EFFORT TO CATALOGUE EVERY MICROBE ON EARTH.

THE MICROBES LIVING on Earth are so plentiful as to be innumerable. Untold. Countless. Not in the hyperbolic sense, but the literal, gobsmacking sense. "It's estimated there are 100 million times as many bacteria as there are stars in the universe," says microbiologist Rob Knight, director of UC San Diego's Microbiome Center for Innovation. "And we know almost nothing about most of them."

https://www.wired.com/story/the-crazy-ambitious-effort-to-catalogue-every-microbe-on-earth/

Posted by biohexx1 biohexx1, November 02, 2017 08:40

Comments

This project is a good idea, as it groups together microscopic observations that would otherwise be distributed across the tree of life.

I noticed something lacking here.


Consider the following two pairs of taxa:

Phylum Tardigrada, Class Heterotardigrada (mainly marine) = 68 observations
Phylum Tardigrada, Class Eutardigrada (mainly freshwater) = 532 observations

. . . freshwater tardigrades are 7.8 times more frequently observed than their marine counterparts.

Phylum Gastrotricha, Order Macrodasyida (mainly marine) = 1 observation
Phylum Gastrotricha, Order Chaetonotida (mainly freshwater) = 195 observations

. . . freshwater gastrotrichs are 195 times more frequently observed than their marine counterparts.


And consider the following exclusively marine microbe phyla:

Chaetognatha = 67 observations
Kinorhyncha = 8 observations
Loricifera = 0 observations
Placozoa = 0 observations


In this project, and on iNaturalist more generally, I think marine microbes are less often observed. Is that because marine microbes are actually less common, or are there biases in sampling? Whatever the cause, I think more should be done to make up for this. Wouldn't it be great to make the first Loricifera observation on iNaturalist? I intend to start sampling more marine material in a targeted effort contribute some interesting observations, and I hope others will too.


Tagging some prominent contributors to this project:

@shanesmicroscope
@roman_romanov
@bdstaylor
@plingfactory
@mnold1
@zookanthos
@sarka
@jane_trembath
@w_martin

Posted by jameskdouch about 1 year ago (Flag)

Not everyone has easy access to coastal regions (https://www.un.org/sustainabledevelopment/wp-content/uploads/2017/05/Ocean-fact-sheet-package.pdf). I'm based only <10 miles from the ocean and <5 miles from an estuary, both with public access, so I have no excuse. I'm especially interested in algae, so I hope to answer your call, @ypna, for more representative biota from a marine environment... with an algal bias. I'm in!

Posted by mnold1 about 1 year ago (Flag)

Yes, I grew up far inland and ocean has always seemed foreign to me. I mean no blame on people who can't access the coast, and no blame on people who can, for that matter. We're all volunteers here and if you find freshwater more interesting, that's fine. But if you don't mind, I suspect the average drop of salty water is more likely to push iNaturalist's boundaries than fresh.

Sorry I only mentioned animals above. I have less knowledge of algae, but if my generalisation holds true, I suspect marine algae are under-represented as well.

It's great to hear you're interested in looking at marine water.

Posted by jameskdouch about 1 year ago (Flag)

The disparity is certainly due to access. People observe what is around them. A human cannot exist without access to freshwater, so it's not surprising that we observe freshwater more. An argument could be put forth that we have more to gain from an understanding of our local environment, in any case, so I don't view this disparity as a problem.

Waxing philosophical (and technical), one might also wonder if the coast is very representative of marine water. I think not, though for the reason stated above, I think the coast is a sensible thing to study if you are on the coast.

The real struggle we face here, IMHO, is one of identification. Every user knows what a bird looks like, often several species of them, but even an experienced microscopist with access to identification resources (another huge problem for the amateur and a whole other topic) can look at something under the microscope and wonder, "What phylum does this even belong in? Is this even life?". Someone posts a blurry bird picture, and within a short time span there are many IDs. I can do my best to document a microscopic specimen with 15 images and several GIFs, and I feel extremely grateful if I ever get a single ID beyond my own. This is not a complaint, but an objective observation of the hurdle we face.

To add to the challenge, the fresh/salt water disparity extends to the literature required to identify as well, purely (again) because of access.

All of that said, we cannot control our curiosity. I certainly can't. If a thing is of interest to you, that is exactly the thing you should study. I seem to be the only one obsessed with peritrichs on iNaturalist, but that does not slow me down!

Posted by shanesmicroscope about 1 year ago (Flag)

Thanks for your response, Shane. Perhaps I've subconsciously underestimated the effects of geography. I consciously know the US has many large inland cities. Here in Australia, due to the interior being mostly desert, something like 95% of the population lives along the coast; in fact we only have one (small) city that isn't coastal, and even that is a planned city and so not representative of natural urban development. I digress.

Most of the ocean is not near the coast, so surely coastal water cannot be representative of all marine life. However, I'm under the impression the open oceans are less diverse and less hospitable to life than the coasts. In any case, the undocumented animal phyla I mentioned above are all coastal – and yet we still haven't seen them.

I agree we could also use more expert identifiers. Perhaps there are rare phyla observations currently sitting at "Stateofmatter Life" already. Keep powering on! One Opercularia observation is better than 100 sparrow observations. I hope in time, as iNaturalist continues to grow rapidly, a small group of observers and identifiers might form and follow our example.

Posted by jameskdouch about 1 year ago (Flag)

Recruiting identifier expertise is an iNat problem in general. I long ago realised that if I wanted something identified that wasn’t abundantly common, I would probably have to do it myself.

When I started my microscope project which was totally new for me, I spent weeks searching the internet, learning and identifying as much as I could before I uploaded it. People like @shanesmicroscope with peritrichs have done the same and developed deeper knowledge of specific areas.

I suggest a new journal thread of this project where we post the websites, books and scientific papers we have used to identify so that we have a handy collection of resources instead of having references scattered in observations which one might never come across. (@ypna your recent Chaetonotidae discussion with Shane as an example).

Posted by jane_trembath about 1 year ago (Flag)

My reason for not posting many marine observations is simply because I don't live anywhere near an ocean. However, I do live near Great Salt Lake and am spending most of my microbiology time on isolating and culturing the microbes that live there. And that's not really freshwater or marine.

There are too many biases to list them all here, but I think one that ought to be pointed out is that most of our microbe observations come from water. Plenty of stuff lives in soil or on plants, or inside other organisms. And I expect none of us have the excuse that we don't live near soil.

Posted by zookanthos about 1 year ago (Flag)

You can send a list of reference books/articles to me and I can post them on the home-page.

Posted by biohexx1 about 1 year ago (Flag)

@jane_trembath Thanks for your response, Jane. Good idea regarding compiling identification resources.

@zookanthos I suppose one benefit of this discussion is that I have realised how privileged I am to live near the ocean. It gives me all the more interested in taking advantage of it. While I'm sure they're there, from my limited experience microorganisms are hard to find in soil.

@biohexx1 Excellent. To get the ball rolling, could you start by adding the following resource?:

Todaro, M. Antonio & Hummon, W.. (2008). An overview and a dichotomous key to genera of the phylum Gastrotricha. Meiofauna Marina. 16. 3-20. (https://www.researchgate.net/publication/236021984_An_overview_and_a_dichotomous_key_to_genera_of_the_phylum_Gastrotricha)

Posted by jameskdouch about 1 year ago (Flag)

Posted!

Posted by biohexx1 about 1 year ago (Flag)

@biohexx1 My favorite resources are:

Synopses of the British Fauna Series.: British Freshwater Ciliate Protozoa (volumes I and II) by C. R. Curds. These are out of print, but can be found at used book sellers.

Foissner's key of indicator ciliate species is very good, but it can give too much confidence at the species level, so usually it is best to back off a taxon level:
http://www.wfoissner.at/data_prot/Foissner_Berger_1996_375-482large.pdf
(it is one among several available from his site: http://www.wfoissner.at/publications.htm)

For identifying algae, these are superb (only I and II are complete thus far):
Freshwater Algae in Northwest Washington, Volume I, Cyanobacteria
https://cedar.wwu.edu/cedarbooks/6/
Freshwater Algae in Northwest Washington, Volume II, Chlorophyta and Rhodophyta
https://cedar.wwu.edu/cedarbooks/1/

Posted by shanesmicroscope about 1 year ago (Flag)

Posted

Posted by biohexx1 about 1 year ago (Flag)

Cheers! (PS, I made a small typo. Instead of "I can give too much confidence at the species level" it should be "it can give too much confidence at the species level." Sometimes I type too fast XD.

Posted by shanesmicroscope about 1 year ago (Flag)

I use these websites, great for beginners:
General https://plingfactory.de/Science/GruKlaOeko/Teichleben/e-TL3.html
General http://www.dr-ralf-wagner.de/index-englisch.htm
General https://boginvertebrates.wordpress.com/

Amoebozoa, especially Testate amoebas https://www.arcella.nl/
Diatoms https://diatoms.org/morphology
Catenulidae: The Catenula of the Eastern United States
John W. Nuttycombe
https://www.jstor.org/stable/2422603?seq=1#metadata_info_tab_contents
More Catenulidae including a key to genus:
Taxonomy and Phylogeny of Catenulida (Platyhelminthes) with Emphasis on the Swedish Fauna KAROLINA LARSSON
https://www.diva-portal.org/smash/get/diva2:171454/FULLTEXT01.pdf

Posted by jane_trembath about 1 year ago (Flag)

Posted!

Posted by biohexx1 about 1 year ago (Flag)

In addition to some already mentioned, here are my go-to websites:
http://protist.i.hosei.ac.jp/Protist_menuE.html - everything!
http://www.digicodes.info/index.html - desmids
http://cfb.unh.edu/phycokey/phycokey.htm - algae and red herrings (University of New Hampshire)
http://www.cfb.unh.edu/cfbkey/html/index.html - zooplankton (University of New Hampshire)

My go-to books for algae and diatoms (if you can find them):
1) Diatoms of North America by William C. Vinyard (1979) Mad River Press. - ISBN 0-916-422-15-1
2) How to Know the Freshwater Algae (3rd edition) by G. W. Prescott (1978) Wm.C. Brown Co. Publishers - ISBN 0-697-04754
3) Common Freshwater Algae of the United States, 2. revised edition by Gary E. Dillard (2008) J.Cramer Berlin Stuttgart - IBSN 978-3-443-5003-7

Posted by mnold1 about 1 year ago (Flag)

Posted!

Posted by biohexx1 about 1 year ago (Flag)

@ypna If you want to find soil microbes, just take some soil, add water and optionally a little bit of food, and then wait a few days. Might not work as well with sand or gravel, but so far it's not failed me. I was surprised to discover there were so many diatoms in my garden.

Posted by zookanthos about 1 year ago (Flag)

Thanks for the tip. When sampling moss I do end up looking at the soil beneath as well.

@lukas_scharer This first comment on this page is quite relevant to you.

Posted by jameskdouch about 1 year ago (Flag)

A reminder to everyone: whenever you open a microscopic observation, please check to see if it has been added to this project. Many haven't, and you can add those observations to this project even if it's not your observation. By doing this we increase the prominence of this project and hopefully entice some into broadening and deepening their microscopic contributions. (Disclaimer: I don't run this project and I get no personal benefit by promoting it. I just want to see more microscopy).

Posted by jameskdouch about 1 year ago (Flag)

I think I've just found a home.

Posted by darineugenius 11 months ago (Flag)

Welcome Darin!

Posted by jameskdouch 11 months ago (Flag)

Question for anyone leading/familiar with this project, is this project only for microbes? Or are non-microbial observations with a microscope allowed? For example the worm in this observation was able to be seen by the naked eye, and these scanning-electron microscope images are of an isopod that wouldn't be classified as a microbe :) Thank you anybody who helps!

Posted by ajamico 6 months ago (Flag)

I think any microbial observation is valid for this group!

Posted by biohexx1 6 months ago (Flag)

I'm not in any way affiliated with this project, but my 2 cents:

-In short, I would argue that any microscopic observation is appropriate for this project. Can you see that worm without a microscope? Who cares. You observed it with a microscope and in so doing were able to pick out features not visible to the naked eye.
-There is no formal, taxonomic definition of "microbe." Microscopic life does not fit neatly into any taxonomic category and is difficult to browse on a site focused on taxonomic relations. That is, to me, the real utility of this project: allowing us to browse microscopic observations easily.
-To add to the above, there is no way to ad hoc map any taxonomic definition to "microbe," either. Some individual protists are visible to the naked eye. Many, many protists form filaments/colonies that are visible to the naked eye. Some animals such as rotifers, on the order of 1000 cells, can be smaller than some single-celled protists.
-Personally, if it were my project I would name it to remove reference to the term "microbe" to avoid confusion. This is functionally a project for collecting observations made through microscopes, as there isn't really any other workable definition.

Posted by shanesmicroscope 6 months ago (Flag)

Gotcha, thank you both for the input! :)

Posted by ajamico 6 months ago (Flag)

I agree with Shane. People have long been using this project to document macroscopic organisms that include microscopic features – and nobody has complained as far as I know. In my opinion it's welcome here. And as Shane points out, the line between microscopic and macroscopic is blurry, making it impossible to satisfactorily enforce a microbe-only policy anyway.

I previously had a talk with the administrator, tiskolin, on the redundancy of the word 'Microbes' in 'Microscopic Microbes', since microbes are by definition microscopic. But now I think it's not just redundant but also confusing, as thatcactusgirl has demonstrated.

@tiskolin – Perhaps the time has come to change the name? I'd like to humbly suggest the plain and simple 'Microscopy'.

Posted by jameskdouch 6 months ago (Flag)

I'm always a fan of alliteration, but yeah I can't have been the first person who was confused by it. To keep the feeling of the current title, how about something like Magnificent, Marvelous, or Miscellaneous Microscopy?

Posted by ajamico 6 months ago (Flag)

I've stated this before, but I'll state it again. This project was created by a very young student (at the time it first came on-line). That student
thought it was a great title for a project, and I'm inclined to agree.

Posted by biohexx1 6 months ago (Flag)

I remember you saying that, and I was inclined to agree that the redundancy wasn't worth interfering with sentimental value. But if people are getting confused, with all due respect, I honestly don't think it's great.

Though it couldn't have been anticipated by anyone at the time, this young student's name now represents almost 14,000 pieces of research-grade data. I wonder how many observations haven't been added to this project because they show barely macroscopic organisms or microscopic parts of macroscopic organisms.

If you insist on the microbe aspect, then I'm confused – should we remove our observations of microcrustaceans, pollen, etc., from this project?

Posted by jameskdouch 6 months ago (Flag)

Of course not, but you are free to do what you will.

Posted by biohexx1 6 months ago (Flag)

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