ve no issue with the question mark or using morphology to make a tentative ID.

My point was simply that “ubiquitous” doesn’t necessarily mean “in every reef tank” and “no reported issues found” isn’t quite the same as “harmless”. Those are still interpretations of the available information.

And no, it’s not revenge. I’m simply applying the same standards you’ve been asking me to apply to my observations. Seems fair enough.

https://pmc.ncbi.nlm.nih.gov/articles/PMC8065943/