[permaculture] UD researchers show how beneficial soil bacteria can boost plant immunity & other related articles on soil life

venaurafarm venaurafarm at bellsouth.net
Mon Sep 17 11:12:50 EDT 2012

This article, downloadable as a .pdf is a must read for permaculture 
designers and teachers and can be considered supplemental reading for 
students of Mollison's Permaculture Designers Manual. This is a 
fascinating report, especially for those interested in soil quality
on a permaculture site, a market farm or homestead garden.


Update on Root Exudation and Rhizosphere Biology
Root Exudation and Rhizosphere Biology1
Travis S. Walker, Harsh Pal Bais, Erich Grotewold, and Jorge M. Vivanco*

"The rhizosphere is a densely populated area in
which the roots must compete with the invading root
systems of neighboring plant species for space, water,
and mineral nutrients, and with soil-borne microorganisms,
including bacteria, fungi, and insects
feeding on an abundant source of organic material
(Ryan and Delhaize, 2001). Thus, root-root, rootmicrobe,
and root-insect communications are likely
continuous occurrences in this biologically active soil
zone, but due to the underground nature of roots,
these intriguing interactions have largely been overlooked.
Root-root and root-microbe communication
can either be positive (symbiotic) to the plant, such as
the association of epiphytes, mycorrhizal fungi, and
nitrogen-fixing bacteria with roots; or negative to the
plant, including interactions with parasitic plants,
pathogenic bacteria, fungi, and insects. Thus, if plant
roots are in constant communication with symbiotic
and pathogenic organisms, how do roots effectively
carry out this communication process within the
A large body of knowledge suggests that root exudates
may act as messengers that communicate and
initiate biological and physical interactions between
roots and soil organisms. This update will focus on
recent advancements in root exudation and rhizosphere
Survival of any plant species in a particular rhizosphere
environment depends primarily on the ability
of the plant to perceive changes in the local environment
that require an adaptive response. Local changes within
the rhizosphere can include the growth and development of
neighboring plant species and microorganisms. Upon encountering
a challenge, roots typically respond by secreting certain
small molecules and proteins (Stintzi and Browse,
2000; Stotz et al., 2000). Root secretions may play
symbiotic or defensive roles as a plant ultimately
engages in positive or negative communication, depending
on the other elements of its rhizosphere. In
contrast to the extensive progress in studying plantplant,
plant-microbe, and plant-insect interactions
that occur in aboveground plant organs such as
leaves and stems, very little research has focused on
root-root, root-microbe, and root-insect interactions
in the rhizosphere. The following sections will examine
the communication process between plant roots
and other organisms in the rhizosphere."



UD researchers show how beneficial
soil bacteria can boost plant immunity

UD researchers show how beneficial soil bacteria can boost plant immunity

9:28 a.m., Aug. 27, 2012--With the help of beneficial bacteria, plants 
can slam the door when disease pathogens come knocking, University of 
Delaware researchers have discovered.

A scientific team under the leadership of Harsh Bais, assistant 
professor of plant and soil sciences in UD’s College of Agriculture and 
Natural Resources, found that when pathogens attempt to invade a plant 
through the tiny open pores in its leaves, a surprising ally comes to 
the rescue. Soil bacteria at the plant’s roots signal the leaf pores to 
close, thwarting infection.

The fascinating defense response is documented in video and micrographs 
of live plants taken by confocal and scanning electron microscopes at 
UD’s Bio-Imaging Center at the Delaware Biotechnology Institute.

The research, which explored the interaction between the soil bacterium 
Bacillus subtilis and the laboratory plant Arabidopsis thaliana, is 
published in the August issue of The Plant Journal. The findings 
underscore both the importance of root-based processes in plant defense 
and the potential for bolstering plant immunity naturally through the 
emerging field of probiotics.

Postdoctoral researcher Amutha Sampath Kumar is the lead author of the 
journal article. In addition to Bais, the co-authors include 
postdoctoral researcher Venkatachalam Lakshmanan, researchers Jeffrey L. 
Caplan, Deborah Powell and Kirk J. Czymmek of UD’s Bio-Imaging Center, 
and Delphis F. Levia, associate professor of geography. The National 
Science Foundation, University of Delaware Research Foundation and 
Delaware Experimental Program to Stimulate Competitive Research (EPSCoR) 
provided funding for the study.

Millions of stomata, consisting of microscopic pores surrounded by guard 
cells, cover the above-ground parts of plants, from the stems to the 
flower petals. The pores resemble tiny mouths, or doors, which the guard 
cells open and close to allow carbon dioxide, oxygen, water and minerals 
in and out of the plant.

Pathogens also can slip through these stomata and begin infecting the 
plant. However, as Bais’s team confirmed, this invasion is halted when 
the beneficial bacterium Bacillus subtilis is present in the soil where 
the plant is rooted. The finding was based on tests of approximately 
3,000 Arabidopsis plants inoculated with the foliar pathogen Pseudomonas 
syringae pathovar tomato DC3000 (PstDC3000) during a year-long period.

When a foliar pathogen attacks, as shown in previous research by Bais 
and his group, the plant recruits Bacillus subtilis to help and 
facilitates its multiplication. The Bacillus subtilis bacteria bind to 
the plant’s roots and invoke abscisic acid and salicylic acid signaling 
pathways to close the stomata.

Abscisic acid and salicylic acid are both important hormones involved in 
plant defense. When a plant encounters adverse environmental conditions, 
such as drought, for example, abscisic acid triggers the stomata to shut 
tightly to prevent the plant from dehydrating.

In addition to ramping up plant disease resistance, the use of this 
rhizobacteria to promote drought tolerance in plants could be a very 
promising avenue, Bais notes.

“Many bacterial pathogens invade plants primarily through stomata on the 
leaf surface,” Bais says. “But how do plants fight off infection? In our 
studies of the whole plant, we see this active enlistment by Bacillus 
subtilis, from root to shoot.”

Strikingly, the research team’s data revealed that of different 
root-associated soil bacteria tested, only Bacillus species were 
effective in closing the stomata and for a prolonged period.

“We know only 1 to 5 percent of what this bug Bacillus subtilis can do, 
but the potential is exciting,” Bais notes, pointing out that there is 
increasing commercial interest in inoculating crop seeds with beneficial 
bacteria to reduce pathogen infection. “Just as you can boost your 
immune system, plants also could be supercharged for immunity.”

Article by Tracey Bryant

Photo by Ambre Alexander


It Takes a Community of Soil Microbes to Protect Plants From Disease
Berkeley Lab scientists decipher immune system for plants beneath our feet

Those vegetables you had for dinner may have once been protected by an 
immune system akin to the one that helps you fight disease. Scientists 
from the U.S. Department of Energy’s Lawrence Berkeley National 
Laboratory (Berkeley Lab) and the Netherland’s Wageningen University 
found that plants rely on a complex community of soil microbes to defend 
themselves against pathogens, much the way mammals harbor a raft of 
microbes to avoid infections.
In a development that could lead to better ways to protect food crops 
from disease, Berkeley Lab scientists unraveled the community of soil 
microbes that protect sugar beets from root fungus. From left, Todd 
DeSantis, Gary Andersen, and Yvette Piceno in the lab where much of the 
research was conducted. Several PhyloChips are on the table next to them.

In a development that could lead to better ways to protect food crops 
from disease, Berkeley Lab scientists unraveled the community of soil 
microbes that protect sugar beets from root fungus. From left, Todd 
DeSantis, Gary Andersen, and Yvette Piceno in the lab where much of the 
research was conducted. Several PhyloChips are on the table next to 
them. (Photo by Roy Kaltschmidt, Berkeley Lab Public Affairs)

The scientists deciphered, for the first time, the group of microbes 
that enables a patch of soil to suppress a plant-killing pathogen. 
Previous research on the phenomenon of disease-suppressive soil had 
identified one or two pathogen-fighting microbes at work.

But the Berkeley Lab-led team found a complex microbial network. After 
analyzing soil from a sugar beet field that had become resistant to a 
pathogen that causes root fungus, the scientists found 17 soil microbes 
fighting to suppress the pathogen. They also determined that all of the 
microbes work together to reduce the incidence of fungal infection. 
Their discovery that plants use a tight-knit army of soil microbes for 
defense could help scientists develop ways to better protect the world’s 
food crops from devastating diseases.

“Individual organisms have been associated with disease-suppressive soil 
before, but we demonstrated that many organisms in combination are 
associated with this phenomenon,” says Gary Andersen of Berkeley Lab’s 
Earth Sciences Division. He conducted the research with fellow Berkeley 
Lab scientists Todd DeSantis and Yvette Piceno as well as several 
scientists from the Netherlands including Wageningen University’s Jos 
Raaijmakers. Their research is published in the May 5 issue of Science 

The Berkeley Lab and Dutch scientists analyzed soil from a sugar beet 
field in the Netherlands. Something in the soil suppressed the presence 
of the pathogen Rhizoctonia solani, which causes root fungus in beets, 
potato, and rice.

The sugar beets’ health followed the typical arc of plants in 
disease-suppressive soil: they enjoyed a few good years, then they 
succumbed to disease, followed by healthy beets again as 
pathogen-fighting microbes were activated and the soil became hostile to 
R. solani. To return the favor, the sugar beets funnel about a fifth of 
their photosynthetically captured carbon through their roots into the 
soil to fuel the microbes.
New research reveals that it takes a community of soil microbes, not 
just one or two, to protect crops. The top image is a healthy sugar beet 
field. The bottom image is a field of sugar beets that is infected with 
the root fungus.

New research reveals that it takes a community of soil microbes, not 
just one or two, to protect crops. The top image is a healthy sugar beet 
field. The bottom image is a field of sugar beets that is infected with 
root fungus.

Disease-suppressive soils are quite common, and scientists have 
identified some of the microbes involved in this underground immune 
system. But they don’t know all of the microbes that participate.

To find out, the scientists used the PhyloChip, which is a credit-card 
sized chip that can detect the presence of 59,000 species of bacteria 
and archaea in samples of air, water, and soil without the need of 
culturing. It was developed at Berkeley Lab to rapidly identify not only 
the most common and abundant organisms in an environmental sample, but 
also very rare types that are present in extremely small numbers. It 
does this by comparing a DNA sequences unique to each bacterial species 
with over one million reference DNA targets on the chip. The PhyloChip 
has shed light on many environmental mysteries, such as what’s killing 
coral reefs near Puerto Rico and what degraded much of the oil from the 
Gulf of Mexico’s Deepwater Horizon spill.

In this case, soil samples from the sugar beet field were modified to 
exhibit six levels of disease suppression. DNA was isolated from the 
samples and sent to Berkeley Lab for analysis. The PhyloChip detected 
more than 33,000 bacterial and archaeal species in the samples, with all 
six having more or less the same types of bacteria.

But when the scientists looked at the abundance of bacteria in each 
sample, they found that each had a unique fingerprint. All of the 
samples in which disease was suppressed had a greater abundance of 17 
unique types of bacteria. These included well-known fungal fighters such 
as Psuedomonas, Burkholderia, Xanthomonas and Actinobacteria. In 
addition, other types of bacteria that have no demonstrated ability to 
fight pathogens on their own were found to act synergistically to 
suppress plant disease.

Based on this, the scientists believe that an uptick in several 
bacterial types is a more important indicator of disease suppression 
than the presence of one or two bacteria that are especially good at 
killing pathogens.

“We now see that the complex phenomenon of disease suppression in soils 
cannot simply be attributed to a single bacterial group, but is most 
likely controlled by a community of organisms,” says Andersen.

Their research will help scientists pursue unanswered questions about 
disease-suppressive soil: Do plants actively recruit beneficial soil 
microorganisms for protection against infection? And if so, how do they 
do it? It will also help scientists elucidate the mechanisms by which 
groups of soil microbes work together to reduce the incidence of plant 

The research was supported in part by the California Environmental 
Protection Agency’s State Water Resources Control Board and the Rathmann 
Family Foundation.

Lawrence Berkeley National Laboratory addresses the world’s most urgent 
scientific challenges by advancing sustainable energy, protecting human 
health, creating new materials, and revealing the origin and fate of the 
universe. Founded in 1931, Berkeley Lab’s scientific expertise has been 
recognized with 12 Nobel prizes. The University of California manages 
Berkeley Lab for the U.S. Department of Energy’s Office of Science. For 
more, visit www.lbl.gov.
Additional information:

     The research is described in a paper entitled “Deciphering the 
Rhizosphere Microbiome for Disease-Suppressive Bacteria” that is 
published in the May 5, 2011 issue of Science Express.

     More information about the PhyloChip.
     The PhyloChip was the recipient of both the 2008 R&D 100 Award and 
first place in the Environment Category of the Wall Street Journal 2008 
Technology Innovation Awards.



Scholarly articles for metagenomic techniques for assessing microbial 
Microbial community gene expression in ocean surface … - Frias-Lopez - 
Cited by 287
Metagenomics: genomic analysis of microbial … - Riesenfeld - Cited by 332
… assessing functional diversity in microbial communities - Schloss - 
Cited by 58
Search Results

     Molecular Techniques to Assess Microbial Community Structure ...
     File Format: PDF/Adobe Acrobat - Quick View
     Chapter 2. Molecular Techniques to Assess Microbial. Community 
Structure, Function, and Dynamics in the Environment. Gurdeep Rastogi 
and Rajesh K. Sani ...
     A statistical toolbox for metagenomics: assessing functional 
diversity ...
     by PD Schloss - 2008 - Cited by 58 - Related articles
     Jump to Methods‎: εij = 1 if i and j are in the same community, 
otherwise it is 0. ... The three metagenomic sequencing projects were 
selected because they ...
     Metagenomic Profile of the Bacterial Communities Associated with ...
     by G Carpi - 2011 - Cited by 7 - Related articles
     With the advent of metagenomic approaches limitations of these 
methods have been overcome, enabling the identification of entire 
microbial communities ...
     We are combining molecular analyses of microbial communities (both 
metagenomic and small subunit rRNA surveys) with techniques to assess 
microbial ...
     Metagenomic analysis of soil microbial communities - doiSerbia
     File Format: PDF/Adobe Acrobat - Quick View
     by L Đokić - 2010 - Related articles
     The composition and size of bacterial communities in ... from 
metagenomic DNA using universal bacterial .... assessed with traditional 
plating methods.
     Metagenomics - Wikipedia, the free encyclopedia
     Metagenomics allows the study of microbial communities like those 
present in this ... genomics techniques to the study of communities of 
microbial organisms ...
     Metagenomic microbial community profiling using unique clade ...
     by N Segata - 2012
     MetaPhlAn (metagenomic phylogenetic analysis) allows the rapid and 
accurate ... Microbial communities are responsible for a broad spectrum 
of biological activities ... However, none of these methods has 
simultaneously achieved both the .... CDS clustering and then an 
extraclade sequence uniqueness assessment; the ...
     File Format: PDF/Adobe Acrobat - View as HTML
     by L DOKIC - Related articles
     The composition and size of bacterial communities in ... from 
metagenomic DNA using universal bacterial .... assessed with traditional 
plating methods.
     Statistical Methods for Detecting Differentially Abundant Features 
in ...
     by JR White - 2009 - Cited by 81 - Related articles
     These studies aim to dramatically expand our understanding of the 
microbial biosphere ... Current metagenomics studies comparing 
communities resemble ... shotgun sequencing methods to assess not only 
the taxonomic composition, but ...
     Assessing microbial diversity | Nature Methods | NPG Nature Asia ...
     Jun 11, 2012 – Home»Research highlights»Assessing microbial 
diversity ... of large microbial communities is reported online this 
week in Nature Methods.

communication between soil bacteria

Scholarly articles for communication between soil bacteria 2012 article
… : communication between bacteria and their hosts - Hughes - Cited by 143

Root exudation and rhizosphere biology - Walker - Cited by 381

Interactions of bacteria, protozoa and plants leading to … - Clarholm - 
Cited by 385


-------- Original Message --------
Subject: Re: Soil microbes protect plant from bacteria

Here's another fascinating recent scientific study on disease
suppressive soils:


I'll be working in the PI's lab in the Netherlands starting in February
and I can't wait to learn more about metagenomic techniques for
assessing microbial communities.


-------- Original Message --------
Subject: Re: Soil microbes protect plant from bacteria
Date: 	Wed, 29 Aug 2012 21:19:50 -0000
From: 	allisonhornor <allisonhornor at hotmail.com>

The composting process itself involves a complex succession of microbes, 
many of which are present on the initial composting feedstock. However, 
distinct communities of microbes are found in the guts of 
microarthropods that congregate in compost and many microbes are present 
in the atmosphere and are just waiting for the right kind of food source 
to colonize. Microbes present in a quiescent (//hibernating) state in 
your soil could also be stimulated by the presence of a suitable 
substrate and grow to a large
population size in your compost.

Also, it's important to remember that disease suppression does not
usually depend on a single species of microbe. Multiple members of the
microbial community are typically involved. So based on my understanding 
of disease suppression, you could definitely have a situation where a 
soil on your property is not disease suppressive, but a compost produced 
out of vegetation grown on your property is.



Inter-kingdom signalling: communication between bacteria and their hosts


Microorganisms and their hosts communicate with each other through an 
array of hormonal signals. This cross-kingdom cell-to-cell signalling 
involves small molecules, such as hormones that are produced by 
eukaryotes and hormone-like chemicals that are produced by bacteria. 
Cell-to-cell signalling between bacteria, usually referred to as quorum 
sensing, was initially described as a means by which bacteria achieve 
signalling in microbial communities to coordinate gene expression within 
a population. Recent evidence shows, however, that quorum-sensing 
signalling is not restricted to bacterial cell-to-cell communication, 
but also allows communication between microorganisms and their hosts.

Prokaryotes and eukaryotes have coexisted for millions of years. It is 
estimated that humans have 1013 human cells and 1014 bacterial cells 
(comprising the endogenous bacterial flora). Eukaryotes have a variable 
relationship with prokaryotes, and these interactions can be either 
beneficial or detrimental. Humans maintain a symbiotic association with 
their intestinal microbial flora, which is crucial for nutrient 
assimilation and development of the innate immune system1. These 
mutually beneficial associations are possible because microorganisms and 
mammals can communicate with each other through various hormone and 
hormone-like chemical compounds. These signals, however, can be 
‘hijacked’ by bacterial pathogens to activate their virulence genes.

The hormonal communication between microorganisms and their hosts, 
dubbed inter-kingdom signalling, is a recent field of research. This 
field evolved from the initial observation that bacteria can communicate 
with each other through hormone-like signals2, a process that was later 
named quorum sensing (QS)3. This field expanded with the realization 
that these bacterial signals can modulate mammalian cell-signal 
transduction4 and that host hormones can cross-signal with QS signals to 
modulate bacterial gene expression5.


Update on Root Exudation and Rhizosphere Biology
Root Exudation and Rhizosphere Biology1
Travis S. Walker, Harsh Pal Bais, Erich Grotewold, and Jorge M. Vivanco*

[provides good reasons for utilizing cover crops, no till agriculture
and never leaving any ground devoid of either compost/mulch or crops]

Interactions of bacteria, protozoa and plants leading to mineralization 
of soil nitrogen
Marianne Clarholm
Department of Microbiology, Swedish University of Agricultural Sciences, 
S-750 07 Uppsala, Sweden

The capacity of bacteria and protozoa to mineralize soil nitrogen was 
studied in microcosms with sterilized soil with or without wheat plants. 
The effect of small additions of glucose or ammonium nitrate or both, 
twice a week was also tested. Plant dry weight and N-content, number of 
microorganisms and biomass plus inorganic N were determined after 6 weeks.

The introduction of plants profoundly influenced the N transformations. 
In the presence of root-derived carbon, much more N was mineralized from 
the organic matter and immobilized mainly in plant biomass. “Total 
observable change in biomass N plus inorganic N” was negative in the 
unvegetated soils without additions, while a mineralization of 1.7 mg N 
microcosm−1 was observed in microcosms with wheat plants grown with 
bacteria only. When protozoa were included, the N taken up by plants 
increased by 75%. Sugar additions resulted in an 18% increase of total N 
in the shoots when protozoa were present, but had no significant effect 
in the absence of grazers. Plants with the same root weight were more 
efficient in their uptake of inorganic N when protozoa were present. 
Plants grown with protozoa also had a lower R/S ratio, indicating a less 
stressed N availability situation. The lowest ratio was found with N 
additions in the presence of protozoa.

The results indicate that, with energy supplied by plant roots or with 
external glucose additions, soil bacteria can mineralize N from the soil 
organic matter to support their own growth. Grazing of the bacteria is 
necessary to make bacterial biomass N available for plant uptake."

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