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

From: Pawlett, Mark <m.pawlett_at_cranfield.ac.uk>
Date: Fri, 18 Feb 2011 11:29:14 +0000

Hi Mary

Yes, sorry for that. But unfortunately the answer is that it's down to mon=
ey. Yes you could get the work done if you was prepared to pay (something =
like about £80 per samples), but it does need lab equipment that you coul=
dn't have in the home.

Really though, it wouldn't benefit the home tea brewer to run individual te=
sts in this way (irrespective of method). You would need money to build a =
historic database to test your system, test the soil, see how they interact=
, and observe over time. This is beyond the scope of most home brewers.

If you want the microbiology of the tea to influence the soil then you will=
 have to ensure that there are no abiotic constraints, the primary one bein=
g pH. If your pH of the tea and soil don't match its highly unlikely that =
your tea microbiology will survive.

The reality is that given the complexity of the soil microbial system it is=
 actually very difficult (for either academic scientist or home brewer) to =
predict the impact of a given tea on the soil microbiology (there has been =
very little, if any convincing research on this that had been published in =
academic journals). Microscopy will give you useful, albeit limited inform=
ation about the tea, but will not tell you how the tea will interact with t=
he soil that you are applying it to.

My advice given the money constraints of most home brewers would be to oper=
ate on a trial and error basis. If it works then fine, if not then alter t=
he brewing process. Of course trial and error where gardens are concerned =
is difficult due to limited space, and that you have to wait some time for =
your results to become apparent.

I'm guessing that my answer didn't help too much (I'm also guessing that so=
me in this group won't like my answers to some questions). But it is very =
important for a group such as this to recognise that lack of research that =
has been dedicated to the impact of compost teas on soil microbiology. Ther=
e has been far more regarding the impact that the tea has as a foliar spray=
. Personally I'd love to have funds to study the interactions between com=
post tea microbiology and that of the soil. Maybe one day.

Please ask if you don't understand any of the above as I am fully aware tha=
t most home-brewers may not understand some scientific lingo that is used.

Mark




From: compost_tea_at_yahoogroups.com [mailto:compost_tea_at_yahoogroups.com] On B=
ehalf Of Mary McCanta
Sent: 17 February 2011 19:14
To: compost_tea_at_yahoogroups.com
Subject: Re: [compost_tea] Re: Compost Tea 'Data' from Yale



Hi Mark -

On a practical level, is there any way for a home compost tea maker to do a=
ny of these tests, like PFLA, or are these all assays that require extensi=
ve lab equipment? I'm afraid I *don't* understand the abiotic and biotic co=
nstraints of the soil (yet) but I do want my compost tea to work! Do you h=
ave any ideas about tests I could do at home that would help ensure that th=
e 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 use=
ful in this context (my "lab" is my basement) then I would greatly apprecia=
te 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 gi=
ve you a phenotypic fingerprint of the microbial community (or as you say t=
he players in the party), without the need to look down a microscope (I gav=
e that up years ago). It will not give species level but groups, e.g. fung=
i:bact, G+ve:G-ve, methanotrophs, AM fungi, stress indicators and some othe=
rs. Protozoa and nematodes would require another method, microscopy is onl=
y one method. Another method called tRFLP (terminal restriction length pol=
ymorphism) will enable you to study in more detail, such as ammonia oxidisi=
ng 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 do=
n'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 fu=
nction, thereby the compost tea will not work. This is about function, but=
 of course the phenotypic signature is important. Yes the 2 are linked, bu=
t there are important situations where the phenotypic fingerprint of the s=
oil microbial community does not change, but the function does, and visa ve=
rsa. You cannot do this stuff using a microscope.

Check out the journal Soil Biology and Biochemistry. You will be hard push=
ed to find any microscopy based techniques to describe soil microbial commu=
nities in the last 10 years. Horticulturalists use the microscopy techniqu=
es as they are easily accessible to them. Not because they are the best me=
thods. Yes, of course the methods that you describe would be useful to a h=
orticulturalist, 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, b=
ut 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 fun=
damental questions that are still unanswered regarding compost tea applicat=
ion. Go on, you know you want to do it. Of course you will be more than h=
appy with the quality of research that we conduct within the department tha=
t I work.

Mark





From: compost_tea_at_yahoogroups.com<mailto:compost_tea_at_yahoogroups.com> [mail=
to:compost_tea_at_yahoogroups.com] On Behalf Of Tim Wilson
Sent: 16 February 2011 19:15
To: compost_tea_at_yahoogroups.com<mailto: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 'co=
mpost tea' or a multiplied microbial extract in liquid one HAS TO observe t=
he existence/numbers of bacteria/archea and the predatory flagellates and n=
aked 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 hypha=
e 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 mic=
robes 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 mic=
roscopy in combination with more detailed methods, which you have outlined =
adequately in your remarks. I believe that E. Ingham, Bryan Griffiths, Mari=
anne Clarholm, Michael Bonkowski and Wilhelm Foissner would likely accord w=
ith this approach to microbial estimations/analysis of soil samples. [if yo=
u 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, co=
mpost 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' popula=
tions of ALL related microbial groups. [bacteria/archaea; protozoa; nematod=
es; 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_...><mailto:m.pawlett_at_...> wrote:
>
> Dear Tim
>
> So, let's open the debate regarding methods used in the world of soil mic=
robiology.
>
> In terms of methods. There are many other methods , and in my opinion, be=
tter methods for example PLFA, 16S rDNA transcriptome analysis, RNAi techno=
logy, molecular matchmaking, RAPD, T-RFLP and FT/MS. Torsvik (1990) estimat=
ed 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 bee=
n described ((Pace 1997 1999). Only approximately 1% of the bacterial popul=
ation 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. Th=
is information was retrieved from a review written by Kirk et al 2004 (Jour=
nal 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 m=
ore 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 metho=
ds described in the report that you refer to not only give microbial biomas=
s, but in addition give a culture-independent method of measuring the catab=
olic functional profile of the soil microbial community. The method is used=
 considerably globally in the world of soil microbiology (refer to the seri=
es 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 micr=
obiology To test this just have a search and let me know whether you come u=
p with any in the last 10 years.
>
> I'd would prefer it if you didn't criticise student (undergrad or MSc) pr=
ojects that are both limited in time and money. If this continues I will di=
scontinue 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>] O=
n 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 p=
art of the methodology. I am consulting a student at a minor western colleg=
e 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 respirat=
ion for overall mass but if one is studying the effects of compost tea in s=
oil, one would think this implies studying the microbial nutrient loop. (it=
 is unfortunate that the one Ingham quote used is not wholly accurate) To a=
ssertain the optimum efficacy of a 'compost tea' or a multiplied microbial =
extract in liquid one HAS TO observe the existence/numbers of bacteria/arch=
ea and the predatory flagellates and naked amoebae. This is what drives the=
 microbial nutrient loop. [true that nematodes and arthropods contribute th=
is 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 rid=
iculous and I'll easily debate anyone on this issue. There is no great expe=
nse 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 ef=
flux 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 ev=
en 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 popul=
ation 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 f=
lagellates 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 the=
re are robins in the back yard.
>
> BTW, Peter of Compostwerks LLC is hardly unamed.
>
> Salutations,
> Tim Wilson
> www.microbeorganics.com<http://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 actuall=
y published. Published scientific papers are all subject to peer review exa=
mination by fellow scientists in the field. This appears to be a student re=
search project report. Nothing more and nothing less. For an undergrad or M=
Sc research project this report is fit for this purpose. Only the very top =
students at either undergraduate or MSc level produce work of sufficient qu=
ality 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 descr=
ibed. Replication is unclear, and there are some problems with the statisti=
cal design. The results and conclusion sections could be clearer. This proj=
ect is not perfect by a long shot, however I certainly would NOT describe t=
his 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 ha=
ve some form of financial investment from the users. I personally (as a Res=
earch Fellow of Soil Microbial Ecology) have had an interest in compost tea=
s research for some time. Despite numerous attempts to find funds for compo=
st tea research from the users and research councils, I have had very littl=
e in terms of financial assistance for research into compost teas. Of cours=
e if anyone has any suggestions as to where I can find funds then I will ce=
rtainly follow it up. It is my intention to supervise a PhD student researc=
h programme on compost teas. Such a programme would allow a student to rese=
arch compost teas for 3 years, but of course financial investment is requir=
ed to have scientifically robust data that can withstand the peer review pr=
ocess necessary for scientific papers.
> >
> > I would also like to stress that the methods used were also suitable. I=
ndeed microscopy would NOT be a suitable method for such work. Catabolic pr=
ofiles are a very important and valid way of describing the functional comp=
onent of the soil microbial community. There are numerous per reviewed pape=
rs 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 differ=
entiate between bacteria and fungi, but rather gives a functional profile o=
f 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 metho=
ds 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 s=
end his questions to the authors of the work to give them a chance to respo=
nd 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><m=
ailto: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: Altern=
ative Land Management at Yale". The paper's root is located at http://envir=
onment.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 meas=
ured 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 e=
ven the basics of equipment involved. It reads as though they're quite resi=
stant to changing there current chemical system.
> >
> > I see lots of logarythmic scatter gram but not much in the way of scien=
ce.
> >
> > I'd expect to see somthing more substantial. This is a dissapointment f=
rom an institution as fine as Yale.
> >
>





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Received on Fri Feb 18 2011 - 15:41:48 EST

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