Bioremediation of brownfield soil

[Carlos Castellanos]

Hey gang,

I am going to be working on a project that involves bioremediation of soil in a contaminated urban brownfield. This will done primarily via a DIY composting approach, using bacteria and other microbes for degrading PAHs (polycyclic aromatic hydrocarbons) such as benzo(a)pyrene). However we would also like to "enhance" the compost by adding bacteria that are known degraders of benzo(a)pyrene (e.g. Mycobacterium vanbaalenii).

My questions is how do we do this? Is it as simple as injecting liquid media containing the bacteria into the compost?

Also, I know we can try to isolate good biodegrading strains from the contaminated soil itself. Is that a good way to go or should we introduce one from the outside?

We will also be looking into phytoremediation (using Brassica juncea or similar) to remove arsenic remove arsenic. So any pointers on that would be appreciated as well.

Thanks,

Carlos

[Dakota Hamill]

You could try isolating strains on selective growth media or by enrichment.  aka dumping in more of the compound you want degraded into soil to see what microbes may utilize it and outcompete others prior to sampling. 

https://pubs.rsc.org/en/content/articlelanding/2017/ra/c7ra09274a

https://www.nature.com/articles/s41598-020-57692-6

Having worked with probiotics before how you prepare them depends a lot on their end use and environment of end use.  How big of a pile of compost are we talking, grandma's back yard or entire front-end loader bays filled with 1,000+ yards?   Daily application if its for cleanup? 

You could use fresh after fermentation in a giant spray-applicator like you see for weed killer.  Or prepare a shelf stable long term liquid formulation (these don't seem to work great long term for non-sporulating bacteria).  

Or, my favorite is to lyophilize the bacteria with a cheap cryoprotectant and after a plate count of the raw material, do a "solid dilution" on an excipient.  This is how most probiotics are made.  Basically mixed onto rice bran, maltodextrin, dendritic salts, some solid carrier that is either inert or will help be a nice powder in the new environment.  You can do this by hand in a mixing bowl, bread mixer, or a cement mixer.  Laboratory powder mixers are expensive.  

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[Dan Kolis]

Sounds like an interesting project.

Most of these 'Im gonna save the world, tonight', projects generate nothing of any utility. Maybe a little P.R. all in about in the usual case.  I'm assuming you wan to actually achieve something that reaches application in the general case. If not, there's no point in reading this...

Controls to verify whats really occuring is unusually significant
Mother nature is not in the fan club of most earth moving, development, or dump operator guys. By wishing pollution prospective materials would just go away, plan 'A' for human management packs up the unwanted one way or the other, keeps it away from sunlight and dry, and squeezes it up denying access at Atmosphere. So handling materials or avoiding it to fabricate them maybe improve them roughly in proportion to same of your remediation attempts. 

Your situation involves the oddity, retrieving samples and doing much of anything, including longish calendar time and any exposure to light, storage temperatures, etc modifies the samples. Your stuck deciding to MAKE pollutant sets from scratch carefully, OR Carefully stabilising and documenting real world samples. Any incidence of pollution involves duplicity and concealment, lying and allegations and falsified records. Also, the damage itself is certainly exceedingly viable in constituencies, quantities and time frames.

I think technology and science not too far off the high school science fair table would be often remarkably effective.  But the complete resistance to applying anything in reality on scale; --very or marginally effective, is a severe constraint.

My first thought is to apply nearly forensic controls on daily work. Maybe look at ISO 900X management systems, with or without paying down external management.

Enumeration and controls of samples, ex: perfect traceability of extraction, storage, dating is unusually important or no matter what you figure out or don't will achieve nothing except the usual mumble: "This work justifies MORE RESEARCH" which like: "SAFETY FIRST", are the two favoured magic statements to support doing nothing, which by definition, is the cheapest option for those stuck with costs. 

I would personally immediately make pollution sets so they can be aged in situ, no matter how difficult that might be to arrange.

Good luck !

Daniel B. Kolis

[John Griessen]

On 5/12/23 08:18, Dan Kolis wrote:
> I would personally immediately make pollution sets so they can be aged in situ

What is meant by pollution set?



It seems to me one needs to look at the in-situ-ation from one's chosen organisms viewpoint
to get much success in a toxin getting degraded.

As in,

How much food do they need along with the toxin to stay alive?

What ratio of normal food to toxic food causes them to eat toxins effectively? (It might be that they will only eat toxins when
normal favorite foods are low, but not low enough to starve)

Does the metabolizing of toxins give you a new toxin as reaction product?

[Dan Kolis]

Q: What is meant by pollution set?

Ref: I would personally immediately make pollution sets so they can be aged in situ

Your latest innovation in nomenclature ( in this case ? ): "A forensically traceable volume of polluted earth managed for experimental assays, experimentation, and remediation".

The feedstock itself should be handled similarly if it's extracted or made to order. Both those tracks have different Background document trails.

My observation on such things is newcomers to traceability become infatuated with time stamps. Uniqueness in controls is more important than when it first encountered some human mind.  I like old fashioned barcodes really, but machine readability is not really the essential issue. However systems like this must be machine readable, of course. You will invariably pick QR codes for new work in 2023. Probably the best is if the enum can be a string in a URL:

https:/allset.project.org/23-1005-2654-a

23-1006-a

etc

Also, you obviously need a lexicon of controlled vocabulary.

Maybe a year code + UUID + pkg code is ok. A system likely to work until year 3000 seems ok for me, for instance !

A so called "Smart" versus "dumb" number is old world stuff. a number can be slightly smart, like 2 digits for year, and 'a' for sample form factor; ( size and containment ). Numbers should be 'just a little smart'.

In case you do double blind tests with lab made versus from the wild samples, I suggest the enum conceal the sources specifically. That is a background idea.

There is generally always a bedrock idea in a work like this. "Make anything that works enough we get paid, somehow", is not really a honorable system. Its easily the #1 system in any project, however.

{ sample Start-of-eval } ===> { process p1, p2, pn } ===> { Eval } ===> { Return to the wild }

Each enumerated is an obvious linear baseline.

Do you think you will be handling a large number of samples, generally or endlessly fuss over singular ones for hours each ? 

Normalised to a labour year of 2000 Hrs hands on labor, how many in a calendar year, max ?

I don't particularly feel enabled by my own preexisting knowledge of biotech for pollution abatement to comment on the microbe munching cycle, specifically. Since human beings do absolutely nothing; (except a bit of midnight concealment, lying and blaming ), there is no surprise hidden pollution problems are astonishingly severe. I almost assume there easier to remedy significantly then prove any act is working. Look at Deinococcus radiodurans ! 

The only reason pollution abatement is not achieved is because no institution worth a rats ass is actually trying. It is not necessarily easy, but is also not very difficult. But of course, any rational approach segregates your project(s) to a subset of kinds of contamination. So, again a lexicon of terms matters, as does proving what you have in the little container before and after you do whatever you do.

Regs,

Daniel B. Kolis

[Carlos Castellanos]

Thanks this is helpful. The compost pile won't need to be big ("grandma's back yard" sounds about right). So the spray-applicator you mentioned, I can simply spray it over the compost?

[Dan Kolis]

Pollutants are disproportionately small chemicals that are not quite in the hierarchies of living matter. Stuff like Benzene's, compounds of tin and lead, etc.

Deciding on life versus life may be a distraction of getting after the bad stuff the way its implemented in reality. Asking Google, it coughs up this bad stuffola shortlist:

Lead (Pb)
Petroleum.
Asbestos.
Polycyclic aromatic.
hydrocarbons (PAHs)
Volatile organic compounds.
(VOCs)
Polychlorinated Biphenyls.

Pretty diverse. Since long chain C-C-C petros have existed 'forever' re-absorption into normal living matter must 100% be due to some human-only stupid weird detail associated with the big leaders in that: Human beings.

How deep "Counts' as on-grade, what 'counts' as pollution matters to. ex: making C anything into CO2 is a little questionable. At any moment one of: air land and sea is excluded from being taken too seriously for pollution. Right now, land is the 'that's ok" one, and air is the most fashionable for concerns, with natural water  in 2nd place.

There's a lot to think about in your problem space, aside from succeeding to turn some X into a different X'

[Dakota Hamill]

You can do whatever you want, no one is doing what you're doing, or if they have it's in some journal somewhere.  So you'd be the first one doing it and there is no "right" way.   Are you measuring the remediation?  You would have to try different application routes and see what worked best.  

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/a3a726cb-b5fb-441c-9bf8-35ff77ca4431n%40googlegroups.com.

[Dan Kolis]

Somebody said:

> You can do whatever you want, no one is doing what you're doing, or if they have it's in some journal somewhere. 

> So you'd be the first one doing it and there is no "right" way.   Are you measuring the remediation?  

> You would have to try different application routes and see what worked best.  

Dan K says:

Well, incredibly subsidised organisations of every flavour pretend. All the required spending to achieve no results... is very challenging.

All the controls on results matter immensely, since the actual work is almost easy. 

Since maybe 1 in 200 pretending professionally are mildly interested in actual results, it's not quite hopeless. But a formidable requirement in serious controls is utterly essential. Almost all institutional arrangements are carefully configured to utterly ignore the bad thing that might happen if you figure out anything too specific that works.

But a heap of enumerations and corrective actions, with paperwork of all sorts, is essential. Succeeding in principle is sort of hobbyist fun, sure.  But "This requires more research" is a perfect magic wand.

The first observation is: one way to not pollute earth matter, is, --not dispose of things haphazardly in it. Facing the duplicity of doing that is a small, but non- trivial part of the process of somewhat.

Still fun, even if its  nearly hopeless; ( Since it implies an action which is an unfunded cost to bear by an institution highly capable of defensive mumbling ).

1 in 200; on the very best of days.

Must be a little something to be done. As mentioned, not doing the bad thing in the first place, is a serious milestone, not achieved.

[Dan Kolis]

Hello,

Are you going to fill in the readers here on this project ? There is a significant number of members here, who know things, have access to unique resources, etc.

You can't get mileage from that unless you cough up significant detail, for starters, on what your plan(s) are.

Where, what and when are three good things to describe most human initiatives, I've noticed.

Regards,

Daniel B. Kolis

  

 

[Dakota Hamill]

Respond to his original thread instead of making five new threads with slightly modified subject lines?  It's too hard to follow the conversation.  

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[Dan Kolis]

This is message is 12 in one thread. it is 12 of 12

When you get an email about a list change that interests you, consider it a non actionable update something has 'happened'. I think the subject lines should mildly permute continuously.  click on the URL at the bottom of the email.

Roughly 1/2 of email users where email pop SNMP is reused to make 'threads' like the subject to stay fixed and server software permute however the programmer decided to do so.

I think its fairly unimportant, but apparently a small number of people are pretty interested in it. I left the subject intact on this one so you can see the difference.

Dear God(s) I hope this is enough and there is no "do it bla bla" because "bla2 bla2 bla2". I could forward 50 messages like that for either notion !

Look at the attachment for clarity. the subject line changes do not alter the linked list, or order, or composition as a set.

Regards,

Dan