Hello, I am teaching a college level mycology class and we will be spending a lot of time culturing fungi from various environmental samples (soil, water, etc). I am wondering if cultured fungi are an acceptable observation to post? Microfungi are generally underrepresented, so from that perspective I think it could be valuable information to add. It seems that this forum https://forum.inaturalist.org/t/are-culture-based-observations-considered-wild/23355 did not reach a consensus. I envision that the observations would include the original sample collection info, then culture info (e.g. which media were used), and images of the culture both from a lower magnification (stereo microscope) as well as higher magnification (compound microscope). Does this sound like a reasonable project for iNaturalist?
Seeing what fungi look like in culture is one way to help identify, so yes, I think tacked on to an observation of the original collection it would be very useful! The media used and the temperature and speed of growth would also be cool information. Fomes inzengae vs. Fomes fomentarius for example: https://imafungus.biomedcentral.com/articles/10.1186/s43008-019-0016-4
If you want confirmatory identifications then you would need to provide sufficiently detailed microscopy of a sporulating culture. You would need to show conidia, conidiophores and mechanism of conidiogenesis, or any other reproductive structures. That is in addition to the substrate/host/habitat from which the samples were collected. For many micro-fungi then sequencing is often needed to differentiate species, and often more than a single barcode locus like ITS.
I think this is a worthwhile project, if you have the resources to sequence these cultures in your class that would be a great addition of information. as mentioned before, this should include all the necessary information regarding the source of the sample , media and conditions it was cultured, as well as microscopy and any additional differentiating details you can provide. you can set up a project with mandatory observation fields to that purpose, making this project more structured and easier to categories in the future (i,e. growth media, sample source, temp , light/dark)
Welcome to the forum, and great question. I think that this is definitely a worthwhile project. I donāt see any issue with uploading observations of these fungi to iNat. I am guessing that some users will probably mark these as Captive/Cultivated, which is probably justified under iNatās guidelines for the use of that term. But that doesnāt mean that the observations donāt belong here. Itās a tough edge case for wild/not wild as fungi like this can really only be observed through captive cultures. But I donāt think that should discourage people from uploading the observations!
Iām not sure but what some of the rules are bendy for projects.
Would it be possible to add these observations into a project and have that fact noted to help prevent the captive/cultivated bin?
Fungi need studied!
If you use the location and time of collection as the observations time/place then Iād have no problem considering these wild. There are some users who post microscopy collected from wild and Iāve not noticed any controversy about it.
I donāt think collecting from the wild and taking a picture later is the issue. If someone collects a water sample, takes it back to the lab, looks under a microscope, finds a rotifer or amoeba or something, and then uploads that with the date/time of the original collection, this can certainly be a WIld, RG observation. Sure, itās possible that the individual might not have been present when the original sample was collected since these kinds of organisms can reproduce quickly, but I think thereās little chance of a problem here.
The issue is that the fungi have been specifically cultured/grown on a medium - the individuals viewed are definitely the offspring of those in the sample and certainly under cultivation. They might also be in a different life stage or have different structures thna those present in the water sample.
āthe individuals viewed are definitely the offspringā
Thatās not always correct. Quite often a piece of fungal tissue taken into culture and genetically it represents the same āindividualā and not itās offspring. It depends how you define an individual and its offspring. Thatās not the same as growing spores, which may then represent different individuals. Although even then it is debatable because often the isolated spores are asexual and the resulting colonies are clones of the original. The notion of an āindividualā for fungi gets a bit fuzzy.
Thanks for all the feedback! Yes, defining an āindividualā for fungi is an interesting and not straightforward question, which is a concept we will be discussing in class. Part of the project does also involve some gene sequencing, which definitely is necessary for some microfungi to make a more confident ID. I could restrict microfungi observations to those for which we obtain sequence data to make it more stringent.
I see no problem. The colony forming unit (is that a term for moulds too or just for bacteria and yeasts?) are wild organisms which you encountered. If you use the date and location where and when you have taken the sample, it should, IMO, qualify for research gate.
But they are still evidence of presence for a wild organism. If there is a colony on a plate, it means that at the time and the location of sampling there has been a spore or conidium of that species present.
As an amateur who is interested in but not knowledgeable about fungi, I would be interested in a photo of the location where the samples were collected, especially if these are fungi visible without magnification. It would help me envision the habitat, substrate, etc. But thatās just a āwould be niceā suggestion, off-topic from your question.
If you do start a project, I hope youāll post the name of it here.
Letās say each observation had as its first image a photo of the collection location (with fungus, if visible). This can then be followed (in the same observation) by diagnostic photos of the cultured organism derived from that collection, plus all the other contextual info suggested by other commenters (e.g. sequences taken from the culture). The date/time and location would reflect the collection.
In that case, perhaps we could avoid getting hung up on whether this is the original organism or offspring. The cultures are provided as evidence to assist with identification of the wild source organism. Of course, it might be inappropriate to add annotations and observation fields based on the culture photos, but thatās a different issue.
Fair point that itās possible that the fungi observable on the plate could be the same individuals in some cases and/or definitions of individual. But even in this case, the organism would likely be significantly different (a different ālife stageā, again depending on what that really means for fungi) than when it was observed in the wild.
In animals, for instance, if thereās a significant change in an organism after itās brought into captivity (hatches from an egg, pupates, becomes sexually mature), itās generally accepted that photos of the organism at this stage should be their own captive observation as opposed to backdated to the original collection. Otherwise, the observation misrepresents the state of the original collection and can give incorrect data about phenology, etc.
This same issue applies to the approach that
If someone finds a seed in the wild and plants it, grows the plant to IDable size (leaves, flowers, whatever), pictures of that individual flowering/leafed plant shouldnāt be backdated to be an observation for the seed collection. The plant is definitely the same individual as the seed and is evidence for the identity of a seed that was wild, but, at that life stage, the organism is in cultivation/captivity, and its form and timing are a result of that.
So, if the same individual fungus has āgrown upā, or now has fruiting bodies, etc. on the plate, maybe at a time it otherwise wouldnāt, this could be an issue.
The solution I have seen suggested, which seems reasonable to me, is similar to what @rupertclayton suggested:
Make an observation for the original observation with whatever evidence there is (photo of water sample, photo of wild caught life stage). Make a second captive observation of the life stage in cultivation (grown plant, eclosed adult, grown fungus) and link to it in the description of the first observation to support the ID there. Itās a bit of a pain/extra work, but I think it is a decent idea and provides additional useful information that a single observation does not.
To be clear, Iām not interested in going around and checking DQAs on cultured fungal observations myself, but part of the thread seemed to deal with whether it is reasonable for users to consider observations like these captive. I think it is pretty reasonable given iNatās guidelines, so if someone were to downvote Wild, I donāt think that should be considered a problem, but a reasonable interpretation of the guidelines.
Regardless of how different users choose to address these types of observations, I do think that theyāre valuable and hope they are uploaded.
To minimize needless confusion, for any observation where the photo/sound evidence could be misinterpreted, itās always a great idea to add context via a note or comment, e.g.
This observation is for a wild-collected fungal organism (photo 1), supplemented by subsequent images of the same or organism (or its offspring) in culture and a DNA sequence taken from the culture. The date/time and location reflect the initial collection.
Although I suggested placing the wild collection photo as the first image, thatās not really necessary, and if you wanted to try to use CV to identify fungal cultures (unlikely to be very helpful at this point), you might want to place a diagnostic image of the cultured specimen as photo #1.
But it solid evidence of what species were present at the place and time of the collection. Isnāt that the point of inat?
Edit - there are a lot of posts since you said this I havenāt read, maybe Iām just repeating conversationā¦
In animals, for instance, if thereās a significant change in an organism after itās brought into captivity (hatches from an egg, pupates, becomes sexually mature), itās generally accepted that photos of the organism at this stage should be their own captive observation as opposed to backdated to the original collection. Otherwise, the observation misrepresents the state of the original collection and can give incorrect data about phenology, etc.
Iām not sure this is agreed on either. Collecting and rearing adult insects from leafminers and galls is very common and frequently the only way to get IDs for the parasite. Itās very common to find RQ observations of insects reared from galls or miners.
And when you talk about hyper parasitism itās more complicated. There is no way to find out what wasp is living inside the grub living inside the plant until the grub matures and a wasp pops out. To me the most correct path is to use the collection location and date for one observation of the miner/gall and a new observation with the collection location and date of the change (adult or parasite emerges). Otherwise whole groups of insects simply wonāt have any āRQā observations. Which ironically doesnāt make sense because if you study hyperparasitic wasps you would almost exclusively be researching these exact samples.
This would be a very important contribution: there are many myco-dependent plants, such as some wild orchids, that have an absolute requirement for them in order to grow-- and they may use one species at germination, then another as the seedlings grow, defining two separate spp. for each phase.
Much of the lit presently just says a need (in general) for mycorrhizae. So identifying the exact species can help in trying to grow and restore populations of rare and endangered plants.
Identifying the fungal partners, Iām all for it.