"observing" unseen Endosymbionts. Should they merit an observation?

Hi
I recently came across two organisms that are not “classically” observed ( no actual observation of the organism) but are inferred from their host, or their hosts association.
I don’t think these should merit an observation and i will try to make my point with examples. but first lets look at what got me here :

https://inaturalist.org/taxa/1538531-Bracoviriform-glomeratae
this is a viriod (some consider it a virus) that facilitates the parasitic life style of Cotesia glomerata on larvae of Pieris brassicae (i wrote P. machon but got the two mixed up)

"An important aspect of the symbiotic polydnavirus is the fact that the virus does not and cannot replicate on its own- it does not contain the genes necessary to replicate itself " (Wikipedia) So in fact , every observation of the parasite ( the parasitic wasp C. glomerata) or its assosiation with P. Machon can be replicated to include the virus, since infection is mediated by it, and cannot happen with out it.

the second example is Wolbachia https://israel.inaturalist.org/taxa/356524-Wolbachia
Wolbachia itself isn’t observed , rather the host is documented and the presence of the symbiont is inferred.

again in both examples ( maybe more out there) the organism is not observed directly. indirect observation of symbionts or parasite is not bad on its own, however if all members of a taxon are known to harbor a symbiont, what’s the point in observing them both ?

I thinks these should not merit an observation , in my opinion this is akin to duplicating every animal observation with enteric bacteria such as E. coli ( that are 100% present in the gut microbiome) . It gives no additional biological data , and the organism in question isn’t really observed but inferred from the mere presence of the host or association, as opposed to observing symptoms of a disease

Would love to hear other opinions, what do you think ?

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these kinds of observations seem so few that it hardly matters.

but conceptually, these sort of observations seem to me to be not much different from someone observing the stump of a tree felled by a beaver as a beaver.

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I know that if I saw a caterpillar in the condition of the example, I would make an observation because it is definitely in the “what’s that? Maybe someone knows…” category.

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We have had this issue come in lichens as well where people have very occasionally posted observations of the photobiont based only on macroscopic images of lichen thalli.

My opinion is that such observations are reasonable if someone has made a particular effort to observe the symbiont as separate from the host - e.g. they have done microscopy of the photobiont layer of a lichen or the bacteriocytes of an aphid, etc. If its presence is merely inferred and based on exactly the same criteria as were used to ID the host I personally don’t like them and don’t think they belong.

I think this situation is quite different from the situation of a beaver-felled tree. An observation of a birch does not imply the presence of a beaver - only birches with the specific signs of beaver interaction do. Meanwhile an aphid will always mean Buchnera, and a Graphis will always mean Trentepohlia.

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With disease, if the specimen shows the symptom of the disease (virus, whatever), I think it’s totally reasonable to ID as the disease. For instance, Covid tests are evidence of Covid (even though the viral particles aren’t visible). Scientists make their own IDs of endosymbionts that cause disease based on similar evidence all the time. Much cheaper and quicker. Getting a DNA/RNA sequence or making an electron microscope image generally isn’t necessary and is cost-prohibitive at a large scale.

If there’s a situation where an endosymbiont is totally ubiquitous in a host taxon (ie, the host is guaranteed to have it), then I wouldn’t duplicate the observation and add the ID. It wouldn’t add any information (anyone looking for the endosymbiont would already be using observations of the host). Though I could see someone who really wants a big species list making a one-off duplicated observation to ID for both the host and endosymbiont. I don’t think that there’s anything wrong with that per se.

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You have a point. Though personally I quite like the addition of the Bracoviriform glomeratae on my lifelist. I have observed the life-cycle of Cotesia glomerata (by the way, it parasitises Pieris brassicae and not Papilio machaon) and when somebody suggested the virus- of which I didn’t know before - I found it a nice addition.

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In my view the point is learning. Seeing such observations/“observations” can open up a whole new world to iNatters, it can inspire deeper learning, new passions and help users have more encounters with nature by sending their searches in new directions. Not everyone is able to make a laboratory grade observation of such things, and if users see a photo of something in a petri dish or something microscopic and they don’t have that kind of access, they may not even open and read about what it is, feeling it’s out of their reach/beyond their abilities. But, if they see a photo of an animal or insect and wonder why it seems mislabeled and look into it, they learn something new and amazing and perhaps see it as something they too can look for and make an observation of. In my view, it makes life richer and helps spread interesting information further.

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What is the point of posting these redundant observations, even though they are worthless to science? I think the answer is hidden in the description of iNaturalist: “iNaturalist is a lot of different things, but at its core, iNaturalist is an online social network of people sharing biodiversity information to help each other learn about nature”.

Getting to know biodiversity is an ongoing-learning process, and here on iNaturalist you can learn individually and together - and, as erin-816 already mentioned, this process itself “can inspire deeper learning, new passions and help users have more encounters with nature by sending their searches in new directions“… Is that not a wonderful thing?

When reading this discussion, I think it is important that we reflect about the different reasons for why someone uses iNaturalist. I surely do not want to annoy anyone – I am not sure if you referred to me, when you mentioned, that “We have had this issue come in lichens as well where people have very occasionally posted observations of the photobiont based only on macroscopic images of lichen thalli.” jlisby. For me it was a nice learning experience to find out which lichen had only one photobiont and which ones could have multiple ones and which ones these where – and posting some of these “results” of my research in the web was like noting down some of these things I had just learned about lichen – completely redundant information for any lichonogist- but cool new information for me, maybe redundant, but not false…

With Bracoviriform glomeratae and Iflavirus dinococcinellae it were even other users that asked me to duplicate the observation in order to have one for the Virus, too, if I remember correctly… (since you mentioned it here, susanne-kasimir). But after learning about the virus, I read also more about it and the interaction – things that I can also pass on in environmental education later on.

I am just thinking about posting an observation of myself as an observation for E.coli… and another one for Buchnera… I hope you will not be annoyed at me - but how cool are the details about the Aphid-Buchnera relationship? - next time in spring I can tell my flatmates that are annoyed at the aphids on their vegetable plants, how cool it is to know that they also have endosymbionts, similar to ours, but of a different genus, that produces amino-acids for them…

By reading the article above I stumbled upon the Genus Blochmannia and their relationshsip with carpenter ants (genus Camponotus and some relatives), where the bacteria also provide a better nutrition. And already I am learning more about both bacteria and ants and evolution and interaction between organisms….

I hope you will forgive me for making a redundant observation now and then – of (not only) these -very much not redundant- endosymbionts, that also deserve our love and attention… [In case of the endosymbionts, even the choice of our own nutrition in many cases gives the impression that we do not have the endosymbionts in mind… so it probably makes sense to learn more about them…]

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I think posting the observation for the endosymbiont as well as the host is fine.

Do not, however, post observations for chloroplasts or mitochondria, for two reasons. First, both occur in all (or very nearly all) individuals of the host species. Also, both have mutated and lost genes to such a great extent that they cannot live independently and truly are part of the host, despite their origin.

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@ guryonatan See maybe also the related discussion here: https://forum.inaturalist.org/t/observations-that-obligatory-imply-the-presence-of-another-species/40933/9

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I agree with this. If there are visible signs of the disease / symbiont, go ahead - but unless someone has gone to the effort of actually finding evidence, it’s just a vague assumption it’s there, and it could well be wrong.

For example, the bacteria that creates nodules on roots of alder trees. If someone finds exposed nodules, that seems like fair evidence, but taking a photo of an alder tree and duplicating it for that when it’s not even shown? Please don’t.

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for me, if a healthy aphid is known to always have Buchnera bacteria, then i think it’s fine to use an aphid as a sign of Buchnera bacteria. it doesn’t matter that the sign of an organism is another organism. as long as it’s a reliable indicator, it’s a reliable indicator.

now, if you were to take a photo of aphid exuvia and say that’s Buchnera, then i think i would say that’s not good because now you’ve got an extra step between exuvia and bacteria.

or if you were to take a photo of dead aphid and say that’s Buchnera, then I would probably also so that’s not good because it’s not clear that a dead aphid will have Buchnera bacteria.

there’s no difference to me between saying that a healthy aphid is a sign of a bacteria that is required to have a healthy aphid vs saying that a diseased leaf is a sign of a bacteria that is required to have a diseased leaf.

but, again, i would say these kinds of observations are relatively few, and i don’t think it’s worth arguing too much about them either way.

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I am now considering opening a feature request to have every observation of a species that reliably implies another species to automatically create an observation of the second species. Wouldn’t that be cool?

But I think I know how that would go :)

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I think they merit an observation if the observer wants to make an observation for it. iNaturalist is about connecting people to nature and their personal experiences with it, if that connection or experience is taking note of an organism implied by another organisms existence, be it a parasitoid virus or a lichen’s photobiont, I see no harm in it.

Plant diseases, viruses, and lichen are all quite niche anyways, viruses and organisms hidden away in obscure information like this will not be common uploads and shouldn’t put that much of a strain on identifiers.

Also I just think they’re cool! I enjoy seeing them, I enjoy learning about them, and I would be open to making similar observations myself if the situation ever arises. I didn’t know braconid wasps utilized viruses until I saw the “unnecessary” observations for them.

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I’ve encountered this situation before with the wasp species discussed in that thread. I have an observation of that wasp, from a pupa I found with a ladybird beetle protecting it. I have 3 observations from that encounter; the wasp, the ladybird beetle, and the virus.

Someone asked me to duplicate the observation for the virus, which I did, but only because the ladybird beetle’s behaviour was evidence of infection by the virus. The same user made the same request for observations that were just pictures of the adult wasps, which didn’t make sense to me.

Similarly I would only post an observation of a lichen-associated algae if I’d actually dissected the lichen and found the algae inside it.

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I will note that iNat asks you to upload evidence, which is a form of scientific rigour.

Ecological education is valuable, both for our fellow iNatters, and for the general public. You “pull on a thread” (you identify a species), and you find it connected to everything else in the universe.

One compromise could be to make ecological notes in a comment under the observation.

One extreme example would be, “Although this human is a casual observation, the following 200 bacterial species are usually found on all humans, so if you have access to microbiome surveying, then you might want to look for them.”

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Erstwhile microgastrine researcher here. I love endosymbionts and the weird stuff they get up to, so I would love the world to know more about 'em, but I think there are some major limitations with inferring an observation.

For polydnaviruses specifically, people know about them as a cool endosymbiosis story, but we’ve done a very poor job communicating what they’re actually like. I’m mostly talking about bracoviruses, I know much less about the ichnoviruses. Calling them a “virus” is expedient but really leads people down the wrong track regarding what they are and how they work. Tagging any eukaryote as alphaproteobacteria because of mitochondria is more reasonable IMHO. Polydnaviruses originated from nudiviruses some 100mya, give or take, but if you look inside a polydnavirus capsid you won’t find any nudrivirus DNA. What’s happened is the wasps have kept the nudivirus genes that make the capsid proteins and then they have other sets of genes that they stick in the capsids: the capsids are just delivery vehicles for a hodgepodge of unrelated genes to do mischief to their caterpillar hosts, with no ability to replicate. The capsid genes, descendent from the nudivirus, don’t go into the capsids. The DNA inside the capsid is not descended from a nudivirus. So I think of polydnaviruses as a functional group of nuclear protein-coding genes, some of which were once derived from a virus, in the genomes of some wasps, not so much as symbiotic viruses.

TLDR: polydnaviruses aren’t viruses, they’re a subset of genes in the nuclear genome of microgastroid and some ichneumonid wasps.

The other point you bring up, things like bucnhera for aphids, I’m not an expert on the known prevalence of buchnera in aphid species, but inferring presence is not observing presence. It’s a reasonable assumption, but not data. I don’t know off the top of my head how many species of aphids there are, or what proportion of those have been screened for buchnera, or if all populations of the species known to harbor buchnera carry the symbiont or if there are any exceptions. Back to microgastrines, we generally assume that all species have polydnaviruses, but there’s something like 20-50k species worldwide and we’ve only checked for evidence of polydnavirus in a handful of those (mostly Microplitis demolitor and several Cotesia spp., probably less than 50 species total including my own unpublished stuff…). I would not be surprised at all if some species lost the ability to produce polydnaviruses along the way, nor would I be suprised to learn that there were populations of aphids that “should” have bucnhera and don’t anymore.

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In case anyone wants to check Kyle’s credentials :wink:
https://www.ideals.illinois.edu/items/107784/bitstreams/351632/data.pdf

Just had a vision of me uploading a picture of the siberian tundra from space and IDing it as “musk ox” … :grin:

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You are correct as to the host! i somehow got the two mixed up in my head

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