Since we are also publishing papers on our research, those act as prior art I think, though my understanding is rudimentary. However as you say I believe it is difficult to patent anything in public domain, particularly if there is official, dated documentation of its release ( such as being published ).
So citing algorithms, production / analysis methodologies, etc. in publication may offer some protection, without the pitfalls of giving away the full blueprints as is required in actual patent filing.
Thank you for the reference to Teresa Scassa’s research. I found one of the papers to which I think you are referring?
https://www.wilsoncenter.org/sites/default/files/Typology_of_Citizen_Science_IP_Rights_Scassa.pdf
She raises relevant points such as:
"Citizen science project coordinators should be concerned about the management of intellectual property rights because of their potential to lead to unanticipated consequences that may hinder the dissemination or use of the research output.
For example, when citizen scientists are invited to contribute content in which they have copyrights, such as photographs or written accounts, it would be difficult for a researcher to disseminate the datasets containing these contents or to reproduce the copyright-protected contributions without authorization."
I’m not sure I agree with this next statement as a whole, since contributing raw data is still a procurement and curation that would not have occurred in the same way by another individual’s hand, but it is also relevant since she thinks this is the case, and I do agree with the second half of the conclusion that detailed prose qualifies as original expression. Perhaps there is some precedent for defining procurement of raw data as not deserving of IP protection? I assume with all the emerging citizen science projects, if there is not already such a case, there will be one eventually. For example, where do we draw the line between what is data and what is design? Is a piece of DNA not a piece of data? Yet it is patented left and right by companies who invest significant effort and research into discovering those pieces of data. How is this qualitatively different from a citizen who has invested significant time and effort in finding just the right RNA sequence to solve a puzzle? It looks like, from the table on pages 10-11, Teresa defines activities at Eterna to be under the category of ‘problem-solving’ and not strictly ‘data gathering’.
“A contributor who provides only raw data to a project has no intellectual property rights in that data; by contrast, observations expressed in detailed prose or in a photograph may qualify as original expressions.”
“In terms of patents in the citizen science context, a key issue might be whether the contribution of any individual participant amounts to inventive activity such that they should be included as a co-inventor in a research project that leads to a patentable invention.”
So with regard to her particular concerns about feasibility of applying licenses that allow redistribution ( commercially or non commercially ) of citizen-science gathered research, I think the important thing is to clearly contextualize and disclose exactly what will and will not be considered distributable IP, and to get clear permission from users on rights for distribution. We have discussed on a few occasions having a EULA popup that new users ( and on introduction, existing users ) would agree to, to be sure among other things of this, and for example general disclaimers for users who are under 18, etc.
It would be good to include in such a EULA clarity and outline of what licenses we use, and which kinds of IP are under which license, and whether anything is exclusively licensed to the user or not. Many websites that accept user generated content of any kind require a carte blanche access to rights for that content, if not to directly exploit it, simply to avoid liability for exactly the issue you mention where US citizens are automatically granted copyright simply by the act of publishing their IP. ( if I understand correctly - on this and everything else I have said please anyone correct me where I am misunderstanding ).
I see in the above paper, a photo of a tree from another citizen science project is included, with a credit to the citizen who took the photo, but I’m not clear on whether their actual permission was obtained. If not, it would be ironic, seeing as citing the author does not necessarily permit use, and certainly not publication. I guess I’ll assume explicit permission was obtained? 
Anyone wishing to see a nice comparison between Patent, Copyright, Trade Secrets, and Database Rights is advised to check out her Table I on page 7 of the above linked paper.
All in all an interesting paper and very relevant to what we are doing, especially during the exciting transition from purely foundational research into actual production pipelines.
Also, yes as you mention below, MIT’s OSI permits sale of the software.
I’ll address applying an individual license for companies wishing to pursue application of specific aspects of our research in Rhiju’s comment below.
