Talk:Bioremediation

Recent Developments in Biotechnology
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Major revision of article
I, rcborden2, am a paid editor and am planning on preparing a major revisions of this page. The current page has a number of significant problems, including the following:


 * 1) The current page has very limited discussion of the two most common approaches, aerobic bioremediation and anaerobic bioremediation.
 * 2) The current page has an undue emphasis on fungal bioremediation (mycoremediation) and genetically engineered microorganisms(GEMs).  While the potential of these two approaches was recognized in the 1980s, they have not developed into widely applied technologies because of regulatory constraints on permitting of GEMs and operational and performance issues with fungal approaches.  The current emphasis on these two approached gives the reader the impression that these are commonly implemented technologies; they are not.
 * 3) There are significant issues with the organization of the article. A wide variety of different topics are briefly mentioned at different places without being developed in detail.
 * 4) Several different topics are included in this article that are not really bioremediation, but are related technologies.  For example, use of biochar as a sorbent to sequester metals can be effective in reducing metals toxicity.  However, sorption is a physical chemical process, not a biological process.  Similarly, use of  microorganisms to treat liquid waste streams is a standard wastewater treatment approach (e.g., activated sludge, trickling filters, rotating biological contactors, etc.).  However, specialists in this area would not refer to this as 'bioremediation', but instead refer to it as biological wastewater treatment.
 * 5) Bioremediation of oil spills in the ocean, on beaches and wetlands is an effective, well developed technology.  However, I am not an expert in this area and am not planning on contributing to this specific area in the near future.
 * 6) Bioremediation and remediation in general are active processes where energy, organisms or  some other material is added to improve treatment.  Monitored natural attenuation (MNA) is a passive process relying on a variety of naturally occurring processes including diffusion, dispersion, sorption, biotic and abiotic degradation. As such, MNA should not be included in the bioremediation article.  Instead, a separate article should be developed on MNA.  I propose to remove MNA from this article and develop a new article, once work on this article is nearing completion.
 * 1) Several different topics are included in this article that are not really bioremediation, but are related technologies.  For example, use of biochar as a sorbent to sequester metals can be effective in reducing metals toxicity.  However, sorption is a physical chemical process, not a biological process.  Similarly, use of  microorganisms to treat liquid waste streams is a standard wastewater treatment approach (e.g., activated sludge, trickling filters, rotating biological contactors, etc.).  However, specialists in this area would not refer to this as 'bioremediation', but instead refer to it as biological wastewater treatment.
 * 2) Bioremediation of oil spills in the ocean, on beaches and wetlands is an effective, well developed technology.  However, I am not an expert in this area and am not planning on contributing to this specific area in the near future.
 * 3) Bioremediation and remediation in general are active processes where energy, organisms or  some other material is added to improve treatment.  Monitored natural attenuation (MNA) is a passive process relying on a variety of naturally occurring processes including diffusion, dispersion, sorption, biotic and abiotic degradation. As such, MNA should not be included in the bioremediation article.  Instead, a separate article should be developed on MNA.  I propose to remove MNA from this article and develop a new article, once work on this article is nearing completion.
 * 1) Bioremediation and remediation in general are active processes where energy, organisms or  some other material is added to improve treatment.  Monitored natural attenuation (MNA) is a passive process relying on a variety of naturally occurring processes including diffusion, dispersion, sorption, biotic and abiotic degradation. As such, MNA should not be included in the bioremediation article.  Instead, a separate article should be developed on MNA.  I propose to remove MNA from this article and develop a new article, once work on this article is nearing completion.
 * 1) Bioremediation and remediation in general are active processes where energy, organisms or  some other material is added to improve treatment.  Monitored natural attenuation (MNA) is a passive process relying on a variety of naturally occurring processes including diffusion, dispersion, sorption, biotic and abiotic degradation. As such, MNA should not be included in the bioremediation article.  Instead, a separate article should be developed on MNA.  I propose to remove MNA from this article and develop a new article, once work on this article is nearing completion.

My proposed outline for the article is as follows:


 * 1) Introduction -- General approach of altering environmental conditions to stimulate growth of microorganisms to degrade the target pollutants.  Most bioremediation processes involve oxidation-reduction reactions where either an electron acceptor (commonly oxygen) is added to stimulate oxidation of a reduced pollutant (e.g. hydrocarbons) or an electron donor is added to reduce oxidized pollutants (nitrate, perchlorate, oxidized metals, chlorinated solvents, explosives and propellants).  In both these approaches, additional nutrients, vitamins, minerals, pH buffers, and microbial cultures may be added to optimize conditions for the microorganisms.
 * 2) Aerobic bioremediation is the most common form of oxidative bioremediation process where oxygen is provided as the electron acceptor for oxidation of hydrocarbons, PAHs, phenols, and other reduced pollutants.  Oxygen is generally the preferred electron acceptor because of the higher energy yield and because oxygen is required for some enzyme systems to initiate the degradation process.  Common approaches for providing oxygen include tilling surface soils (land farming), windrow composting and circulating air through the vadose zone (bioventing) using blowers or passive barometric pumping.  Simulating aerobic biodegradation in groundwater is more challenging due to the relatively low solubility of oxygen in water.  Approaches for oxygen addition below the  water  table  include: a) extracting groundwater, aerating it at the surface and then recirculating the oxygenated water through the aquifer; b) injecting air below the water table (air sparging); and c) addition of hydrogen peroxide, calcium peroxide or magnesium peroxide which decomposes releasing oxygen.  In some cases,  alternative electron acceptors have been used including nitrate (NO3) and sulfate (SO4).
 * 3) Anaerobic bioremediation involve the addition of an electron donor to: 1) deplete O2, NO3-, and reactive sediment-bound Mn[III/IV], Fe[III], and SO4+2; and 2) stimulate the biological and/or chemical reduction of the oxidized pollutants.  This approach can be employed to treat a broad range of contaminants including chloroethenes, chloroethanes, chloromethanes, chlorinated cyclic hydrocarbons, various energetics (e.g., perchlorate, RDX, TNT), and nitrate.  Hexavalent chromium (Cr[VI]) and uranium (U[VI]) can be reduced to less mobile and/or less toxic forms (e.g., Cr[III], U[IV]).  Similarly, reduction of sulfate to sulfide (sulfidogenesis) can be used to precipitate certain metals (e.g., zinc, cadmium, and cobalt) The choice of substrate and the method of injection depend on the contaminant type and distribution in the aquifer, hydrogeology, and remediation objectives.  Substrate can be added using conventional well installations, by direct-push technology, or by excavation and backfill such as permeable reactive barriers (PRB).  Slow-release products composed of edible oils or solid substrates tend to stay in place for an extended treatment period.  Soluble substrates or soluble fermentation products of slow-release substrates can potentially migrate via advection and diffusion, providing broader but shorter-lived treatment zones.  The added organic substrates are first fermented to hydrogen (H2) and volatile fatty acids (VFAs).  The VFAs, including acetate, lactate, propionate and butyrate, provide carbon and energy for bacterial metabolism.
 * 4) Nutrients - In some cases, major inorganic nutrients (N, P), micronutrients, vitamins, and other materials are added to improve conditions for microbial respiration.
 * 5) pH Adjustment - Acids, bases and buffers may be added to adjust and maintain the pH in an appropriate range for the desired bioremediation process.
 * 6) Bioaugmentation - In many cases, addition of specialized microorganisms is not required since the microflora has evolved to degrade a wide variety of pollutants.  However under certain circumstances, addition of specialized microbial cultures (bioaugmentation) can accelerate pollutant degradation.  Bioaugmentation is typically most effective when treating xenobiotic chemicals (e.g. certain pesticides, chlorinated solvents, etc.) and unusual or harsh environmental conditions (high or low pH, high salinity, low temperatures, inhibitory compounds, radioactivity).
 * 7) Specialized Treatments and complementary approaches - The items in the list above cover the major approaches used to stimulate bioremediation.  However, there are numerous modifications to this basic approach.  A few of these will be mentioned here including current material on biochar to sequester metals and reduce toxicity, phytoremediation, etc.
 * 1) pH Adjustment - Acids, bases and buffers may be added to adjust and maintain the pH in an appropriate range for the desired bioremediation process.
 * 2) Bioaugmentation - In many cases, addition of specialized microorganisms is not required since the microflora has evolved to degrade a wide variety of pollutants.  However under certain circumstances, addition of specialized microbial cultures (bioaugmentation) can accelerate pollutant degradation.  Bioaugmentation is typically most effective when treating xenobiotic chemicals (e.g. certain pesticides, chlorinated solvents, etc.) and unusual or harsh environmental conditions (high or low pH, high salinity, low temperatures, inhibitory compounds, radioactivity).
 * 3) Specialized Treatments and complementary approaches - The items in the list above cover the major approaches used to stimulate bioremediation.  However, there are numerous modifications to this basic approach.  A few of these will be mentioned here including current material on biochar to sequester metals and reduce toxicity, phytoremediation, etc.
 * 1) Bioaugmentation - In many cases, addition of specialized microorganisms is not required since the microflora has evolved to degrade a wide variety of pollutants.  However under certain circumstances, addition of specialized microbial cultures (bioaugmentation) can accelerate pollutant degradation.  Bioaugmentation is typically most effective when treating xenobiotic chemicals (e.g. certain pesticides, chlorinated solvents, etc.) and unusual or harsh environmental conditions (high or low pH, high salinity, low temperatures, inhibitory compounds, radioactivity).
 * 2) Specialized Treatments and complementary approaches - The items in the list above cover the major approaches used to stimulate bioremediation.  However, there are numerous modifications to this basic approach.  A few of these will be mentioned here including current material on biochar to sequester metals and reduce toxicity, phytoremediation, etc.
 * 1) Specialized Treatments and complementary approaches - The items in the list above cover the major approaches used to stimulate bioremediation.  However, there are numerous modifications to this basic approach.  A few of these will be mentioned here including current material on biochar to sequester metals and reduce toxicity, phytoremediation, etc.

In the outline above, I have not yet included references. Once I get feedback on the proposed approach, I will fill in additional detail and provide extensive referencing. I will avoid self-referencing. The primary references will be US Government documents (USEPA, SERDP, ESTCP) which public domain and may be copied and distributed freely. All tables and figures will be from public domain sources.

Thanks Rcborden2 (talk) 19:07, 28 January 2017 (UTC)


 * Well, in the main this sounds very good. There are not enough volunteers about to fix all the outdated, poorly written and poorly cited science articles; both your comments on the existing text and proposals for improvement are on target and welcome. But why are you being paid to do this task, and how can we be assured you will edit neutrally as is required? Chiswick Chap (talk) 19:24, 28 January 2017 (UTC)


 * The agency that is funding this work is the Environmental Technology Certification Program (ESTCP) which is described in more detail on my user page. They fund a great deal of research on bioremediation, but recognize that much of this work never reaches the intended audience.  This work is part of a technology transfer effort to more widely communicate their research results.  I will do my very best to present neutral, unbiased science.  The other editors of this page will need to check my references to ensure the writing is neutral, complete, and appropriately referenced. In addition to the public domain references I mentioned above, I will also include peer reviewed journals.  Usually, the reports are free to download, but you need to pay to access the peer reviewed journals.Rcborden2 (talk) 16:46, 29 January 2017 (UTC)


 * Support: Thanks. I've seen also your very helpful statement on your user page. I'm in favour. Chiswick Chap (talk) 16:46, 29 January 2017 (UTC)


 * Please read WP:LEAD - what you are calling the "introduction" just summarizes the body of the article.  You should concentrate on improving the body of the article, and when you are done, update the lead to summararize the body.
 * Also please use more recent refs (last five years or so - going further back than that is generally problematic), and please avoid primary sources (a paper in the scientific literature in which people do experiments and describe them and the results, is a primary source in Wikipedia). Please use literature review articles in the scientific literature when you go that literature; publications by the EPA like the current ref #1 are great.  There are probably great sources from the WHO and EU like those as well.
 * It is really helpful if you use reference templates. There is an automated tool available in the toolbar above the edit window that will autofill and often will provide useful links, so that others can verify that the content accurately summarizes the source, and so that people can easily go find the sources and learn more (links are not necessary but they are very much preferred).Jytdog (talk)   21:54, 8 October 2017 (UTC)

Sdunyak (talk) 15:52, 13 February 2018 (UTC)I will be working through Michigan State University with another person to contribute to the bioaugmentation section of this paper. It is lacking properly sourced content, depth, and a proper explanation/background of the purpose, uses, and problems with bioaugmentation.

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Deleted Mycoremediation section
Few months ago Mycoremediation became a section of Bioremediation, since the content was little and lacked of references. I rewrote the article and added all the needed references so I place it back in its own page and deleted the section here. I added link to mycoremediation in See also and at the beginning, together with phytoremediation and the others. Basically, I'm using the same pattern as with phytoremediation.

Hope that is ok with everyone. --Beleriandcrises (talk) 11:52, 2 October 2017 (UTC)
 * I was thinking of adding more details about mutualistic Mycorrhizal remediation to the Mycoremediation article under "Synergy with Phytoremediation" but I may have enough information to dedicate to a whole article on the topic. I have a rough outline in my Sandbox. Whatsit369 (talk) 00:04, 16 October 2017 (UTC)
 * I went ahead and created a Mycorrhizal Bioremediation page, and will work on incorporating its links and info into other pages. Whatsit369 (talk) 18:54, 2 June 2018 (UTC)

Addition of a disadvantages section
Hi, I am thinking of including a section on the disadvantages of bioremediation. The 3 sources that I will be using are:

'''Bioremediation. An overview*''' by M. Vidali https://www.iupac.org/publications/pac/pdf/2001/pdf/7307x1163.pdf

A comprehensive overview of elements in bioremediation by Juwarkar, Asha A; Singh, Sanjeev K; Mudhoo, Ackmez https://link.springer.com/article/10.1007/s11157-010-9215-6

Factors limiting bioremediation technologies by R. Boopathy http://www.sciencedirect.com/science/article/pii/S0960852499001443?via%3Dihub

Lizhuang97 (talk) 21:17, 8 October 2017 (UTC)
 * The first ref is 16 years old and the third is 17 years old; there is generally no good reason to use refs that are this old. The 2nd ref is fine date-wise and in terms of the kind of source it is. Jytdog (talk) 21:55, 8 October 2017 (UTC)

Sourcing
this is field that has moved a lot. way too many refs from 1980s and 1990s. We should be using recent, authoritative reviews and government publications here. Jytdog (talk) 21:39, 8 October 2017 (UTC)


 * I understand the concern about older references. However, most of the good work on bioremediation of hydrocarbons was done in the 1980s and there really are not good overview articles.  The work on anaerobic bio is much more recent and current.


 * Also, I am trying to figure out how to effectively edit. Others are editing my changes before I have even finished adding them.  — Preceding unsigned comment added by Rcborden2 (talk • contribs) 23:01, 9 October 2017 (UTC)
 * I replied on your talk page, where you posted the same thing. We can keep the "how-to" discussion there, and use this page to discuss specific content issues as they arise... Jytdog (talk) 23:22, 9 October 2017 (UTC)
 * The article currently has the banner "This article needs additional citations for verification.". The article previously had an excellent set of references that someone removed.  They should be restored.Rcborden2 (talk) 00:42, 10 October 2017 (UTC)
 * The article formerly had a set of out-dated and badly formatted citations. Please understand that editing Wikipedia is not like writing some scientific paper. The editing community has developed policies and guidelines that govern content.  Please start engaging with them. We understand that it is hard for experts to adapt - the essay WP:EXPERT discusses that. Jytdog (talk) 00:48, 10 October 2017 (UTC)

In this page, there is content that needs to be cited. For example under the aerobic section of the page the sentence "Oxygen is generally the preferred electron acceptor because of the higher energy yield and because oxygen is required for some enzyme systems to initiate the degradation process." must be cited. The information is specific and not common knowledge, therefore, it should be backed by a reliable source.Dbanyaib (talk) 22:09, 6 November 2017 (UTC)

Another problem I have found with this Wikipedia page is overrepresentation. Of the few sources cited, half of them are from the same government agency, the EPA. Having this many citations from one source can create a bias in the paper because this organizations viewpoint outways the other sources cited on the page. Dbanyaib (talk) 22:09, 6 November 2017 (UTC)

Another example of a sentence that should be cited in the article is "However, the amount of oxygen that can be provided by this method is limited by the low solubility of oxygen in water (8 to 10 mg/L for water in equilibrium with air at typical temperatures)." Any specific numbers or data like the ones used in this sentence require a reliable source showing that it is indeed true.Dbanyaib (talk) 22:24, 6 November 2017 (UTC)

Caption
User:Vaselineeeeeeee, not sure what is going on. this and the restoration here were unsourced. The source added here talks about a place in Idaho and the various kinds of pollutants, but doesn't mention bioremediation nor the whey etc they are pumping in. The file at the commons gives a bit of quotation from the image source, so i found that (it is here) - they say they are using bioremediation to remove TCE, not radioactive stuff. Jytdog (talk) 14:43, 13 October 2017 (UTC)


 * Take a look at Bioremediation of radioactive waste. If the searching you've done shows it's not radioactive waste, then maybe something needs to be done on that page as well. The image is clearly showing a radioactive waste symbol on the apparatus. If you're about the sourcing and not about controlling this page as I've seen you've recently pushed other editors away, then consistency among articles is important. Vaselineeeeeeee★★★ 14:49, 13 October 2017 (UTC)

Picture and its caption
The source provided for this image at the commons is somebody's the Department of Energy's Flickr account. The caption at the commons takes the quote at the Flicr page, and I tracked that down the source of the words which is the ref provided in the caption now) but that source doesn't discuss radiation. The picture clearly has something that looks like the radiation symbol on it. There is no sign of any bioremediation going on in the picture.  So this is a mess.



Image was used also at
 * Biostimulation
 * Geomicrobiology
 * Bioremediation of radioactive waste
 * In situ bioremediation

-- Jytdog (talk) 21:40, 14 October 2017 (UTC) (corrected per below Jytdog (talk) 01:57, 15 October 2017 (UTC))


 * It's not "somebody's" Flickr account, it's the U.S. Department of Energy Flickr account. Oddly enough, the link in your source doesn't have the image, but another page with the same title and nearly identical address includes the picture and discusses it. It does not discuss the radiation symbol, and I agree that is a puzzle, but not a justification for removing a reliably sourced image from multiple pages. RockMagnetist (DCO visiting scholar) (talk) 00:08, 15 October 2017 (UTC)
 * Why people have cows over discussion is beyond me - it is not like I am seeking to delete this. Just discuss it.
 * My attention was called to this image by by this edit which actually said that bioremediation was being used to remove radioactive matter. If you look at the list you will see it was also used in the Bioremediation of radioactive waste article.
 * I don't think the image is helpful to illuminate anything - it is tank marked with a symbol people associate with radiation sitting out on the plains. Whey and sodium lactate are not dangerous materials and nothing in the picture suggests those materials or anything like that being pumped into the well.
 * Good point on the source of the image though. Jytdog (talk) 01:57, 15 October 2017 (UTC)


 * Sorry I gave you the impression that I'm having a cow. Not really. I just think that you were overstating the problem, and it would have been better to start a discussion before removing the image. I agree that it isn't particularly illuminating, but it is hard to find good images on bioremediation (even if you ignore the copyright restrictions), and I think that images make a page more inviting to the reader even if they don't add much information. If you can find a better image, I'd be happy to use it.


 * Looking at the link I provided, I see that the trichloroethylene was used to remove grease from nuclear engines. So maybe there is some nuclear contamination. RockMagnetist (DCO visiting scholar) (talk) 04:42, 15 October 2017 (UTC)


 * For what little it may be worth, I have seen such signs on equipment where flow sensing is undertaken using detectors using radio isotopes. Presumably this avoids using mechanical flow measurement in remote areas where failure might take a long time to detect and rectify. An example (perhaps not a good one) is here.  Velella  Velella Talk 09:54, 15 October 2017 (UTC)


 * better pics
 * from flikr
 * stuff being pumped into the ground, guy with clipboard
 * similar but inside where the stuff is mixed
 * 2 women scientists with soil in petri dishes testing bacteria to see what works
 * methane tanks for feeding bioremediation bacteria
 * from commons
 * File:Biosorption,_biomineralization_and_bioaccumulation_of_radionuclides_(en).png (for radiation article)

-- Jytdog (talk) 21:07, 15 October 2017 (UTC)
 * I don't think most of those figures are better. Instead of a well doing nothing, we have three pictures of a guy looking at a pressure meter/valve/methane tank doing nothing. At least the well is in a scenic spot and comes with an informative caption and citation. The biosorption/etc. figure is a good match for a section of that name, but is a little too big and information-rich for a section in Geomicrobiology that is summarizing the whole subject. The two scientists might be a good choice, though. I'll add it to Commons and try it out. RockMagnetist (DCO visiting scholar) (talk) 23:08, 15 October 2017 (UTC)
 * I have added the two scientists image, and I think it is an improvement. Thanks! RockMagnetist (DCO visiting scholar) (talk) 23:17, 15 October 2017 (UTC)

Vague
The information presented on this page is often vague and does not take the appropriate time to explain the complicated topics covered so that the general public would be able to understand what exactly is being expressed. Any word or phrase used on this page that is not common knowledge should be explained in a sentence or two following or preceding their use in writing.Dbanyaib (talk) 22:10, 6 November 2017 (UTC)

An example of this lack of specific explanation is "Under ideal conditions, the biodegradation rates of the low- to moderate-weight aliphatic, alicyclic, and aromatic compounds can be very high." The article mentions biodegradation which has yet to be explained in the article and there is not a link to another article explaining it. Dbanyaib (talk) 22:31, 6 November 2017 (UTC)

Metals Section
There current sections on heavy metals (chromium, cadmium, lead,) have lots of background information on these metals that is not directly linked to bioremediation. I proposed to combine these sections into a single section on metals. The section will discuss several different metals remediation approaches including biosorption (focus of current articles), redox changes to immobilize, and sulfide precipitation. Rcborden2 (talk) 13:44, 26 August 2018 (UTC)

Summary of edits
I have recently restructured/updated the flow of the article and added sources. I have also moved the section about oxidation-reduction reactions to the “bioventing” section. I have taken away the separate “aerobic” and “anaerobic” sections as there was little information about anaerobic bioremediation. The previous anaerobic section was moved to the “biostimulation” section. I have used in-situ and ex-situ to separate each bioremediation process. With these edits there is still a lot of opportunity to expand on anaerobic bioremediation. Please let me know if there are any suggestions or changes that should be made. StolteKate (talk)

Slightly misleading
While many of us wish and hope that bioremediation was widely employed and highly effective, I worry that it is neither. So I really toned down this article so that innocent readers are not led to believe that these techniques are being used on a large scale. These green topics attract a lot of hopeful editors who want promise to be reality, but readers are here to collect sober knowledge on the current situation. Stated more bluntly, bioremediation is largely inadvertent, and human induced processes such as biostimulation are rare. I could find no large scale apps, e.g. oil spills, chemical disasters, etc that were solved by bioremediation. Hopefully, I am wrong.--Smokefoot (talk) 16:45, 6 March 2022 (UTC)

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