RE: [compost_tea] Re: Compost Tea 'Data' from Yale

From: Pawlett, Mark <m.pawlett_at_cranfield.ac.uk>
Date: Sun, 20 Feb 2011 10:36:32 +0000

Hi

Thanks v much for the feedback.

any good research would require laboratory work and field trials. You are right, it is important to describe what CTs do to plants. There is plenty of info on its effects as a foliar spray, but very little regarding the effects on the soil and how they affect nutrient cycling processes. That is really my main interest.

Here's hoping that one day I'll have some cash to do some good quality research that will benefit all users.

Mark



________________________________________
From: compost_tea_at_yahoogroups.com [compost_tea_at_yahoogroups.com] On Behalf Of Jason Kalka [shortstop42000_at_yahoo.com]
Sent: 18 February 2011 17:55
To: compost_tea_at_yahoogroups.com
Subject: RE: [compost_tea] Re: Compost Tea 'Data' from Yale

Mark,
I think you bring up excellent points about testing. I think before even attempting these tests you must realize what the results will mean for your plants. I see a lot of these posts and wonder if the posters realize what the various microbes will actually do for their crops. I think results in the garden outweigh anything done in the lab.

Just my two cents.

Jason Kalka
Amature gardener


________________________________
From: Pawlett, Mark <m.pawlett_at_cranfield.ac.uk>
Sent: February 18, 2011 5:56 AM
To: compost_tea_at_yahoogroups.com <compost_tea_at_yahoogroups.com>
Subject: RE: [compost_tea] Re: Compost Tea 'Data' from Yale


Hi

Ok, the debate as I see it is whether the methods that many compost tea enthusiasts use at the moment are sufficient. Due to the complexity of the soil microbial system it is my opinion that microbial and culture based methods are insufficient in describing the interactions of CT and the soil microbial community. The microscopy method used do go some way towards describing the compost tea, but do little if anything in terms of describing the interactions with the soil.

All method have weaknesses. The important thing is to recognise the weaknesses. I wonder if the CT community understands the weaknesses of using microscopy as their main technique?

How about that as a starting point ☺

The link looks great, but unfortunately its not in my neighbourhood. I’m in UK.

Please keep me informed regarding your research. I’d be very interested if you publish anything. Also, if you require collaboration from us then please contact me (m.pawlett_at_cranfield.ac.uk<mailto:m.pawlett_at_cranfield.ac.uk>) and we’ll try and work something out.

Enjoy Seattle.

Mark




From: compost_tea_at_yahoogroups.com [mailto:compost_tea_at_yahoogroups.com] On Behalf Of Tim Wilson
Sent: 17 February 2011 18:28
To: compost_tea_at_yahoogroups.com
Subject: [compost_tea] Re: Compost Tea 'Data' from Yale



Mark,

I still do not see where the debate is. I have no argument with what you have stated and it is not much different than what I have stated.

In particulr though you have not really addressed the weakness I pointed out except to say; "Protozoa and nematodes would require another method, microscopy is only one method"

With my microscopes I can view the active protozoa and nematodes in soil or compost, etc. so indeed it is another tool in the kit for the horticulturist. From some of the studies I've read from USDA and other institutes, which did not include evalution of protists and nematodes of any kind, a microscope would have easily solved this. To the best of my knowledge, the microscope is the favoured tool for seeing protozoa and nematodes in soil and water at the University of British Columbia, the University of Toronto,Institut für Zoologie, Technische Universität Darmstadt, Washington State University, etc. etc.

You might be interested in attending this if you can afford it. It is in my neighborhood.; http://www.3dcourse.ubc.ca/2009/public.php?page=companies

Your questioning applications of compost tea and the microbes contained therein surviving in the soil into which they enter, is quite valid. It is a crap shoot but informally I have observed soil microbial populations changed over a period of time with repeated applications. Along with this, I believe soil properties such as pH have been altered by these (microbes) applications. However, this is all anecdotal information. I'm not saying that I will have published works on the subject but I intend to do some research on this subject (survival of ACT microbes in the soil) over the next 2 years. Right now I'm in the midst of constructing a new laboratory space.

This is going to likely be my last response to you until March as I'm leaving for Seattle to set up a soil microscopy exhibit at a garden show and I'm going mad with preparations.

I am sponsoring a student doing a self-determined study through a Washington institution, with donations of a microscope and resource materials. I don't believe he has a masters but degrees don't mean much to me. I find that many people with degrees sometimes have tunnel vision as a result of imprinting by their favourite instructor/supervisor.

Salutations,
Tim

--- In compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com>, "Pawlett, Mark" <m.pawlett_at_...> wrote:
>
> Hi Tim
>
> The PLFA method (there are others but this one is relatively cheap) will give you a phenotypic fingerprint of the microbial community (or as you say the players in the party), without the need to look down a microscope (I gave that up years ago). It will not give species level but groups, e.g. fungi:bact, G+ve:G-ve, methanotrophs, AM fungi, stress indicators and some others. Protozoa and nematodes would require another method, microscopy is only one method. Another method called tRFLP (terminal restriction length polymorphism) will enable you to study in more detail, such as ammonia oxidising bacteria.
>
> But what is the most important thing here. To define what is there or the function (I'm not taking about the whole food web, rather the bacterial and fungal component). You can make a spectacular compost tea, but if you don't understand the abiotic and biotic constraints of the soil that you are going to apply it to the microbiology will not survive or genes will not function, thereby the compost tea will not work. This is about function, but of course the phenotypic signature is important. Yes the 2 are linked, but there are important situations where the phenotypic fingerprint of the soil microbial community does not change, but the function does, and visa versa. You cannot do this stuff using a microscope.
>
> Check out the journal Soil Biology and Biochemistry. You will be hard pushed to find any microscopy based techniques to describe soil microbial communities in the last 10 years. Horticulturalists use the microscopy techniques as they are easily accessible to them. Not because they are the best methods. Yes, of course the methods that you describe would be useful to a horticulturalist, I'm sure nobody would deny that. But there are more tools in the tool kit of soil microbiology than the ones that you describe. The bridge between the academic and the horticulturalist does need crossing, but that's a wider issue.
>
> Of course, if you want to put your money where your mouth is why don't you fund a MSc student to compare methods, and at the same time answer some fundamental questions that are still unanswered regarding compost tea application. Go on, you know you want to do it. Of course you will be more than happy with the quality of research that we conduct within the department that I work.
>
> Mark
>
>
>
>
>
> From: compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com> [mailto:compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com>] On Behalf Of Tim Wilson
> Sent: 16 February 2011 19:15
> To: compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com>
> Subject: [compost_tea] Re: Compost Tea 'Data' from Yale
>
>
>
> Hi Mark,
>
> I agree and believe that I already stated that it is important to have more than one method of microbial analysis so you have no argument there.
>
> To repeat what I actually said, "To assertain the optimum efficacy of a 'compost tea' or a multiplied microbial extract in liquid one HAS TO observe the existence/numbers of bacteria/archea and the predatory flagellates and naked amoebae."
>
> This is necessary to actually see what players, microbially speaking are at the party. It is a simple thing to peer (pun intended) into a sample down a microscope tube to SEE if there are indeed bacteria/archaea, fungal hyphae and/or conidia, various protozoa and nematodes. One can view this in soil/compost samples as is or after applying various foodstocks to see what microbes are emergent.
>
> I'm glad that you have quoted one of my dear friends <GRIN> Vigdis because, I believe, it was she who originally stressed the importance of direct microscopy in combination with more detailed methods, which you have outlined adequately in your remarks. I believe that E. Ingham, Bryan Griffiths, Marianne Clarholm, Michael Bonkowski and Wilhelm Foissner would likely accord with this approach to microbial estimations/analysis of soil samples. [if you really want I'll dig up the citations]
>
> For the purpose of horticultural activities, one can usually depend on the microscope alone as a tool to evaluate the general microbial population of one's soil, compost and compost tea. This, however, as you have pointed out is not up to par with the measurements required to publish an article. My point still bears out that microbially related studies of compost, soil, compost tea etc. are just as much not up to par if microscopy is not included unless some other technique utilized reveals the 'at least general' populations of ALL related microbial groups. [bacteria/archaea; protozoa; nematodes; fungi]
>
> So when does the debate begin? <enormous grin>
>
> BTW, you will note, I did not attack the student but criticize
> the instructors for failing to provide better guidance. As noted previously, the use of a microscope can be far from expensive and even less expensive than the methods named. I assume Yale can afford some microscopes(?)
>
> Salutations,
> Tim
>
> --- In compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com>, "Pawlett, Mark" <m.pawlett_at_> wrote:
> >
> > Dear Tim
> >
> > So, let's open the debate regarding methods used in the world of soil microbiology.
> >
> > In terms of methods. There are many other methods , and in my opinion, better methods for example PLFA, 16S rDNA transcriptome analysis, RNAi technology, molecular matchmaking, RAPD, T-RFLP and FT/MS. Torsvik (1990) estimated that in 1g of soil there are 4000 different genomic units, based on DNA-DNA reasociation. It is also estimated that 5000 bacterial species have been described ((Pace 1997 1999). Only approximately 1% of the bacterial population can be cultured by standard laboratory practices, and it is not know (in my opinion unlikely) that this 1% represents the bacterial population (Torsvik 1999). An estimated 1, 500, 5000 fungi species exist in the world (Giller 1997) but fungi are much harder to culture in the lab than fungi. This information was retrieved from a review written by Kirk et al 2004 (Journal of Microbial Methods 58: 169-188). Some of these methods are expensive, however some (e.g. PLFA) is certainly not too expensive to anyone already using the other methods of analysis. It may be cheaper, and would provide more useful information.
> >
> > Catabolic profiles are culture independent methods. As such they are not subject to the same biases. Of course it is important to remember that all methods have bias. The important thing it to recognise that bias. The methods described in the report that you refer to not only give microbial biomass, but in addition give a culture-independent method of measuring the catabolic functional profile of the soil microbial community. The method is used considerably globally in the world of soil microbiology (refer to the series of papers started by Degens and Harris starting I think in 1999).
> >
> > Simple methods are only important if they are relevant. It is worthwhile noting that study that involves only microscopy or culture based techniques would not be published in any reputable peer reviewed journal of soil microbiology To test this just have a search and let me know whether you come up with any in the last 10 years.
> >
> > I'd would prefer it if you didn't criticise student (undergrad or MSc) projects that are both limited in time and money. If this continues I will discontinue the debate. Lets now stick to published, peer reviewed, facts and see where it goes. In the above I have referenced the published articles, and you can assume that anything that is not referenced is my opinion.
> >
> > Thanks
> >
> > Mark
> >
> >
> >
> >
> > From: compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com> [mailto:compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com>] On Behalf Of Tim Wilson
> > Sent: 16 February 2011 00:21
> > To: compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com>
> > Subject: [compost_tea] Re: Compost Tea 'Data' from Yale
> >
> >
> >
> > Well, I thought about shutting up but....
> >
> > I skimmed through the student's paper and yes it is a student project and not a journal article. That is no excuse for not including microscopy as part of the methodology. I am consulting a student at a minor western college who is conducting a similar study with much more detail applied.
> >
> > Your statement "Indeed microscopy would NOT be a suitable method for such work. Catabolic profiles are a very important and valid way of describing the functional component of the soil microbial community."
> >
> > seems to me off base. Sure there is value in measuring microbial respiration for overall mass but if one is studying the effects of compost tea in soil, one would think this implies studying the microbial nutrient loop. (it is unfortunate that the one Ingham quote used is not wholly accurate) To assertain the optimum efficacy of a 'compost tea' or a multiplied microbial extract in liquid one HAS TO observe the existence/numbers of bacteria/archea and the predatory flagellates and naked amoebae. This is what drives the microbial nutrient loop. [true that nematodes and arthropods contribute this in the soil but are virtually impossible to maintain in compost tea]. To not include microscopy and related microbial counts in such a study is ridiculous and I'll easily debate anyone on this issue. There is no great expense involved in this. If you set up the study, I'll provide the microscope and counting wells. Don't get me wrong. This should be included with CO2 efflux and respiration related staining as well. The expensive part comes in when we want to ID the microbes to species.
> >
> > I am ranting but I get so sick to death with these studies that do not even encompass the simplest things. Look at the studies conducted by the USDA and Canadian Min of Ag where they did not even consider the protozoa population when they determined that e-coli can grow in compost tea (only after inoculating it with e-coli of course). Protozoa eat e-coli. Hello.
> >
> > Looking down a microscope tube to see if there are bacteria/archaea and flagellates and naked amoebae is so simple that even a caveman can do it.
> >
> > I don't know why it is considered expensive to evaluate whether there are nematodes in ones compost or soil. It is as tough as looking to see if there are robins in the back yard.
> >
> > BTW, Peter of Compostwerks LLC is hardly unamed.
> >
> > Salutations,
> > Tim Wilson
> > www.microbeorganics.com
> >
> > --- In compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com>, "Pawlett, Mark" <m.pawlett_at_> wrote:
> > >
> > > Hi All
> > >
> > > Just to make this clear. I can't see any evidence that this was actually published. Published scientific papers are all subject to peer review examination by fellow scientists in the field. This appears to be a student research project report. Nothing more and nothing less. For an undergrad or MSc research project this report is fit for this purpose. Only the very top students at either undergraduate or MSc level produce work of sufficient quality to publish in a scientific journal.
> > >
> > > You are quite correct in some of your statements, there are some flaws in the experiment. The compost tea, soil and compost are inadequately described. Replication is unclear, and there are some problems with the statistical design. The results and conclusion sections could be clearer. This project is not perfect by a long shot, however I certainly would NOT describe this as shocking.
> > >
> > > Student projects have limited time and money. As such they cannot cover all analysis (e.g. nematodes). In order to gain both it is necessary to have some form of financial investment from the users. I personally (as a Research Fellow of Soil Microbial Ecology) have had an interest in compost teas research for some time. Despite numerous attempts to find funds for compost tea research from the users and research councils, I have had very little in terms of financial assistance for research into compost teas. Of course if anyone has any suggestions as to where I can find funds then I will certainly follow it up. It is my intention to supervise a PhD student research programme on compost teas. Such a programme would allow a student to research compost teas for 3 years, but of course financial investment is required to have scientifically robust data that can withstand the peer review process necessary for scientific papers.
> > >
> > > I would also like to stress that the methods used were also suitable. Indeed microscopy would NOT be a suitable method for such work. Catabolic profiles are a very important and valid way of describing the functional component of the soil microbial community. There are numerous per reviewed papers that are available that demonstrate this. Microscopy has inherent flaws in terms of bias.
> > >
> > > The methods DO NOT only give data on bacteria. The data does not differentiate between bacteria and fungi, but rather gives a functional profile of the soil microbial community as a whole. Thus data includes both bacteria and fungi. A more detailed study would allow the research to use the methods to differentiate between fungi and bacteria. But the substrates used in the method are suitable, would be utilised fungal community, and have been published in peer reviewed scientific journals.
> > >
> > > I wonder whether the un-named writer of the below had the courtesy to send his questions to the authors of the work to give them a chance to respond before sending into the group.
> > >
> > > Dr Mark Pawlett
> > > Research Fellow of Soil Microbial Ecology at Cranfield University.
> > >
> > >
> > >
> > >
> > > From: compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com> [mailto:compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com>] On Behalf Of Peter
> > > Sent: 15 February 2011 00:22
> > > To: compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.com>
> > > Subject: [compost_tea] Compost Tea 'Data' from Yale
> > >
> > >
> > >
> > > Hi folks;
> > >
> > > I just came across a published paper entitled "Closing the Loop: Alternative Land Management at Yale". The paper's root is located at http://environment.yale.edu/hixon/student-research/student-research-interns/
> > >
> > > The paper is located here; http://environment.yale.edu/hixon/files/pdf/2010_Emily_Stevenson.pdf
> > >
> > > Does anyone else find this paper a bit shocking? Here's another case of flawed methodology and misunderstanding on how biological systems perform in the real world.
> > >
> > > There seems to be a complete disconnect on how compost tea is made.
> > >
> > > * Too many foods (certainly an anerobic tea they're referencing here)
> > > * No testing of compost tea
> > > * No mention of brewer design aside from a 'bubbler'
> > > * No DO data
> > >
> > > No testing on their 'food waste' compost.
> > >
> > > No mention of microscopy...at all.
> > >
> > > Flawed methodology in before/after soil testing. Only bacteria are measured using narrow range of foods. Where's the data on fungi, nematodes and prots??
> > >
> > > There's a misunderstanding of organic matter accumulation in soils. Can we expect appreciable increase in OM using 1,500 grams of compost, making tea, diluting 1:1 and applying multiple times in a 6 X 6 meter area?
> > >
> > > There's a major disconnect as to how to apply CT on a large scale and even the basics of equipment involved. It reads as though they're quite resistant to changing there current chemical system.
> > >
> > > I see lots of logarythmic scatter gram but not much in the way of science.
> > >
> > > I'd expect to see somthing more substantial. This is a dissapointment from an institution as fine as Yale.
> > >
> >
>



Received on Sun Feb 20 2011 - 15:17:27 EST

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