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

From: Mary McCanta <mary_at_mccanta.com>
Date: Thu, 17 Feb 2011 11:14:23 -0800

Hi Mark -

On a practical level, is there any way for a home compost tea maker to
do any of these tests, like PFLA, or are these all assays that require
extensive lab equipment? I'm afraid I *don't* understand the abiotic and
biotic constraints of the soil (yet) but I do want my compost tea to
work! Do you have any ideas about tests I could do at home that would
help ensure that the tea I'm making will work for my particular soil?
Right now microscopy is the only way I know of to inexpensively check
the contents of the tea, and I can do pH tests on my soil, but if you
have other tests that would be useful in this context (my "lab" is my
basement) then I would greatly appreciate it.

Thanks! - Mary



On 2/17/2011 2:58 AM, Pawlett, Mark 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_at_yahoogroups.com] *On Behalf Of *Tim Wilson
> *Sent:* 16 February 2011 19:15
> *To:* compost_tea_at_yahoogroups.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>, "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_at_yahoogroups.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>
> > 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>,
> "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_at_yahoogroups.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>
> > > 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 Thu Feb 17 2011 - 14:23:12 EST

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