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

From: Jason Kalka <shortstop42000_at_yahoo.com>
Date: Fri, 18 Feb 2011 11:55:17 -0600


Mark,
I think you bring up excellent points about testing. I think before even a=
ttempting 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

-----Original Message-----
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 ent=
husiasts use at the moment are sufficient.  Due to the complexity of the =
soil microbial system it is my opinion that microbial and culture based met=
hods are insufficient in describing the interactions of CT and the soil mic=
robial community.  The microscopy method used do go some way towards desc=
ribing the compost tea, but do little if anything in terms of describing th=
e interactions with the soil.
 
All method have weaknesses.  The important thing is to recognise the weak=
nesses.  I wonder if the CT community understands the weaknesses of using=
 microscopy as their main technique?
 
How about that as a starting point J
 
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 intereste=
d if you publish anything.  Also, if you require collaboration from us th=
en please contact me (m.pawlett_at_cranfield.ac.uk) and we’ll try and work s=
omething 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 h=
ave stated and it is not much different than what I have stated.

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

 With my microscopes I can view the active protozoa and nematodes in soil o=
r compost, etc. so indeed it is another tool in the kit for the horticultur=
ist. From some of the studies I've read from USDA and other institutes, whi=
ch did not include evalution of protists and nematodes of any kind, a micro=
scope would have easily solved this. To the best of my knowledge, the micro=
scope is the favoured tool for seeing protozoa and nematodes in soil and wa=
ter at the University of British Columbia, the University of Toronto,Instit=
ut für Zoologie, Technische Universität Darmstadt, Washington State Uni=
versity, etc. etc.

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

 Your questioning applications of compost tea and the microbes contained th=
erein surviving in the soil into which they enter, is quite valid. It is a =
crap shoot but informally I have observed soil microbial populations change=
d over a period of time with repeated applications. Along with this, I beli=
eve soil properties such as pH have been altered by these (microbes) applic=
ations. However, this is all anecdotal information. I'm not saying that I w=
ill 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 leav=
ing 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 Washingt=
on institution, with donations of a microscope and resource materials. I do=
n'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 impri=
nting by their favourite instructor/supervisor.

 Salutations,
 Tim

 --- In compost_tea_at_yahoogroups.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 sa=
y 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. fu=
ngi:bact, G+ve:G-ve, methanotrophs, AM fungi, stress indicators and some ot=
hers. Protozoa and nematodes would require another method, microscopy is on=
ly 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 th=
e function (I'm not taking about the whole food web, rather the bacterial a=
nd 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, 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 pu=
shed to find any microscopy based techniques to describe soil microbial com=
munities in the last 10 years. Horticulturalists use the microscopy techniq=
ues 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 ho=
rticulturalist, I'm sure nobody would deny that. But there are more tools i=
n the tool kit of soil microbiology than the ones that you describe. The br=
idge 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 y=
ou fund a MSc student to compare methods, and at the same time answer some =
fundamental questions that are still unanswered regarding compost tea appli=
cation. 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 th=
at I work.
>
> Mark
>
>
>
>
>
> From: compost_tea_at_yahoogroups.com [mailto:compost_tea_at_yahoogroups.com] O=
n 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 m=
ore 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 observ=
e the existence/numbers of bacteria/archea and the predatory flagellates an=
d 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 do=
wn a microscope tube to SEE if there are indeed bacteria/archaea, fungal hy=
phae and/or conidia, various protozoa and nematodes. One can view this in s=
oil/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 becau=
se, I believe, it was she who originally stressed the importance of direct =
microscopy in combination with more detailed methods, which you have outlin=
ed adequately in your remarks. I believe that E. Ingham, Bryan Griffiths, M=
arianne Clarholm, Michael Bonkowski and Wilhelm Foissner would likely accor=
d 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 t=
he 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 inclu=
ded unless some other technique utilized reveals the 'at least general' pop=
ulations of ALL related microbial groups. [bacteria/archaea; protozoa; nema=
todes; 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 previou=
sly, the use of a microscope can be far from expensive and even less expens=
ive 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 tec=
hnology, molecular matchmaking, RAPD, T-RFLP and FT/MS. Torsvik (1990) esti=
mated that in 1g of soil there are 4000 different genomic units, based on D=
NA-DNA reasociation. It is also estimated that 5000 bacterial species have =
been described ((Pace 1997 1999). Only approximately 1% of the bacterial po=
pulation can be cultured by standard laboratory practices, and it is not kn=
ow (in my opinion unlikely) that this 1% represents the bacterial populatio=
n (Torsvik 1999). An estimated 1, 500, 5000 fungi species exist in the worl=
d (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 (J=
ournal of Microbial Methods 58: 169-188). Some of these methods are expensi=
ve, however some (e.g. PLFA) is certainly not too expensive to anyone alrea=
dy using the other methods of analysis. It may be cheaper, and would provid=
e more useful information.
> >
> > Catabolic profiles are culture independent methods. As such they are n=
ot subject to the same biases. Of course it is important to remember that a=
ll methods have bias. The important thing it to recognise that bias. The me=
thods described in the report that you refer to not only give microbial bio=
mass, but in addition give a culture-independent method of measuring the ca=
tabolic functional profile of the soil microbial community. The method is u=
sed considerably globally in the world of soil microbiology (refer to the s=
eries of papers started by Degens and Harris starting I think in 1999).
> >
> > Simple methods are only important if they are relevant. It is worthwhi=
le noting that study that involves only microscopy or culture based techniq=
ues would not be published in any reputable peer reviewed journal of soil m=
icrobiology To test this just have a search and let me know whether you com=
e 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 article=
s, 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 a=
s part of the methodology. I am consulting a student at a minor western col=
lege who is conducting a similar study with much more detail applied.
> >
> > Your statement "Indeed microscopy would NOT be a suitable method for s=
uch work. Catabolic profiles are a very important and valid way of describi=
ng the functional component of the soil microbial community."
> >
> > seems to me off base. Sure there is value in measuring microbial respi=
ration for overall mass but if one is studying the effects of compost tea i=
n soil, one would think this implies studying the microbial nutrient loop. =
(it is unfortunate that the one Ingham quote used is not wholly accurate) T=
o assertain the optimum efficacy of a 'compost tea' or a multiplied microbi=
al extract in liquid one HAS TO observe the existence/numbers of bacteria/a=
rchea 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 e=
xpense involved in this. If you set up the study, I'll provide the microsco=
pe 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 U=
SDA and Canadian Min of Ag where they did not even consider the protozoa po=
pulation when they determined that e-coli can grow in compost tea (only aft=
er inoculating it with e-coli of course). Protozoa eat e-coli. Hello.
> >
> > Looking down a microscope tube to see if there are bacteria/archaea an=
d 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.co=
m><mailto:compost_tea%40yahoogroups.com>, "Pawlett, Mark" <m.pawlett_at_> wrot=
e:
> > >
> > > Hi All
> > >
> > > Just to make this clear. I can't see any evidence that this was actu=
ally 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 o=
r MSc research project this report is fit for this purpose. Only the very t=
op 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 fla=
ws in the experiment. The compost tea, soil and compost are inadequately de=
scribed. Replication is unclear, and there are some problems with the stati=
stical design. The results and conclusion sections could be clearer. This p=
roject is not perfect by a long shot, however I certainly would NOT describ=
e this as shocking.
> > >
> > > Student projects have limited time and money. As such they cannot co=
ver 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 co=
mpost tea research from the users and research councils, I have had very li=
ttle in terms of financial assistance for research into compost teas. Of co=
urse 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 rese=
arch programme on compost teas. Such a programme would allow a student to r=
esearch compost teas for 3 years, but of course financial investment is req=
uired 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 c=
omponent of the soil microbial community. There are numerous per reviewed p=
apers that are available that demonstrate this. Microscopy has inherent fla=
ws in terms of bias.
> > >
> > > The methods DO NOT only give data on bacteria. The data does not dif=
ferentiate between bacteria and fungi, but rather gives a functional profil=
e of the soil microbial community as a whole. Thus data includes both bacte=
ria and fungi. A more detailed study would allow the research to use the me=
thods to differentiate between fungi and bacteria. But the substrates used =
in the method are suitable, would be utilised fungal community, and have be=
en published in peer reviewed scientific journals.
> > >
> > > I wonder whether the un-named writer of the below had the courtesy t=
o send his questions to the authors of the work to give them a chance to re=
spond 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.c=
om><mailto:compost_tea%40yahoogroups.com> [mailto:compost_tea_at_yahoogroups.c=
om<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>
> > > Subject: [compost_tea] Compost Tea 'Data' from Yale
> > >
> > >
> > >
> > > Hi folks;
> > >
> > > I just came across a published paper entitled "Closing the Loop: Alt=
ernative Land Management at Yale". The paper's root is located at http://en=
vironment.yale.edu/hixon/student-research/student-research-interns/
> > >
> > > The paper is located here; http://environment.yale.edu/hixon/files/p=
df/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 perfo=
rm 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 m=
easured using narrow range of foods. Where's the data on fungi, nematodes a=
nd prots??
> > >
> > > There's a misunderstanding of organic matter accumulation in soils. =
Can we expect appreciable increase in OM using 1,500 grams of compost, maki=
ng 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 an=
d even the basics of equipment involved. It reads as though they're quite r=
esistant to changing there current chemical system.
> > >
> > > I see lots of logarythmic scatter gram but not much in the way of sc=
ience.
> > >
> > > I'd expect to see somthing more substantial. This is a dissapointmen=
t from an institution as fine as Yale.
> > >
> >
>




Received on Fri Feb 18 2011 - 15:42:03 EST

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