Mark,
You stated;
"but fungi are much harder to culture in the lab than fungi"
I presume you meant bacteria at one end of the statement.
Tim
--- In compost_tea_at_yahoogroups.com, "Pawlett, Mark" <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, b=
etter methods for example PLFA, 16S rDNA transcriptome analysis, RNAi tech=
nology, 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 =
population can be cultured by standard laboratory practices, and it is not =
know (in my opinion unlikely) that this 1% represents the bacterial populat=
ion (Torsvik 1999). An estimated 1, 500, 5000 fungi species exist in the w=
orld (Giller 1997) but fungi are much harder to culture in the lab than fun=
gi. This information was retrieved from a review written by Kirk et al 200=
4 (Journal of Microbial Methods 58: 169-188). Some of these methods are exp=
ensive, however some (e.g. PLFA) is certainly not too expensive to anyone a=
lready using the other methods of analysis. It may be cheaper, and would p=
rovide 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 al=
l methods have bias. The important thing it to recognise that bias. The m=
ethods described in the report that you refer to not only give microbial bi=
omass, but in addition give a culture-independent method of measuring the c=
atabolic 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 technique=
s would not be published in any reputable peer reviewed journal of soil mic=
robiology 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) pr=
ojects that are both limited in time and money. If this continues I will d=
iscontinue the debate. Lets now stick to published, peer reviewed, facts a=
nd 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_at_yahoogroups.com] On=
Behalf 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=
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
>
> --- 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 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_at_yahoogroups.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>
> > 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.
> >
>
Received on Wed Feb 16 2011 - 15:25:00 EST