microbial bioremediation of toxic heavy metals
looking for examples of in situ microbial bioremediation of legacy heavy metals on the shoreline of Newtown Creek, so far using portable metals testing XRF + genetics labs. since 2021 we are taking soil microbiology samples along the multi THM contaminated shoreline, plus some cleaner sites (restored brownfields, urban farms, community gardens, native wildflower nurseries, old growth forests, restored river grasses) for reference
we're a growing team of volunteer microbiologists + geochemists which welcomes assistance from coders to help us find or create tools to make data visualizations of our local data. csv + raw files available upon request
keywords metagenomics, metallomics, bioavailability, bioremediation, bioimmobilization, biomineralization, biotransformation, biogeochemistry, geomicrobiology, geomycology, heavy metal toxicology, metal uptake
Danny Thu 9 Feb 2023 3:27PM
Just as an update this grant is no longer active. But I am now in conversation with Suzanne Pierre from the critical ecology lab about her interests in using the BwoB facilities for her research.
Danny Mon 15 Aug 2022 7:14PM
@JORGE DIAZ Do you have any thoughts about this project or are you otherwise able to connect us to resources that might help us progress further? Your questions about approach or methodology could be incredibly useful to help us refine the possibilities here and/or create interesting new avenues to consider.
Danny Wed 31 Aug 2022 2:37PM
Oh whoops I think I thought you were someone else :S Well we're still interested in your thoughts, but I understand if you are thinking that this is not in your area expertise
Danny Wed 31 Aug 2022 2:38PM
@Guillermo L.C. Oh gosh I got you mixed up with someone else. In any case, do you have any thoughts about this project or are you otherwise able to connect us to resources that might help us progress further? Your questions about approach or methodology could be incredibly useful to help us refine the possibilities here and/or create interesting new avenues to consider.
Guillermo L.C. Wed 31 Aug 2022 2:42PM
Hello! Give me a minute and I'll share some relevant research on microorganisms-minerals/metals interactions with a wealth of methods that could be implemented!
Guillermo L.C. Wed 31 Aug 2022 3:09PM
Is it possible to get more information about the project? What have been the findings, current questions and what is planned for the future? It will help me narrow down what can I share!
Danny Wed 31 Aug 2022 3:59PM
Yes of course! Beyond what is in the context of the thread it's my understanding that we have a wealth of 16S and ITS amplicon data from various sites matched with XRF readings of the heavy metals from those same sites. One line of investigation centers on correlating microbial OTUs with metal levels. But we also have access to some of the sites on a more long term basis and are interested in developing a strategy to remediate the site perhaps centered on trialing various amendments on small test plots. I've been meeting with @j sinopoli semi-regularly (and typically at 15:00 EDT [UTC-4]) to understand the scope of the project so perhaps he can tell you more. We could also try and schedule a call with all three of us to have a discussion.
Guillermo L.C. Thu 1 Sep 2022 1:41PM
If I understand this correctly, you currently have ID'd several microorganisms that are thriving in presence of different heavy metals and trihalomethanes(?).
I think the next steps would be in working further into the microbiological aspect, e.g. classify the organisms, determine their relationships, and get to grow them in a laboratory setting for further work.
In terms of the metals side do you know the concentrations in the environment and has this decreased as a function of the presence of the IDd microorganisms?(research question for the prep of a proposal right here).
As for the call, id be happy to discuss this by means of a call as well, it will definitely help defining a direction and getting to know the existing results! I will be back from my holidays on the 08.09 so we can find a date for the coming weeks!
Danny Tue 13 Sep 2022 3:23PM
@Guillermo L.C. We have a shared zotero library concerning this project. It can be accessed here. I will approve your request to join it so you can share papers with us and see what we have collected on the subject.
Others who are interested in working on this project too are welcome to request to join
Patrick Ferner Wed 30 Nov 2022 3:43PM
Hello! I'm a software engineer looking to help out and I think I could be of use with data processing and data visualization. @j sinopoli are you looking help at this time?
j sinopoli Wed 30 Nov 2022 6:43PM
hi Patrick yes thanks that would be great, are you here in NYC? let's talk sometime
j sinopoli Sat 3 Dec 2022 5:40PM
we'd be grateful for any help
we have 3 separate csv/ods spreadsheets of soil 16S archaea/bacteria + ITS fungi + XRF heavy metals ppm data, so now we're looking for clear visual ways to overlay, correlate or otherwise to decipherably visualize our taxa abundance + ppm csv data. we've also been fantasizing about finding better advanced search spreadsheet lookup tools (ie by phyla genus or species while filtering out low abundances etc)
Danny Fri 5 May 2023 1:53PM
@j sinopoli Was talking to a friend yesterday and I learned that Pumping Station 1 in Chicago has a working NMR which potentially could be used to ID pyromorphite (at least there is enough NMR sensitive Pb in the world for it to theoretically be visible). I'd be curious as to what our AI faerie oracle has to say about how to approach the method.
Danny · Mon 15 Aug 2022 7:11PM
@j sinopoli I know we talked about it offline, but could you share your thoughts with the thread concerning this Public Lab opportunity for funding.
It would be nice to make some of our discussion around the opportunity more transparent because it represents chance for someone to help weave together local communities (including Biotech Without Borders, j's community connections, and whatever other groups folks have relationships with) around the idea of community-based remediation or surveillance efforts. Particularly, I think it would be useful to hear if you are interested in this opportunity or how you might support someone who is interested in the opportunity. Also what groups do you know who might be interested in collaborating with us around to support a fellow?
For the record I am interested in applying for this (although I haven't been working on my application... yet) but I am also happy to operate in a supporting role for a potential fellow. I went to one of the Public Lab open calls to ask some questions about previously funded fellows and they provided a handful of projects as examples stressing that projects can be at any stage.
The most important element is that the projects are based in a local issue although team members can be from any geography. Public Lab itself is very interested in open source measurements as well as with DIY equipment. I specifically asked if the fellowship must already have a clear plan on how their work will impact the issue at hand and they said that the project itself could be planning (involving appropriate stakeholders, etc). The project could also be R&D into some sort of measurement/remediation tool/methodology or it could be researching to find viable commercial services for measurement/remediation.