Subject: More really good stuff ___ Key references - covering important topics in soil health and soil quality

From: "Lawrence F. London, Jr." <[email-masked]>
Date: Mon, 19 Sep 2005 01:08:26 -0400

Here's the article on red clover and micronutrient mining with VAM's 
(you'll really like this one - has to do with the value of commercial 
mycorrhizal inoculants) - this is a really good article; glad I had the 
foresight to archive it from bionet.plants in 1995 - thank God for 
Usenet, Unix, ibiblio and the Internet.

Nice photographs!

LL
()()()()()
 From [email-masked] Fri Mar  3 21:36:59 EST 1995
Article: 5512 of bionet.plants
(Brendan A. Niemira)
Newsgroups: bionet.plants
Subject: Re: Mycorhizzae vs. Fertilizer
Date: Thu, 02 Mar 1995  11:04 est
Organization: Michigan State University

In Article <[email-masked]> "[email-masked] 
(Eric Grunden)" says:
 >
 > If a person was to isolate a fungus that would form a
 > mycorhizzae relationship with an agronomic crop, would
 > innoculation of that fungus into the field (once it
 > became established) be an effective method for reducing
 > the need for commercial fertilization? Wouldn't the
 > "strength/abundance" of the fungi grow exponentially with
 > the passing of years?

For agronomic crops, you're talking about vesicular arbuscular 
mycorrhizae (VAM),
a symbiotic endomycorrhizal fungus.  These are ubiquitous anyway, and 
not very
host-specific, so there is very little need to inoculate the field in order
to introduce them.  The big trick is getting them to colonize your crop 
plant
to such an extent that fertilizer inputs can be reduced.  You can a) 
build up
the population in the soil such that even moderately active fungi result in
heavy coloniazation, b) put something in the soil to stimulate the activity
of smaller populations to get heavy colonization.

Crop rotations have been shown to have a definite impact on the population
dynamics of VAM, and work is currently being done (by me, among others) to
determine how the different crop plants differentially select for certain
species of VAM among all that are availible in the soil.

Other workers have shown that certain natural, plant-produced chemicals can
stimulate the existing VAM to higher levels of activity.  These 
chemicals were
originally derived from red clover, a popular sequence in crop 
rotations.  This
may shed some light on why rotations are effective w/regard to VAM.

Good luck.
...........

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Brendan A. Niemira           |   "You know your Shelley, Bertie." 

Dept. Botany and Plant Path  |   "Oh, am I?"
Michigan State University    |       P.G. Wodehouse
[email-masked]     |       *The Code of the Woosters*
         All opinions expressed are entirely my own.

<><><><>

From: "ARS News Service" <[email-masked]>
To: "ARS News List" <[email-masked]>
Subject: High CO2 Stimulates Soil-Building "Glue"
Date: Wed, Aug 11, 1999, 11:03 AM

STORY LEAD:
High CO2 Stimulates Soil-Building "Glue"

-----------
ARS News Service
Agricultural Research Service, USDA
Don Comis, (301) 504-1625, [email-masked]
August 12, 1999
-----------

In the first examination of the effects of high atmospheric carbon dioxide
levels on soil structure, an Agricultural Research Service scientist and
cooperators found that the gas stimulates soil-dwelling fungi to produce
more of a unique protein that greatly amplifies a soil's ability to store
carbon.

The study's results are described in a letter published in the August 12
issue of Nature magazine. One of the letter's authors, ARS soil scientist
Sara F. Wright, previously discovered the protein and named it glomalin. She
suspects it may be the primary glue that holds soil together. Now it appears
that a little of this glue goes a long way toward helping soils keep carbon
out of the atmosphere in the form of carbon dioxide.

Carbon dioxide is a greenhouse gas contributing to possible global warming.

The lead author, Matthias C. Rillig, is with the Carnegie Institution of
Washington at Stanford, Calif., as is Christopher B. Field. The fourth
author, Michael F. Allen, is with the University of California at Riverside.
The researchers studied three different ecosystems: two grasslands in
northern California and chaparral in southern California. In all three, they
found that as more carbon dioxide was pumped into open-top chambers placed
over grassland plants growing outdoors, or in a greenhouse built around
shrubs, glomalin levels rose, along with soil stability.

The high carbon dioxide levels in the air increase the amount of carbon
taken in by plant roots. That gives the fungi more food and enables them to
produce more glomalin. The glomalin glues soil particles together and helps
them clump, improving soil structure. This eases the passage of air and
water through soil, boosting plant yields. It also helps soil resist erosion
and hold in soil carbon -- valuable organic matter that holds nutrients to
recycle slowly to plants.

Farmers can increase glomalin levels further by avoiding plowing and by
growing cover crops year-round if feasible. Fungi need live roots to produce
glomalin.

----------
Scientific contact: Sara F. Wright, ARS Soil Microbial Systems Laboratory,
Beltsville, Md., phone (301) 504-8156, fax 504-8370,
[email-masked].
----------
This item is one of the news releases and story leads that ARS Information
distributes on weekdays to fax and e-mail subscribers. You can also get the
latest ARS news on the World Wide Web at
http://www.ars.usda.gov/is/pr/thelatest.htm.
* Feedback and questions to ARS News Service via e-mail: [email-masked].
* ARS Information Staff, 5601 Sunnyside Ave., Room 1-2251, Beltsville MD
20705- 5128, (301) 504-1617, fax 504-1648.

<><><>

 From [email-masked] Tue Mar 28 12:36:19 2000
Date: Tue, 28 Mar 2000 09:51:57 -0500
From: ARS News Service <[email-masked]>
To: ARS News List <[email-masked]>
Subject: Adding Microbes to Transplant Mix

STORY LEAD:
Adding Microbes to Transplant Mix Helps Increase Crop Yields

-----------
ARS News Service
Agricultural Research Service, USDA
Jesus Garcia, (301) 504-1627, [email-masked]
March 28, 2000
-----------

Tomato and pepper farmers can now add microbes along with their transplant
mix to the arsenal of production practices used to reduce yield losses
caused by soilborne pathogens--including root-knot nematodes.

The microbe-amended transplant mix is being developed by Agricultural
Research Service scientists at the U.S. Horticultural Research Laboratory in
Fort Pierce, Fla., led by Nancy K. Burelle, in cooperation with Gustafson
LLC of Plano, Texas. The transplant mix, called BioYield 213, is amended
with two naturally occurring soil microorganisms--Paenobacillus macerans and
Bacillus amyloliquefacien.

The mix provides the microorganisms with the environment they need to grow
on the root surface of seedlings. Once this occurs, the microbes then
stimulate vigorous growth and improve the health of the transplanted
seedling by triggering the plant's resistance mechanisms. This research is
part of an ongoing ARS effort to provide farmers with alternatives to the
use of methyl bromide, an ozone-depleting soil fumigant being phased out by
2005.

Benefits continue to be observed in seedlings out in the field. Greenhouse
producers can expect to grow seedlings in a shorter time period and farmers
can anticipate 5 to 20 percent yield increases in tomatoes, bell peppers and
even strawberries. The mix will be made commercially available to transplant
producers in the fall after grower trials are concluded.

This research is helping scientists gauge the effectiveness of other
alternatives to methyl bromide. For example, when this technology is
combined with alternative soil treatments such as Telone II and PLANTPRO 45,
levels of crop productivity approach those achieved with methyl bromide. But
results also indicate that combining the new formulations with the commonly
used practice of solarization--a process that creates an inhospitable
environment for detrimental microbes by covering the soil with plastic to
heat it, for 6 to 8 weeks in the summer--does not enhance control of
root-knot nematodes.

As the phasing out of methyl bromide proceeds, this technology will provide
growers with an effective, economical and sustainable alternative component
that they can use with existing methods.

ARS is the chief research agency of the U.S. Department of Agriculture.

----------
Scientific contact: Nancy K. Burelle, ARS U.S. Horticultural Research
Laboratory, Fort Pierce, Fla., phone (561) 462-5861, fax (561) 462-5986,
[email-masked].
----------
This item is one of the news releases and story leads that ARS Information
distributes on weekdays to fax and e-mail subscribers. You can also get the
latest ARS news on the World Wide Web at
http://www.ars.usda.gov/is/pr/thelatest.htm.
* Feedback and questions to ARS News Service via e-mail: [email-masked].
* ARS Information Staff, 5601 Sunnyside Ave., Room 1-2251, Beltsville MD
20705-5128, (301) 504- 1617, fax 504-1648.

<><><>

Date:         Fri, 11 May 2001 08:18:07 -0500
  Reply-To:     Sustainable Agriculture Network Discussion Group
                <[email-masked]>
  Sender:       Sustainable Agriculture Network Discussion Group
                <[email-masked]>
  From:         "Wilson, Dale" <[email-masked]>
  Subject:      Chitin in laymans terms
  Content-Type: text/plain; charset="iso-8859-1"

  Sanjay,

  > Could someone please give us an explanation in LAYMAN'S
  > language, as to what is Chitin?

  Two basic strategies for mechanical support are found among living things,
  bones/muscles and tough, hard shells.  Plants, fungi, insects, 
spiders, and
  crustaceans (including lots of tiny, tiny soil creatures) have shells or
  cell walls.  Most of these exoskeletons and walls are made of sugar
  molecules spun together to make long chains.  The sugar molecules are
  connected by a kind of linkage or bond that is very resistant to breakdown
  (unlike starch, which is easily broken into sugar). The plants make cell
  walls mainly out of cellulose, the main constituent of cotton and 
wood.  The
  animals (and most fungi) that make cell walls and exoskeletons make 
them out
  of a substance very similar to cellulose called chitin, also fiberous and
  hard to break down.  It is almost identical chemically to cellulose, 
except
  the sugar molecules have an amino group (contains N) stuck on the side.

  The fact that chitin contains all this nitrogen has important implications
  ecologically.  Nitrogen is a scarce resource in most systems (well, not if
  you apply 200 lb/a!), and chitin is an important source of N, and sugar in
  many systems.  There has been great pressure for the evolution of 
organisms
  that can exploit this resource.  In soils with a large currency of chitin
  (soils with a lot of fungi) there are also many organisms that eat chitin
  for breakfast.  In such situations, chitin is less effective as armor 
plate.
  It so happens that nematodes use chitin as armor plate, and of course most
  fungi do to.  Soil with a high rate of formation and breakdown of 
chitin is
  less hospitable to nematodes and fungi.  Flora must spend more energy
  defending itself.  Plants have ways of exploiting this situation at the
  root/soil interface.  It is all wonderfully complex and, well, miraculous
  (also very violent on a tiny scale).

  Dale

Date:         Thu, 10 May 2001 23:58:28 -0700
  Reply-To:     Sustainable Agriculture Network Discussion Group
                <[email-masked]>
  Sender:       Sustainable Agriculture Network Discussion Group
                <[email-masked]>
  From:         Don Lotter <[email-masked]>
  Subject:      Chitin, microbes, and soil: an addition to the discussion
  Content-Type: text/plain; charset="iso-8859-1"; format=flowed

  I've been skimming over the discussion on chitin in soil the last week or
  two.  Rodriguez-Kabana's work on chitin in soil has been really good. 
  Here
  is the first part of one of his papers.  Here is the intro to a paper 
by him:
  Don Lotter

  Naturally-occurring nematode suppressiveness has been reported for 
several
  agricultural systems (Stirling et al., 1979; Kerry, 1982; Kluepfel et 
al.,
  1993), but suppressiveness can also be induced by crop rotation with
  antagonistic plants such as switchgrass (Panicum virgatum) 
(Kokalis-Burelle
  et al., 1995) and velvetbean (Mucuna deeringiana) (Vargas et al., 
1994) or
  organic amendments including pine bark (Kokalis-Burelle et al., 1994),
  hemicellulose (Culbreath et al., 1985) and chitin (Mankau and Das, 1969;
  Spiegel et al., 1986; Rodríguez-Kábana and Morgan-Jones, 1987). A major
  component of the suppressiveness of chitin amendments is believed to be
  biotic and several reports confirm increased numbers of nematode
  antagonistic microorganisms associated with chitin-induced suppressive
  soils (Godoy et al., 1983; Rodríguez-Kábana et al., 1984). Extensive work
  has been done over the past years on fungi associated with chitin
  amendments (Godoy et al., 1983; Rodríguez-Kábana et al., 1984); however,
  information on bacterial community structure and the role of bacteria in
  chitin-induced suppressiveness is still very limited. We chose chitin
  amendments as a model system to study the effect of suppressiveness on
  bacterial diversity in the soil and endorhiza. Endophytic bacteria were
  included in this study because they colonize the same root tissues as
  sedentary plant-parasitic nematodes. This association of endophytic
  bacteria with nematodes throughout the nematode life cycles makes these
  bacteria excellent candidates for biocontrol strategies.

  Chitin is a structural component of some fungi, insects, various
  crustaceans and nematode eggs. In egg shells of tylenchoid nematodes,
  chitin is located between the outer vitelline layer and the inner lipid
  layer and may occur in association with proteins (Bird and Bird, 
1991). The
  breakdown of this polymer by chitinases can cause premature hatch,
  resulting in fewer viable juveniles (Mercer et al., 1992). In the soil,
  chitinases are produced by some actinomycetes (Mitchell and Alexander,
  1962), fungi (Mian et al., 1982) and bacteria (Ordentlich et al., 1988;
  Inbar and Chet, 1991), but chitinases are also released by many plants as
  part of their defense mechanism against various pathogens (Punja and 
Zhang,
  1993) and plant-parasitic nematodes (Roberts et al., 1992). Chitinases
  depolymerize the chitin polymer into N-acetylglucosamine and chitobiose.
  Further microbial activity results in the deamination of the sugar and
  accumulation of ammonium ions and nitrates (Rodríguez-Kábana et al., 
1983).
  Nematicidal concentrations of ammonia in association with a newly formed
  chitinolytic microflora are believed to cause nematode suppressiveness
  (Mian et al., 1982; Godoy et al., 1983). Benhamou et al. (1994) have 
shown
  that chitosan, the deacetylated derivative of chitin, induces systemic
  plant resistance against Fusarium oxysporum f.sp. radicis-lycopersici in
  tomato when applied as a seed treatment or soil amendment. This suggests
  that plant defense mechanisms might contribute to the overall nematode
  suppression. Our objective was to determine if the chitin-mediated
  suppression of plant parasitic nematodes is related to changes in 
bacterial
  communities in soils, rhizospheres or within cotton roots.

  From:
  Chitin-mediated changes in bacterial communities of the soil, rhizosphere
  and within roots of cotton in relation to nematode control

  Soil Biology and Biochemistry
  Volume 31, Issue 4  April 1999   Pages 551-560
  J. Hallmann1, R. Rodríguez-Kábana and J. W. Kloepper*

  Biological Control Institute, Alabama Agricultural Experiment Station,
  Department of Plant Pathology, Auburn University, Auburn, AL 
36849-5409, USA

  Abstract
  Changes in microbial communities associated with nematode control were
  studied by comparing population numbers of fungi and bacteria in the soil
  and in internal root tissues (endorhiza) in non-amended and 
chitin-amended
  soils. Addition of chitin to soil at 1% (w/w) eliminated plant-parasitic
  nematodes in a first planting of cotton cv. `Rowden' and significantly
  reduced Meloidogyne incognita infestation in a second planting, 
confirming
  long-term nematode suppressiveness induced by this organic amendment. The
  chitin amendment was associated with an increase in fungal and bacterial
  populations, especially those with chitinolytic activity. The bacterial
  communities of soil, rhizosphere and endorhiza were assessed by examining
  the taxonomic diversity of recoverable bacteria based on identification
  with fatty acid analysis of sample sizes of 35 soil and rhizosphere
  bacteria and 25 endophytic bacteria. All major bacterial species which
  formed at least 2% of the total population in non-amended soils and
  rhizospheres also occurred with chitin amendment. In contrast,
  chitin-amended soils and rhizospheres yielded several species which were
  not found without chitin amendment, including Aureobacterium testaceum,
  Corynebacterium aquaticum and Rathayibacter tritici. Burkholderia cepacia
  was recovered from both amended and non-amended soils and 
rhizospheres, but
  it was most abundant with chitin amendment at the end of the first cotton
  planting. Soil was probably the major source for bacterial endophytes of
  cotton roots, since nearly all endophytic bacteria were also found in the
  soil or rhizosphere. However, two dominant genera in the soil and
  rhizosphere, Bacillus and Arthrobacter, were not detected as endophytes.
  Chitin amendment exhibited a further specific influence on the endophytic
  bacterial community; Phyllobacterium rubiacearum was not a common 
endophyte
  following chitin amendment, even though chitin amendment stimulated its
  populations in non-planted soil. Burkholderia cepacia, found in similar
  numbers in the soil of both treatments, was the dominant endophyte in
  plants grown in chitin-amended soil but rarely colonized cotton roots 
grown
  in non-amended soil. These results indicate that application of an 
organic
  amendment can lead to modifications of the bacterial communities of the
  soil, rhizosphere and endorhiza.

 From "The American Heritage Dictionary of the English Language",
  American Heritage Publishing Co., INC. and Houghton Mifflin Company.

  chi-tin  n. A simitransparant horny substance, primarily a
  mucopolysaccharide, forming the principal component of crustacean
  shells, insect exoskeletons, and the cell walls of certain fungi.

Date:         Wed, 6 Jun 2001 10:38:09 +0200
  Reply-To:     [email-masked]
  Sender:       Sustainable Agriculture Network Discussion Group
                <[email-masked]>
  From:         Klaus Wiegand <[email-masked]>
  Organization: Landw. U.-& Forsch.-Anstalt Speyer
  Subject:      chitin

  relating to the recent discussion (raised by dale wilson) on
  chitin-producing fungi, i ran upon an interesting paper on that
  topic:

  Are chitinolytic rhizosphere bacteria really beneficial to
  plants?
  Wietse de Boer & J.A. van Veen
  Netherlands Institute of Ecology, Centre for Terrestrial Ecology,
  Department of Plant-Micro-organism Interactions,
  P.O. Box 40,
  6666 ZG Heteren,
  The Netherlands.
  E-Mail: [email-masked]

  The observations of mycolysis by chitinolytic bacteria have
  stimulated research on possible application of these bacteria for
  biocontrol purposes. The focus has been on rhizosphere bacteria
  as they should be adapted to the environment where
  plant-pathogenic fungi infect roots.  Chitinolytic rhizosphere
  isolates, showing in vitro antifungal effects have therefore been
  tested for their ability to protect plants against infection by
  plant pathogens.  In several cases these strains reduced disease
  symptoms significantly under controlled greenhouse conditions.
  However, application of such strains under field conditions has
  been far less successful, and it is not at all clear that
  mycolytic activities should be expected under field conditions.
  Before this issue can be resolved information is needed about the
  ecological function of bacterial chitinases including
  environmental conditions that might promote chitinase production
  and mycolytic activity.

  In this paper it will be argued that chitinases of rhizosphere
  bacteria are most likely involved in mycoparasitism and defence
  against lysis by fungi.  Obviously, mycoparasitic growth of
  chitinolytic rhizosphere bacteria could be an important mechanism
  to control plant-pathogenic fungi.  However, chitinase production
  in soil bacteria, including potential biocontrol strains, is
  repressed by small organic substrates like sugars and amino
  acids. This indicates that mycolytic activity does only occur
  when no other growth substrates are available i.e. under
  starvation conditions.  Hence, the release of organic compounds
  by the root is expected to repress mycolytic activities of most
  chitinolytic rhizosphere bacteria.  This does, however, not
  suggest that the search for biocontrol strains is futile, but
  indicates that knowledge of chitinase expression and repression
  must be taken into account during this process.

  A potential negative effect of chitinolytic bacteria may be
  exterted on mycorrhizal development.  In fact, the starvation
  conditions in the bulk soil, into which mycorrhizal hyphae are
  extending from the root, should promote mycolytic activities.
  Therefore, study of interactions between chitinolytic strains and
  mycorrhizal fungi should be part of biocontrol studies.

  -----

  klaus

Date:         Wed, 6 Jun 2001 08:42:05 -0500
  Reply-To:     Sustainable Agriculture Network Discussion Group
                <[email-masked]>
  Sender:       Sustainable Agriculture Network Discussion Group
                <[email-masked]>
  From:         "Wilson, Dale" <[email-masked]>
  Subject:      Re: chitin
  Content-Type: text/plain; charset="iso-8859-1"

  Klaus,

  > i ran upon an interesting paper on that topic:

  This is a really interesting subject.  The other day we had Gary 
Harman here
  for a little seminar.  Gary is the guy who developed the
  rhizoplane-competent Trichoderma harzianum strain T-22.  He showed nice
  pictures of how the Trichoderma eats little holes in the cell wall of 
other
  fungi using chitinase (among other enzyme tricks).

  > "application of such strains under field conditions has
  > been far less successful, and it is not at all clear that
  > mycolytic activities should be expected under field conditions.
  > Before this issue can be resolved information is needed about the
  > ecological function of bacterial chitinases including
  > environmental conditions that might promote chitinase production
  > and mycolytic activity." (de Boer and van Veen)

  Trichoderma too has been more consistently beneficial in the 
greenhouse.  I
  think that the field soil environment is a veritable zoo, including, 
besides
  fungi, bacteria, and actinomycetes, microarthropods (and protozoa?) that
  feed on fungi.  Greenhouse soils are probably much simpler systems. 
BTW, we
  see consistent and somewhat mysterious growth enhancement in the field 
from
  seed treatment with systemic neonicotinoid insecticides.  Probably, we are
  suppressing some little critter in the root zone.

  > "chitinase production
  > in soil bacteria, including potential biocontrol strains, is
  > repressed by small organic substrates like sugars and amino
  > acids. This indicates that mycolytic activity does only occur
  > when no other growth substrates are available i.e. under
  > starvation conditions." (de Boer and van Veen)

  And this may be where plant roots come in.  They leak small organic
  molecules onto the rhizoplane and alter the ecology.  And they snap up 
N and
  P.  So rhizoplane colonizers are confronted with a substrate-rich, but
  nutrient-poor niche, that may favor mycoparasites that can obtain N by
  breaking down fungi.  Iron availability too may be a key player in some of
  these systems (thinking of some of the Pseudomonads).  God this is
  interesting!

  What I think is happening (and I am going way, way out on a 
speculative limb
  here!) is that plants exploit this situation, producing a mycoparasitic
  environment on the rhizoplane, creating rapid N-turnover, and suck out N
  from the system.

  Gary presented evidence that colonization by his strain of Trichoderma can
  often greatly enhance N uptake, reducing the need for N application.  I
  can't vouch for their data, and they ARE trying to peddle their wares, but
  the results looked pretty encouraging.

  I just did a little literature search: "(chitinase or chitinolytic) and
  (hyperparasitism or mycoparasitism)"  All eight papers were about
  fungus-fungus parasitism.  Also did a search on "(chitinase or 
chitinolytic)
  and biocontrol"  I will send these if anyone is interested.

  Dale

Date:         Thu, 7 Jun 2001 08:02:19 +0800
  Reply-To:     Sustainable Agriculture Network Discussion Group
                <[email-masked]>
  Sender:       Sustainable Agriculture Network Discussion Group
                <[email-masked]>
  From:         David Menne <[email-masked]>
  Subject:      Re: chitin
  Content-Type: text/plain; charset=us-ascii

  Researching references for an article "Enzymatically improving infant 
nutrition
  in developing countries [particularly KwaZulu/Natal]" (see
  http://www.plantsfood.com/infantenzyme.htm), I came across the interesting
  claims that chitinases have proven active against human pathogens such as
  Listeria monocytogenes, Clostridium botulinum, Bacillus cereus, 
Staphylococcus
  aureus and E coli.

  I have a general interest in the mechanics of what I suppose one could 
call
  health-promoting food production; and possibly a need to be aware of 
destructive
  food production processes [such as boiling the hostel cabbage to a pulp -
  Greytown High School boarding hostel, 1950's]; and would value any related
  references which might/should turn up or be in the databases of those 
following
  this thread.

<><><>