Dear Tim
So, let's open the debate regarding methods used in the world of soil micro=
biology.
In terms of methods. There are many other methods , and in my opinion, bet=
ter methods for example PLFA, 16S rDNA transcriptome analysis, RNAi techno=
logy, molecular matchmaking, RAPD, T-RFLP and FT/MS. Torsvik (1990) estima=
ted 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 b=
een 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 wor=
ld (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 expen=
sive, however some (e.g. PLFA) is certainly not too expensive to anyone alr=
eady using the other methods of analysis. It may be cheaper, and would pro=
vide more useful information.
Catabolic profiles are culture independent methods. As such they are not s=
ubject 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 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 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 worthwhile n=
oting that study that involves only microscopy or culture based techniques =
would not be published in any reputable peer reviewed journal of soil micro=
biology 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) proj=
ects that are both limited in time and money. If this continues I will dis=
continue 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_at_yahoogroups.com] On B=
ehalf Of Tim Wilson
Sent: 16 February 2011 00:21
To: compost_tea_at_yahoogroups.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 n=
ot a journal article. That is no excuse for not including microscopy as par=
t 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 w=
ork. Catabolic profiles are a very important and valid way of describing th=
e functional component of the soil microbial community."
seems to me off base. Sure there is value in measuring microbial respiratio=
n for overall mass but if one is studying the effects of compost tea in soi=
l, one would think this implies studying the microbial nutrient loop. (it i=
s unfortunate that the one Ingham quote used is not wholly accurate) To ass=
ertain the optimum efficacy of a 'compost tea' or a multiplied microbial ex=
tract in liquid one HAS TO observe the existence/numbers of bacteria/archea=
and the predatory flagellates and naked amoebae. This is what drives the m=
icrobial nutrient loop. [true that nematodes and arthropods contribute this=
in the soil but are virtually impossible to maintain in compost tea]. To n=
ot include microscopy and related microbial counts in such a study is ridic=
ulous and I'll easily debate anyone on this issue. There is no great expens=
e involved in this. If you set up the study, I'll provide the microscope an=
d counting wells. Don't get me wrong. This should be included with CO2 effl=
ux and respiration related staining as well. The expensive part comes in wh=
en 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 a=
nd Canadian Min of Ag where they did not even consider the protozoa populat=
ion when they determined that e-coli can grow in compost tea (only after in=
oculating it with e-coli of course). Protozoa eat e-coli. Hello.
Looking down a microscope tube to see if there are bacteria/archaea and fla=
gellates 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 n=
ematodes 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>, "=
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 exami=
nation by fellow scientists in the field. This appears to be a student rese=
arch 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 st=
udents at either undergraduate or MSc level produce work of sufficient qual=
ity 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 describ=
ed. Replication is unclear, and there are some problems with the statistica=
l design. The results and conclusion sections could be clearer. This projec=
t is not perfect by a long shot, however I certainly would NOT describe thi=
s as shocking.
>
> Student projects have limited time and money. As such they cannot cover a=
ll 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 Resea=
rch 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 cert=
ainly 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 resear=
ch compost teas for 3 years, but of course financial investment is required=
to have scientifically robust data that can withstand the peer review proc=
ess necessary for scientific papers.
>
> I would also like to stress that the methods used were also suitable. Ind=
eed microscopy would NOT be a suitable method for such work. Catabolic prof=
iles are a very important and valid way of describing the functional compon=
ent 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 differen=
tiate between bacteria and fungi, but rather gives a functional profile of =
the soil microbial community as a whole. Thus data includes both bacteria a=
nd fungi. A more detailed study would allow the research to use the methods=
to differentiate between fungi and bacteria. But the substrates used in th=
e method are suitable, would be utilised fungal community, and have been pu=
blished in peer reviewed scientific journals.
>
> I wonder whether the un-named writer of the below had the courtesy to sen=
d 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_at_yahoogroups.com<mailto:compost_tea%40yahoogroups.com>] O=
n Behalf Of Peter
> Sent: 15 February 2011 00:22
> To: compost_tea_at_yahoogroups.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: Alternat=
ive Land Management at Yale". The paper's root is located at
http://environ=
ment.yale.edu/hixon/student-research/student-research-interns/
>
> The paper is located here; http://environment.yale.edu/hixon/files/pdf/20=
10_Emily_Stevenson.pdf
>
> Does anyone else find this paper a bit shocking? Here's another case of f=
lawed 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 measur=
ed using narrow range of foods. Where's the data on fungi, nematodes and pr=
ots??
>
> There's a misunderstanding of organic matter accumulation in soils. Can w=
e expect appreciable increase in OM using 1,500 grams of compost, making te=
a, 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 eve=
n the basics of equipment involved. It reads as though they're quite resist=
ant 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 fro=
m an institution as fine as Yale.
>
Received on Wed Feb 16 2011 - 13:44:44 EST