Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

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Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#1 Post by linuxusr » Thu Sep 02, 2021 5:12 pm

Using “how to know the protozoa,” Second Edition, Jahn. I bought this book 25 years ago. It is now out of print but available used.

Infusion: alfalfa and timothy hay in aquarium water with a pinch of
peptone; a single ciliate type appeared after 24 hours.

w.m. with methyl cellulose
BF with 200x and 400x TM; video with Zeiss Axiocam 208 Color

I am guessing that locomotion is via cilia which appear to encircle the organism laterally.

The organism, when elongated, and slightly pear shaped, moves in a shallow parabolic curve, very rapidly, A to B, rotates in milliseconds, and returns B to A. It can also rotate on its horizontal axis. Other times, the specimen is spherical and rotates, slowly, 360 degrees, possibly ingesting bacteria.

The cytoplasm consists of hundreds of discrete bodies and are very dynamic. I don’t know what these bodies are but I doubt they are organelles. I don’t know if there are sol/gel interactions.
After viewing anatomy of Euplotes, these discrete bodies could be food vacuoles.

On the anterior surface appears to be a rotating ciliated crown. 1/5 body length distal from the posterior end is either a nucleus or a vacuole, I suspect, a nucleus.

A key feature of this specimen is an oral cavity, at a 45 degree angle, laterally, and from the ventral (dorsal) side appearing as a depression or dimple. Within the oral cavity and extending outside of the cell are three cirri.

1. with cilia indicates Phylum Ciliophora
2. with membranelles and cirri; membranelles in mouth; undulating membrane bordering oral zone; no cirri on body indicate Subphylum Oligohymenophora
3. typically there are three small membranelles in the lateral cavity that contains the mouth indicates Class Hymenostomea
4. mouth lateral and in a small buccal cavity indicate Order Hymenostomatida
5. Order Hymenostomatida includes 14 Families, one of which is Family Parameciidae. However, the shallow buccal cavity and three cirri of my specimen indicates Family Tetrahymenidae. By visual comparison of drawings species T. patula is a candidate.

I’d appreciate any additions or subtractions you could contribute. For one thing, there is a crying need for a dictionary of the biology of the eukaryotic cell. This is a sub-speciality within microbiology. However, when I google “dictionary of protozoology” I get a definition of protozoology! (I believe that protozoology is now deprecated in favor of protistology). Unfortunately, the key I am using has no glossary and the author frequently does not define anatomical terms. It is hard to make observations when you do now know what a word means. As an example, compare cirrus (cirri) and membranelle. Some sources say that they are synonymous; others that cirri are a type of membranelle but I cannot find a definition of the latter even though the author uses the term. Cirri, plural for cirrus, are sometimes described as a tuft of cilia. A single cirrus is a group of cilia fused together. When ventral, they may be used for locomotion. Since, here, in the buccal cavity, I suspect they play a role in ingestion.

At Amazon in the U.S. I have found Paul Singleton’s Dictionary of Microbiology and Molecular Biology, Second Edition, used, for about $28.00 USD. The Third Edition costs are whopping $154.00 USD. It’s impossible to preview this book virtually and there are no reviews, so it’s impossible to say if it will be useful or not.

This is my first timehttps://imgur.com/4fLlfPK linking to photo and video. Please let me know if you have problems or if you have suggestions.

1. https://imgur.com/4fLlfPK image

2. https://imgur.com/a/zCEhZQD video
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#2 Post by Bruce Taylor » Fri Sep 03, 2021 3:45 pm

As you've found, ciliatology has its own vocabulary and identification requires familiarity with some specialized anatomical terms. I understand that it can be frustrating. :) Luckily, a very good glossary is available. The late Denis Lynn included one in the 2nd edition of The Ciliated Protozoa (2008). https://www.springer.com/gp/book/9781402082382 All the terms that interest you are carefully defined, there. Digital copies are widely available.

The text you're using is more than forty years old, and gives a very abbreviated view of ciliate diversity. It's a good starting place, but ciliate taxonomy has changed a lot since it was written.
On the anterior surface appears to be a rotating ciliated crown.
Hymenostomes (including tetrahymenids) have nothing like this. Anterior ciliary wreaths (membranelles, typically) are found in a few major ciliate groups (oligotrichs, choreotrichs, peritrichs, some heterotrichs, some litostomateans), but not hymenostomes.

Tetrahymenids have a paroral membrane on the right side of the oral opening, and three polykinetids (short membranous ciliary groups) on the left side of the mouth. The latter are not normally described as "cirri" (which are usually conically tapered, functioning like little limbs). In the light microscope the paroral membrane is often fairly conspicuous. It looks like a small sheet or sail.

Your images are not too clear, unfortunately, but do not look like Tetrahymena, to me. A longer video would probably help, if you could upload footage to YouTube. I don't see enough to offer an alternative suggestion, but we do seem to see a few dangling cirri, which would point to something in class Spirotrichea, possibly an oligotrich.

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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#3 Post by linuxusr » Sat Sep 04, 2021 4:46 pm

Bruce Taylor wrote:
Fri Sep 03, 2021 3:45 pm
As you've found, ciliatology has its own vocabulary and identification requires familiarity with some specialized anatomical terms. I understand that it can be frustrating. :) Luckily, a very good glossary is available. The late Denis Lynn included one in the 2nd edition of The Ciliated Protozoa (2008). https://www.springer.com/gp/book/9781402082382 All the terms that interest you are carefully defined, there. Digital copies are widely available.

The text you're using is more than forty years old, and gives a very abbreviated view of ciliate diversity. It's a good starting place, but ciliate taxonomy has changed a lot since it was written.
On the anterior surface appears to be a rotating ciliated crown.
Hymenostomes (including tetrahymenids) have nothing like this. Anterior ciliary wreaths (membranelles, typically) are found in a few major ciliate groups (oligotrichs, choreotrichs, peritrichs, some heterotrichs, some litostomateans), but not hymenostomes.

Tetrahymenids have a paroral membrane on the right side of the oral opening, and three polykinetids (short membranous ciliary groups) on the left side of the mouth. The latter are not normally described as "cirri" (which are usually conically tapered, functioning like little limbs). In the light microscope the paroral membrane is often fairly conspicuous. It looks like a small sheet or sail.

Your images are not too clear, unfortunately, but do not look like Tetrahymena, to me. A longer video would probably help, if you could upload footage to YouTube. I don't see enough to offer an alternative suggestion, but we do seem to see a few dangling cirri, which would point to something in class Spirotrichea, possibly an oligotrich.

Wilfred Bion, the English psychoanalyst said that truth is more important than cure. The analogy is not perfect but whether or not I can identify this specimen (“cure”) at least you have set me on the path of finding tools (“truth”) what will help me with identification in the future, so thanks for your suggestions and recommendations. Of course, the field of view is very narrow here because our discussion is limited to only one phylum, Phylum Ciliophora, and there remains Phyla Mastigophora, Sarcodina, and Mastigophora as well as the algae, all of the above include specimens that we might find in our infusions and natural resources.

You referenced Denis Lynn’s, Second Edition, The Ciliated Protozoa(2008) as being indispensable for a glossary of biological terms of which I am in much need. However, this text is not available on the Net as a free .pdf download. I tried well over 100 links using Google, Bing, and duckduckgo search engines. Nearly 100% of links are to spurious sites, possibly phishing cites, that ask for registration prior to downloading. I tried registering on multiple cites, only to be offered iPhone prizes, solicitation of credit card information, etc. One site, laughably, was named LibraryofBook [ sic ].

However, I was able to download useful bits and pieces of his text. Here I note that there are three editions and the one you cite is the second. Lynn gives a useful summary of the three editions in a document titled 2008_bookmatter_TheCiliatedProtozoa.pdf Alas, I failed to copy/paste the URL of this Preface to the second edition, so I think it will be useful to quote the first part here:

Soon after I began graduate studies in Protozoology
at the University of Toronto in September 1969,
Jacques Berger brought in his copy of the First
Edition of “The Ciliated Protozoa” as required
reading. This book synthesized the “state of knowl-
edge” of ciliate systematics at that time, and
it brought the formal study of ciliate diversity,
especially in its nomenclatural aspects, to a highly
professional level. In the following decade events
occurred that set me on the path to pursuing ciliate
research. John Corliss, the author of that little-big
ciliate book visited Jacques in Toronto, and I met
him. John suggested that I visit Gene Small at the
Department of Zoology, University of Maryland,
USA. In 1971, I met Gene, whose enthusiasm for
“these wee bugs” was infectious, and whose intui-
tive grasp of the systematic significance of particu-
lar features was marvellous. I resolved to return to
Maryland to work with Gene, taking a “sabbatical”
leave from my doctoral thesis research to do so.
There was, of course, another wonderful reason for
the move to Maryland in September 1972 – I had
met Dr. Portia Holt who, at the time, was working
as a postdoctoral fellow with Dr. Corliss. So the
1972–1973 period was a rich experience of immer-
sion in ciliate systematics, coupled with immersion
in my developing relationship with my future wife,
Portia. During this time, John Corliss, Head of the
Department of Zoology, provided financial assist-
ance as well as academic support. At that time,
John was beginning preparations for the Second
Edition of “The Ciliated Protozoa”, having just
co-authored a major revision of the ciliate mac-
rosystem with his colleagues in France. By 1974,
these co-authored and authored papers on the new
macrosystem were published, including his paper
entitled “The changing world of ciliate systemat-
ics: historical analysis of past efforts and a newly
proposed phylogenetic scheme of classification
for the protistan phylum Ciliophora”. This was the
“Age of Ultrastructure,” as John called it, but the
“newly proposed phylogenetic scheme” was only
moderately influenced by these new data.
While in Maryland, Gene Small and I became
deeply involved in discussing the implications of
ultrastructural features, and these discussions lead
to my publication of “the structural conservatism
hypothesis” in 1976. Applying that idea, Gene and
I proposed a radically different macrosystem for
the ciliates in 1981, which I supported by a major
review of the comparative ultrastructure of ciliate
kinetids, demonstrating the conservative nature
of these important cortical components. While
ultrastructural study still formed an element of my
research program in the 1980s, Gene encouraged
me to consider moving into molecular phylogenet-
ics to test the robustness of our ideas, which had
now been slightly modified with publication of
the First Edition of “An Illustrated Guide to the
Protozoa”. In an ultimately productive sabbatical
year in 1986–1987, I worked with Mitch Sogin
at the National Jewish Hospital, Denver, to learn
the techniques of cloning and sequencing. Mitch
and I were finally able to provide one of the first
larger comparative datasets on genetic diversity
of ciliates based on the small subunit rRNA gene
sequences, derived at that time by reverse tran-
scriptase sequencing. On the other side of the
Atlantic, our colleagues in France, led by André
Adoutte, were using the same approach with the
large subunit rRNA gene and generating an even
larger dataset. Both approaches demonstrated two
things: firstly, confirmation that the ultrastructural
approach informed by structural conservatism was
providing resolution of the major natural assem-
blages or clades of ciliates; and secondly, genetic
distances between groups of ciliates were as vast as
the genetic distances between plants and animals
– THE major eukaryotic kingdoms at that time!


Following the Preface in this .pdf are the chapters and detailed subheadings. (Can I make this text document available to you via upload? I don’t see such a menu item.)

Lynn’s second edition is available at Amazon for about $250.00. Confusingly, one can also find The Ciliated Protozoa: Characterization, Classification and Guide to the Literature
by John O. Corliss for the much lower price of less than $75.00 new. Understanding the difference between Lynn’s and Corliss’ second edition is most confusing. John O. Corliss is a name that looms much larger than Lynn’s. For example, I have an article from International Journal of Systematic and Evolutionary Microbiology (2003), 53, 1707–1714 titled The collapse of the two-kingdom system, the rise of protistology and the founding of the InternationalSociety for Evolutionary Protistology (ISEP) In that article, J.O. Corliss is cited 12 times and Lynn not once.

Lynn’s second edition is also available on https://www.springer.com/la/book/9781402082382 for $249.00 in softcover and $349.00 in hardcover. It is sad that for us amateurs that the most indispensable works are prohibitively expensive. However, there is an option here. For $29.95 each I can download the chapter “Glossary of Terms and Concepts Useful in Ciliate Systematics” as well as “The Ciliate Taxa Including Families and Genera.” There’s no way to know if Corliss’ book includes the glossary. I might buy that first and, if not, then add these chapters for a total cost of $75.00 - $135.00 unless one of you can provide me the link to the entire .pdf!

An additional somewhat useful resource is Wikipedia’s article on Phylum Ciliophora https://en.wikipedia.org/wiki/Ciliate

(to be continued)
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#4 Post by Wes » Sat Sep 04, 2021 6:42 pm

linuxusr wrote:
Sat Sep 04, 2021 4:46 pm
You referenced Denis Lynn’s, Second Edition, The Ciliated Protozoa(2008) as being indispensable for a glossary of biological terms of which I am in much need.
Voilá!

edit
Last edited by Wes on Sun Sep 05, 2021 8:38 am, edited 1 time in total.
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#5 Post by 75RR » Sat Sep 04, 2021 7:48 pm

Wes wrote:
Sat Sep 04, 2021 6:42 pm
linuxusr wrote:
Sat Sep 04, 2021 4:46 pm
You referenced Denis Lynn’s, Second Edition, The Ciliated Protozoa(2008) as being indispensable for a glossary of biological terms of which I am in much need.
Voilá!
Can you recheck link, not working for me.
Last edited by 75RR on Sun Sep 05, 2021 9:43 am, edited 1 time in total.
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#6 Post by Wes » Sat Sep 04, 2021 8:05 pm

75RR wrote:
Sat Sep 04, 2021 7:48 pm
Can you recheck link, not working for me.
It works fine but might be blocked by the ISP in certain jurisdictions. Try a proxy server, a VPN or the Tor browser.
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#7 Post by linuxusr » Sat Sep 04, 2021 11:58 pm

Wes wrote:
Sat Sep 04, 2021 8:05 pm
75RR wrote:
Sat Sep 04, 2021 7:48 pm
Can you recheck link, not working for me.
It works fine but might be blocked by the ISP in certain jurisdictions. Try a proxy server, a VPN or the Tor browser.
@Wes
@75RR

Voilá! is the word! I have the complete text at 11.7 MB. Great! The link worked for me and I did not use a VPN. The path that worked for me: Click on the text icon < Click on Cloudfare gateway.

Worked immediately. I am in the Dominican Republic. There are two other gateways. They bypass the Tor option. The link's webpage describes multiple options for downloading.
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#8 Post by linuxusr » Mon Sep 06, 2021 12:26 am

@ Bruce Taylor

Now that we have the link and text of Denis Lynn, I did find very clear definitions of types and functions of cirri as well as a definition of membranelle. You are correct that Jahn's work, "how to know the protista," Second Edition, is dated, being about 40 years old. I note his citation of Corliss, J.O. 1961. The Ciliated Protozoa. Jahn cites J. Protozoology, 1964 of the Society of Protozoologists for the latest "accepted" taxonomy of the protista. Jahn makes several changes and in his scheme he identifies the Protista as a Kingdom, the Protozoa as a Subkingdom, and these phyla: Phylum Ciliophora, Sarcodina, Mastigophora, and Sporozoa. Is the taxonomy of the protista through this level of generalization now obsolescent? Is there an agreed upon and available taxonomic key that we at Microbe Hunters can agree upon so that we can speak the same language as we reference specimens?

Taxonomy is one thread of Jahn's work. The other thread is the morphology of representative specimens with descriptions and diagrams. These anatomical features are unchanging unless viewed under the the broad expanse of evolutionary time. Further, we as amateur microscopists, are limited to LM observations and not EM observations or the observations that Lynn investigates of "ultrastructure" and the sequencing of ribosomal RNA. We can study these things but they are out of our field of view when we look through our light microscopes. So I do think that Jahn's book is useful for recognizing anatomical features that we observe in common.

I have uploaded videos of the same specimen to YouTube. Maybe these are better:

https://youtu.be/osPJd2scteg
https://youtu.be/opb2UHAX11A
https://youtu.be/dM9QegmQrpU

Meanwhile, I'm going to learn how to do video editing in Linux so I can produce better videos of specimens in the future. What I'm lacking now is an agreed upon (if that's possible) key. What do you use?? I think that fixing a taxon as an end in itself is not that interesting although it is certainly necessary to have an identification. More interesting, I think, is the behaviour and anatomy of the specimens we look at.
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#9 Post by Bruce Taylor » Wed Sep 08, 2021 1:44 pm

linuxusr wrote:
Mon Sep 06, 2021 12:26 am
Jahn cites J. Protozoology, 1964 of the Society of Protozoologists for the latest "accepted" taxonomy of the protista. Jahn makes several changes and in his scheme he identifies the Protista as a Kingdom, the Protozoa as a Subkingdom, and these phyla: Phylum Ciliophora, Sarcodina, Mastigophora, and Sporozoa. Is the taxonomy of the protista through this level of generalization now obsolescent?
Yes, very obsolescent. :D

Sarcodina was found to contain a dog's-breakfast of amoeboid organisms from all over the eukaryote tree, so it was abandoned. Its organisms are now distributed in a variety of unrelated groups, including Amoebozoa, Cercozoa, Opisthokonta and Heterokonta (stramenopiles).

Mastigophora was a catch-all for flagellated organisms. However, it turns out that having flagella is the ancestral condition of all eukaryotes, and flagellated forms occur in every major group. As a taxonomic concept for high-level classification, it is useless.

Sporozoa was a similar mishmash of organisms, which are now placed in Apicomplexa, Fungi, Rhizaria...and even Animalia!

Ciliophora...well, that one turned out to be a natural (monophyletic) group! :D It is still with us, as a phylum under the supergroup Alveolata, under the clade SAR (stramenopiles, Alveolata, Rhizaria).
Is there an agreed upon and available taxonomic key that we at Microbe Hunters can agree upon so that we can speak the same language as we reference specimens?
High-level classification is a work in progress. The International Society of Protistologists endorses an unranked classification scheme that is updated every few years as new phylogenetic information comes in. The current version is here: https://onlinelibrary.wiley.com/doi/ful ... /jeu.12691

There are quite a few ranked schemes, most of which accept some "non-natural" (i.e. non-monophyletic) groups, such as "Kingdom Protozoa" and "Kingdom Chromista." A fairly typical ranked scheme is used on the World Register of Marine Species (WoRMS): https://www.marinespecies.org/

For ciliates, the classification used in Denis Lynn's book is largely current (though there have been changes, since then). A fairly up-to-date ciliate taxonomy is available here: https://www.nature.com/articles/srep24874 That one has a very nice graphic showing all the classes and orders in Ciliophora.

Shortly before his death, the great ciliatologist Wilhelm Foissner made most of his work available through his website. See: http://www.wfoissner.at/publications.htm and http://www.wfoissner.at/data_prot/

An old work that remains very useful is Kahl's 4-volume revision of the ciliates. I've scanned my own copy and uploaded it to Internet Archive: https://archive.org/search.php?query=wi ... er+ciliata

There are other handy texts...too many to list, though I should mention the excellent genus keys in Curds et al., British and other Freshwater Ciliated Protozoa. https://www.amazon.ca/British-Other-Fre ... 0521285585

The most useful resource of all is: https://scholar.google.com/ ;)
So I do think that Jahn's book is useful for recognizing anatomical features that we observe in common.
It's definitely still useful! It's very sketchy and incomplete, though. Some 8,000 nominal species of ciliate have been described, and there could be another 30,000 undescribed ones out there. No "field guide" can do justice to that kind of diversity.

Also, many groups that were identified in the light microscope have undergone big changes. Vorticella has become difficult to identify in simple LM, because many traditional species actually belong in the genus Pseudovorticella. Trachelophyllum can no longer be reliably identified without electron microscopy. Dileptus has been split into half a dozen genera (Pseudomonilicaryon, Rimaleptus, etc.).

So, it's best to think of books like Jahn's as stepping stones to further research. :)

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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#10 Post by linuxusr » Wed Sep 08, 2021 4:10 pm

@ Bruce Taylor

Your thoughtful and carefully researched response is much appreciated. I will be digesting and getting back to this thread in a couple of days . . .
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#11 Post by linuxusr » Sat Sep 11, 2021 6:33 pm

@Bruce Taylor

I have viewed and downloaded from most of your links.

Since high level classification is a work in progress, as you state, the conclusion to be drawn is that we in the forum as amateur microscopists, at best, can do no better than to agree on a provisional taxonomy. Hopefully, after digesting your sources, we may be able to do that. In order to clarify a usable taxonomy for the protista (eukaryotes), I am reading the “Revisions” article (2018), from The Journal of Eukaryotic Biology. As you indicated, the research represented in this article is under the auspices of The International Society of Protistologists. Secondly, I am reading the Science Reports article from nature on revisions in the phylum Ciliophora. After reading these two sources I want to look at how they reconcile, or do not, with the taxonomy presented in Lynn (and Corliss’) Third Edition The Ciliated Protozoa.

Want I will want to know as I do these readings is if Lynn’s presentation will serve as a usable protist taxonomic bible, for the time being, or, if not, what changes should be adapted to Lynn’s work based on these readings.

Meanwhile, using Lynn, I am thinking about a way I might cobble together a key that I could use in place of Jahn’s. This key would begin with pictures and then proceed to text. As they say, “A picture is worth a thousand words.” Jahn even suggests as a method, instead of using the key, just to flip through the pages, looking at the figures, and trying to find a match. This is much faster than reading text. Lynn not only has TEM images of representatives of each Class, but also drawings for representative Families within each Class. Using Linux with a one button PrtSc, it took me only one hour to go through the whole book snapping screenshots of all the pictures.

I then created two folders, one for each of his subphyla for phylum Ciliophora. In one subphyla are only about two classes and in the other about ten. Per each subphylum folder, I then make a folder which I label by its Class, one folder per Class. Since Lynn devotes one chapter to each Class, it’s very easy to take screenshots of pictures of representatives for each class. Also I screenshot the first page of each chapter which encapsulates a brief introduction to that class, for example, maybe the key feature is that they are sessile.

The procedure would be something like this: a. View generic images of all classes; select most probable classes, b. Look at representative images for each of these classes. Select most probable class and image. c. Proceed to text and try to identify by morphology.

I have photographs and videos of some specimens that are very distinctive. I will try this method and see if I can get an identification.

What do you think about this idea?

If we can agree on a usable taxonomy, I think I’ll go to the website sub-forum and suggest a “sticky” for taxonomy.

Oh, and when you say “great” that is an understatement for that prolific Austrian scholar W. Foissner! And kudos to him that he permits downloads of entire texts on our subject for educational use. Down the line I will also suggest a sticky for reference and study links that are now scattered around the MH website, buried in various posts.

After I read the two articles mentioned and see what alterations to Lynn may be necessary as well as try out my informal key method, I’ll post back.
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#12 Post by linuxusr » Sun Sep 12, 2021 10:27 pm

@ Bruce Taylor
@ Et al

I am still working on the above. Meanwhile, does anyone have a link for a .pdf for Lee's An Illustrated Guide to the Protozoa, Second Edition? It costs more than $150.00 on Amazon and I cannot preview it. On the face it says that it is published under the auspices of the Society of Protozoologists. When I search this society I find that it has been renamed the International Society of Protozoologists or ISOP. In 1954 this society began publishing the Journal of Eukaryotic Microbiology The website of the society is protistologists.org When you go to this site you will find Lee's Second Edition for sale, This indicates to me that the Second Edition is the last edition. Also you are asked to contact someone if you are interested in purchase. Ha! Compare that with W. Foissner who makes his works available for educational use . . .
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#13 Post by linuxusr » Tue Sep 14, 2021 11:10 pm

@Bruce Taylor

The task I set for myself was to use some of the taxonomic articles you suggested to see if they corroborated, or not, the taxonomy suggested by Lynn in his “The Ciliated Protozoa,” Third Edition.

The comparison articles I used were from Scientific Reports, 2016, on the data based evolutionary hypothesis of cilitated protists with a revised classification of phylum Ciliophora. I paraphrased the title as it is available in the foregoing link; and “Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes” from Journal of Eukaryotic Biology, 2018; and "Monograph of the Spathidiida", Foissner and Xu, 2007.

The taxon I want to corroborate in Lynn is CLASS. As you ascend taxa, morphology becomes more distinctive. This becomes obvious when you descend taxa and see that at the species level that morphological differences are the least distinctive. I figure if I can begin a specimen identification with CLASS, that that’s a good starting point. We shall see if that is the case when I start my crude but simple pictorial key method using Lynn.

Indeed, with a few exceptions, there is corroboration.

The “Revisons” article pertains to eukaryotes and is a 2012 update from ISOP (International Society of Protozoologists). The authors confirm the two subphyla of Lynn, POSTCILIODESMATOPHORA and INTRAMACRONUCLEATA which the authors of “Revisions” describe as branches but not subphyla. I assume that “branch” and “clade” are synonymous. Of the eleven CLASSES described by Lynn, the authors of “Revisions” agree with nine of them (as CLASSES). The exceptions are that two CLASSES of Lynn, the HETEROTRICHIDA and ARMORPHOREA, are identified as Orders by the former authors. And the same authors add a CLASS absent in Lynn, the PROSTOMATEA.

On the whole, then, the CLASS designations of Lynn and these ISOP authors are in agreement. A few other points in this article that I wish to draw attention to:

(1) Historically, the International Code for Zoological Nomenclature was the body responsible for protista taxonomy whereas algae, plants, and fungi were under the auspices of the International Code of Nomenclature for Algae, Fungi, and Plants. These codes are now deprecated,

(2) Criticism and rejection of prokaryotic/eukaryotic taxonomy, Ruggiero, 2015,

(3) The eukaryotes form two domains: a. Amorphea, b. Diaphoretickes. N.B. I find it puzzling that here, and in Lynn, that no mention is made of taxa and their relationships above the level of CLASS. It’s probably assumed knowledge which I lack. Can you speak to this, Bruce? And, currently, what is the status of Kingdom Protista; Subkingdom Protozoa?

(4) With respect to my N.B., the authors of “Revisions” make an important point. There are, in a sense, two taxonomies of the eukaryotes that operate in parallel and at different rates. One incorporates phylogenetic trees whose foundation rests on genetic sequencing of various proteins. But, based on these studies, when a new relationship is discovered and there needs to be an official change in the nomenclature, the ISOP must vote and reach agreement. Likely, I’m thinking, there must be publishing and peer review as well. This is a slow process. And that is why in parallel to this slowly emerging taxonomy, there will always be a second taxonomy, in part obsolescent, that is used for heuristic purposes, for the classroom. People must have a common language they can use even if, in future, some of those terms and relationships will change.

I was most surprised to find appended to this article, Table 2, a taxonomy of eukaryotic and multicellular organisms, including H. sapiens, and dated to 1758, Linnaeus! (H. sapiens is described as the least inclusive clade!) All taxa naming include the discoverer. Besides many historical taxa, one finds many from the 21st century; discoveries based on TEM, molecular biology, and genetic sequencing are well represented as well.

I have to study more to understand this taxonomy but there’s much that’s very clear in the descriptions and there’s a good chance that this Table 2 could be used in concert with the text of Lynn.

Now turning to the Scientific Reports article. Two already extant branches are equivalent to Lynn’s two subphyla. These authors add a third branch, the Mesodiniea, basal to the two above branches. These authors confirm seven of Lynn’s twelve classes as monophyla. The other four classes of Lynn are not mentioned! Except for these “missing classes,” these authors more or less corroborate Lynn’s Third Edition taxonomy.


Foissner and Xu’s “Monograph of the Spathidiida (Ciliophora, Haptoria) . . . “ describes taxa from Family through species. I am saving identification from the Family level and down (and the corroboration question) for another day.

I’m now going to start identification of speciments (eukaryotes) using Lynn’s pictorial identifications of CLASS, then if successful there, proceeding downward through lower taxa and the more detailed written descriptions. I’m only going to select specimens that have some outstanding morphology rather than being nondescript.
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#14 Post by Bruce Taylor » Sat Sep 18, 2021 11:25 am

linuxusr wrote:
Sun Sep 12, 2021 10:27 pm
@ Bruce Taylor
@ Et al

I am still working on the above. Meanwhile, does anyone have a link for a .pdf for Lee's An Illustrated Guide to the Protozoa, Second Edition? It costs more than $150.00 on Amazon and I cannot preview it.
I don't think digital copies exist. The 2 volumes contain contributions from many individuals, and it is possible that ISOP is not at liberty to provide free copies? They used to give away hard copies to new members. It's a nice book to have, but it is about 20 years old, now, and much of it was out of date already on the day it was published. In any case, the information it contains is all available elsewhere.

Another big, fat compendium to look for is the Handbook of the Protists: https://www.springer.com/gp/book/9783319281476 That one is available in digital form.

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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#15 Post by Wes » Sat Sep 18, 2021 11:35 am

Bruce Taylor wrote:
Sat Sep 18, 2021 11:25 am
Another big, fat compendium to look for is the Handbook of the Protists: https://www.springer.com/gp/book/9783319281476 That one is available in digital form.
This one is truly great, and you can get it for free.
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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#16 Post by Bruce Taylor » Sat Sep 18, 2021 11:44 am

The “Revisons” article pertains to eukaryotes and is a 2012 update from ISOP (International Society of Protozoologists).
The 2019 revision is based on the 2012 classification, which was itself a revision of Adl et al., 2005. The organization used to be called the International Society of Protozoologists, but in 2005 members voted to change the name to the International Society of Protistologists.
The authors confirm the two subphyla of Lynn, POSTCILIODESMATOPHORA and INTRAMACRONUCLEATA which the authors of “Revisions” describe as branches but not subphyla.
Those subphyla have broad acceptance. Note that Lynn was among the authors.
And the same authors add a CLASS absent in Lynn, the PROSTOMATEA.
Lynn accepts Class Prostomatea. See Chapter 13, p. 257.
(2) Criticism and rejection of prokaryotic/eukaryotic taxonomy, Ruggiero, 2015,
Ruggiero et al., 2015 takes a very different approach to classification, accepting paraphyletic groups such as Cavalier-Smith’s “Kingdom Protozoa”, in order to preserve familiar groups such as Kingdoms Animalia and Fungi (both of which are submerged in Opisthokonta, in purely phylogenetic classifications, commingled with “protozoan”) groups like choanoflagellates and nucleariids). The scheme was adopted as the basis of classification on Catalogue of Life (Michael Ruggiero was chairman of the global team on that project), and is influential on some other databases.
(3) The eukaryotes form two domains: a. Amorphea, b. Diaphoretickes. N.B. I find it puzzling that here, and in Lynn, that no mention is made of taxa and their relationships above the level of CLASS. It’s probably assumed knowledge which I lack. Can you speak to this, Bruce? And, currently, what is the status of Kingdom Protista; Subkingdom Protozoa?
To your first question, Lynn does include two taxa above class, as mentioned above…the subphyla Postciliodesmatophora and Intramacronucleata. However, since Ciliophora is itself a phylum, he would not have any reason to mention the groups above it (Alveolata, SAR and TSAR).

To the second question, there are still people who use “Kingdom Protista”. It is considered obsolete by many, but it still appears in some high school biology curricula, and you’ll often run across it in educational texts and websites. Of course, the lower-case “protist” is widely used as a term of convenience for “organisms that are not plants, animals or fungi”; and “protistologist” is a handy word for the people who study such things. However, Protista is not a natural (monophyletic) group, because its members are widely dispersed across the eukaryote tree. The most recent ancestor of all protists would also be the most recent ancestor of all eukaryotes. So, the only natural group that would be comprehensive enough to include all so-called “protists” would be Eukaryota itself!

Kingdom Protozoa is still used as a formal taxon by some people. Thomas Cavalier-Smith kept a stripped-down version of it, which actually excludes such classic “protozoa” as ciliates, dinoflagellates and apicomplexans (e.g. the parasite that causes malaria)! This is the “Kingdom Protozoa” that we see in Ruggiero et al., 2015. You’ll see it in use on Catalogue of Life, as noted above, and on the World Registry of Marine Species, and on iNaturalist (where I curate ciliates).
And that is why in parallel to this slowly emerging taxonomy, there will always be a second taxonomy, in part obsolescent, that is used for heuristic purposes, for the classroom. People must have a common language they can use even if, in future, some of those terms and relationships will change.
Hence the wide acceptance of Ruggiero et al., 2015. I don’t like the system much, but I recognize its usefulness for general-purpose educational resources, where people expect to see Animals, Plants and Fungi given high status.
Now turning to the Scientific Reports article. Two already extant branches are equivalent to Lynn’s two subphyla. These authors add a third branch, the Mesodiniea, basal to the two above branches.
Recent work has called that into question, and (for now) genus Mesodinium has been restored to Litostomatea, where Lynn had it (https://doi.org/10.1093/gbe/evz233).
Foissner and Xu’s “Monograph of the Spathidiida (Ciliophora, Haptoria) . . . “ describes taxa from Family through species.
But that book only covers spathidiids, a specific group of haptorian ciliates. Note, too, that Foissner and his Austrian colleagues tend to use nomenclature that differs somewhat from that of Lynn at the higher ranks. For instance, they use the group Gymnostomatea where most scholars would use Litostomatea, and have never adopted Lynn & Small’s subclass Stichotrichia (which Gao et al., 2016 have also abandoned, incidentally).

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Re: Keying a Ciliate: Probable Candidate for Family Tetrahymenidae

#17 Post by Bruce Taylor » Sat Sep 18, 2021 12:45 pm

linuxusr wrote:
Tue Sep 14, 2021 11:10 pm
The taxon I want to corroborate in Lynn is CLASS. As you ascend taxa, morphology becomes more distinctive. This becomes obvious when you descend taxa and see that at the species level that morphological differences are the least distinctive. I figure if I can begin a specimen identification with CLASS, that that’s a good starting point. We shall see if that is the case when I start my crude but simple pictorial key method using Lynn.
I’m generally in favor of “top-down” identification, where possible, but Lynn’s classes are not a very useful starting place for identification in the light microscope. For example, there are no inherited morphological features (synapomorphies) that define Oligohymenophorea. It is probably a valid group (it is supported by molecular analysis), but it contains ciliates as different-looking as the peritrichs (e.g. Vorticella) and the peniculids (e.g. Paramecium), not to mention the long-bodied philasterids, or the mouthless Astomatia! The class Phyllopharyngea contains flat, mobile basket-mouthed creatures like Chilodonella…and sessile tentacled creatures like the Suctoria. Spirotrichea includes the loricate funnel-shaped tintinnids, but also flattened "walking ciliates" like hypotrichs and euplotids. And so on.

I don't know whether you're familiar with the pictorial keys Foissner and his collaborators made for their revision of ciliate "indicator species". If not, you should have a look: https://onlinelibrary.wiley.com/doi/abs ... .tb01775.x Their key and the 4-volume work it references are not comprehensive. The monographs are (mostly) restricted to ciliates listed by ecologist Sladacek as useful indicators of water quality. However, the authors use similar keys in other works. For instance, there is one in Foissner & Berger's book on freshwater plankton ciliates: https://www.researchgate.net/publicatio ... n_Ciliates

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