[permaculture] Interesting recent research on beneficial soil microorganisms.

Lawrence F. London, Jr. lflj at bellsouth.net
Sat Apr 27 04:20:07 EDT 2013

Interesting recent research on beneficial soil microorganisms.


Horticultural Hijacking: The Dark Side of Beneficial Soil Bacteria

"According to research reported by a University of Delaware scientific
team in the September online edition of Plant Physiology, the most
highly cited plant journal, a power struggle ensues as the plant and the
"good" bacteria vie over who will control the plant's immune system.

"For the brief period when the beneficial soil bacterium Bacillus
subtilis is associated with the plant, the bacterium hijacks the plant's
immune system," says Harsh Bais, assistant professor of plant and soil
sciences, whose laboratory group led the research at the Delaware
Biotechnology Institute.

In studies of microbe-associated molecular patterns (MAMPs), a hot area
of plant research, the UD team found that B. subtilis produces a small
antimicrobial protein that suppresses the root defense response
momentarily in the lab plant Arabidopsis.

"It's the first time we've shown classically how suppression by a benign
bacteria works," Bais says. "There are shades of gray -- the bacteria
that we view as beneficial don't always work toward helping plants."

In the past, Bais' lab has shown that plants under aerial attack send an
SOS message, through secretions of the chemical compound malate, to
recruit the beneficial B. subtilis to come help.

In more recent work, Bais and his collaborators showed that MAMP
perception of pathogens at the leaf level could trigger a similar
response in plants. Through an intraplant, long-distance signaling, from
root to shoot, beneficial bacteria are recruited to forge a system-wide
defense, boosting the plant's immune system, the team demonstrated. In
that study, the Bais team also questioned the overall tradeoffs involved
in plants that are associated with so-called beneficial microbes.

In the latest work, involving the testing of more than 1,000 plants, the
researchers shed more light on the relationship. They show that B.
subtilis uses a secreted peptide to suppress the immune response in
plants. It is known that plants synthesize several antimicrobial
compounds to ward off bacteria, Bais says.

The team also shows that when plant leaves were treated with a foliar
MAMP -- flagellin, a structural protein in the flagellum, the tail-like
appendage that bacteria use like a propeller -- it triggered the
recruitment of beneficial bacteria to the plant roots.

"The ability of beneficial bacteria to suppress plant immunity may
facilitate efficient colonization of rhizobacteria on the roots," Bais
says. Rhizobacteria form an important symbiotic relationship with the
plant, fostering its growth by converting nitrogen in the air into a
nutrient form the plant can use.

"We don't know how long beneficial bacteria could suppress the plant
immune response, but we do know there is a very strong warfare under way
underground," Bais says, noting that his lab is continuing to explore
these interesting questions. "We are just beginning to understand this
interaction between plants and beneficial soil bacteria.""


Bacteria are social microorganisms: MIT researchers

"Bacteria can have social structures similar to plants and animals, new
MIT research reveals. Bacteria can produce chemical compounds that kill
or slow the growth of other populations of bacteria in the environment,
but not harm their own. "Bacteria typically have been considered purely
selfish organisms and bacterial populations as groups of clones," said
Otto Cordero, a theoretical biologist and lead researcher on the paper.
"This result contrasts with what we know about animal and plant
populations, in which individuals can divide labors, perform different
complementary roles and act synergistically." Cordero and colleagues
from MIT, along with researchers from the French Research Institute for
Exploitation of the Sea and Woods Hole Oceanographic Institution in
Massachusetts, studied whether population-level organization exists for
bacteria in the wild. They reasoned social structure can reduce conflict
within populations of plants and animals and determine aggression
towards competing biological populations. "Think of a population of
lions in the Serengeti or a population of fish in a lake," said Cordero.
But could the same be true for populations of bacteria?"


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


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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