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

From: Pawlett, Mark <m.pawlett_at_cranfield.ac.uk>
Date: Fri, 18 Feb 2011 11:56:27 +0000

Hi

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

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

How about that as a starting point :)

The link looks great, but unfortunately its not in my neighbourhood. I'm i=
n 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 ple=
ase 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 B=
ehalf 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 ha=
ve stated and it is not much different than what I have stated.

In particulr though you have not really addressed the weakness I pointed ou=
t except to say; "Protozoa and nematodes would require another method, micr=
oscopy 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 horticulturi=
st. From some of the studies I've read from USDA and other institutes, whic=
h did not include evalution of protists and nematodes of any kind, a micros=
cope would have easily solved this. To the best of my knowledge, the micros=
cope is the favoured tool for seeing protozoa and nematodes in soil and wat=
er at the University of British Columbia, the University of Toronto,Institu=
t für Zoologie, Technische Universität Darmstadt, Washington State Univ=
ersity, 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 the=
rein surviving in the soil into which they enter, is quite valid. It is a c=
rap shoot but informally I have observed soil microbial populations changed=
 over a period of time with repeated applications. Along with this, I belie=
ve soil properties such as pH have been altered by these (microbes) applica=
tions. However, this is all anecdotal information. I'm not saying that I wi=
ll 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 leavi=
ng 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 Washingto=
n 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 imprin=
ting 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 g=
ave that up years ago). It will not give species level but groups, e.g. fun=
gi:bact, G+ve:G-ve, methanotrophs, AM fungi, stress indicators and some oth=
ers. Protozoa and nematodes would require another method, microscopy is onl=
y one method. Another method called tRFLP (terminal restriction length poly=
morphism) will enable you to study in more detail, such as ammonia oxidisin=
g 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 an=
d 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 g=
oing to apply it to the microbiology will not survive or genes will not fun=
ction, thereby the compost tea will not work. This is about function, but o=
f course the phenotypic signature is important. Yes the 2 are linked, but t=
here 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 pus=
hed to find any microscopy based techniques to describe soil microbial comm=
unities in the last 10 years. Horticulturalists use the microscopy techniqu=
es as they are easily accessible to them. Not because they are the best met=
hods. Yes, of course the methods that you describe would be useful to a hor=
ticulturalist, 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 bri=
dge between the academic and the horticulturalist does need crossing, but t=
hat's a wider issue.
>
> Of course, if you want to put your money where your mouth is why don't yo=
u fund a MSc student to compare methods, and at the same time answer some f=
undamental questions that are still unanswered regarding compost tea applic=
ation. 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%40yahoogroups.com> [=
mailto:compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com>] O=
n 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 mo=
re 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 dow=
n a microscope tube to SEE if there are indeed bacteria/archaea, fungal hyp=
hae and/or conidia, various protozoa and nematodes. One can view this in so=
il/compost samples as is or after applying various foodstocks to see what m=
icrobes are emergent.
>
> I'm glad that you have quoted one of my dear friends <GRIN> Vigdis becaus=
e, I believe, it was she who originally stressed the importance of direct m=
icroscopy in combination with more detailed methods, which you have outline=
d adequately in your remarks. I believe that E. Ingham, Bryan Griffiths, Ma=
rianne 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 th=
e microscope alone as a tool to evaluate the general microbial population o=
f one's soil, compost and compost tea. This, however, as you have pointed o=
ut is not up to par with the measurements required to publish an article. M=
y 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 includ=
ed unless some other technique utilized reveals the 'at least general' popu=
lations of ALL related microbial groups. [bacteria/archaea; protozoa; nemat=
odes; 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 previous=
ly, the use of a microscope can be far from expensive and even less expensi=
ve 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 m=
icrobiology.
> >
> > In terms of methods. There are many other methods , and in my opinion, =
better methods for example PLFA, 16S rDNA transcriptome analysis, RNAi tech=
nology, molecular matchmaking, RAPD, T-RFLP and FT/MS. Torsvik (1990) estim=
ated that in 1g of soil there are 4000 different genomic units, based on DN=
A-DNA reasociation. It is also estimated that 5000 bacterial species have b=
een described ((Pace 1997 1999). Only approximately 1% of the bacterial pop=
ulation can be cultured by standard laboratory practices, and it is not kno=
w (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 (Jo=
urnal of Microbial Methods 58: 169-188). Some of these methods are expensiv=
e, however some (e.g. PLFA) is certainly not too expensive to anyone alread=
y 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 no=
t subject to the same biases. Of course it is important to remember that al=
l methods have bias. The important thing it to recognise that bias. The met=
hods described in the report that you refer to not only give microbial biom=
ass, but in addition give a culture-independent method of measuring the cat=
abolic functional profile of the soil microbial community. The method is us=
ed considerably globally in the world of soil microbiology (refer to the se=
ries of papers started by Degens and Harris starting I think in 1999).
> >
> > Simple methods are only important if they are relevant. It is worthwhil=
e noting that study that involves only microscopy or culture based techniqu=
es would not be published in any reputable peer reviewed journal of soil mi=
crobiology 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 a=
nd 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><m=
ailto: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 a=
nd 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 coll=
ege who is conducting a similar study with much more detail applied.
> >
> > Your statement "Indeed microscopy would NOT be a suitable method for su=
ch work. Catabolic profiles are a very important and valid way of describin=
g the functional component of the soil microbial community."
> >
> > seems to me off base. Sure there is value in measuring microbial respir=
ation 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 microbia=
l extract in liquid one HAS TO observe the existence/numbers of bacteria/ar=
chea and the predatory flagellates and naked amoebae. This is what drives t=
he 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 r=
idiculous and I'll easily debate anyone on this issue. There is no great ex=
pense involved in this. If you set up the study, I'll provide the microscop=
e 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 i=
n 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 US=
DA and Canadian Min of Ag where they did not even consider the protozoa pop=
ulation when they determined that e-coli can grow in compost tea (only afte=
r 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 a=
re nematodes in ones compost or soil. It is as tough as looking to see if t=
here 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.co=
m>, "Pawlett, Mark" <m.pawlett_at_> wrote:
> > >
> > > Hi All
> > >
> > > Just to make this clear. I can't see any evidence that this was actua=
lly published. Published scientific papers are all subject to peer review e=
xamination 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 to=
p 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 flaw=
s in the experiment. The compost tea, soil and compost are inadequately des=
cribed. Replication is unclear, and there are some problems with the statis=
tical design. The results and conclusion sections could be clearer. This pr=
oject 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 cov=
er 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 R=
esearch Fellow of Soil Microbial Ecology) have had an interest in compost t=
eas research for some time. Despite numerous attempts to find funds for com=
post tea research from the users and research councils, I have had very lit=
tle in terms of financial assistance for research into compost teas. Of cou=
rse 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 resea=
rch programme on compost teas. Such a programme would allow a student to re=
search compost teas for 3 years, but of course financial investment is requ=
ired 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 co=
mponent of the soil microbial community. There are numerous per reviewed pa=
pers that are available that demonstrate this. Microscopy has inherent flaw=
s in terms of bias.
> > >
> > > The methods DO NOT only give data on bacteria. The data does not diff=
erentiate between bacteria and fungi, but rather gives a functional profile=
 of the soil microbial community as a whole. Thus data includes both bacter=
ia and fungi. A more detailed study would allow the research to use the met=
hods to differentiate between fungi and bacteria. But the substrates used i=
n the method are suitable, would be utilised fungal community, and have bee=
n 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 res=
pond 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.co=
m><mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.c=
om> [mailto:compost_tea_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.co=
m><mailto:compost_tea%40yahoogroups.com><mailto:compost_tea%40yahoogroups.c=
om>] 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: Alte=
rnative Land Management at Yale". The paper's root is located at http://env=
ironment.yale.edu/hixon/student-research/student-research-interns/
> > >
> > > The paper is located here; http://environment.yale.edu/hixon/files/pd=
f/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 perfor=
m 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 me=
asured using narrow range of foods. Where's the data on fungi, nematodes an=
d prots??
> > >
> > > There's a misunderstanding of organic matter accumulation in soils. C=
an we expect appreciable increase in OM using 1,500 grams of compost, makin=
g 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 re=
sistant to changing there current chemical system.
> > >
> > > I see lots of logarythmic scatter gram but not much in the way of sci=
ence.
> > >
> > > I'd expect to see somthing more substantial. This is a dissapointment=
 from an institution as fine as Yale.
> > >
> >
>





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Received on Fri Feb 18 2011 - 15:41:46 EST

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