Skip to Content.
Sympa Menu

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

permaculture@lists.ibiblio.org

Subject: permaculture

List archive

Chronological Thread  
  • From: venaurafarm <venaurafarm@bellsouth.net>
  • To: permaculture <permaculture@lists.ibiblio.org>, Market Farming <marketfarming@lists.ibiblio.org>
  • Subject: [permaculture] UD researchers show how beneficial soil bacteria can boost plant immunity & other related articles on soil life
  • Date: Mon, 17 Sep 2012 11:12:50 -0400


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*
http://www.ziektefaq.info/pdf/exudation/2.pdf

"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
rhizosphere?
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
biology.
ROOT-RHIZOSPHERE COMMUNICATION
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."

<>

1)

UD researchers show how beneficial
soil bacteria can boost plant immunity
http://www.udel.edu/udaily/2013/aug/beneficial-soil-bacteria-082712.html

UD researchers show how beneficial soil bacteria can boost plant immunity
TEXT SIZE
E-mail

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


2)

It Takes a Community of Soil Microbes to Protect Plants From Disease
Berkeley Lab scientists decipher immune system for plants beneath our feet
http://newscenter.lbl.gov/news-releases/2011/05/05/community-soil-microbes/

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 Express.

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 disease.

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.

3)

https://www.google.com/search?q=metagenomic+techniques+for+assessing+microbial+communities&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en-US:official&client=firefox-a

Scholarly articles for metagenomic techniques for assessing microbial communities
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

[PDF]
Molecular Techniques to Assess Microbial Community Structure ...
www.springer.com/cda/.../cda.../9781441979308-c1.pdf?...
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 ...
www.biomedcentral.com/1471-2105/9/34/
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 ...
www.plosone.org/.../info%3Adoi%2F10.1371%2Fjournal.pon...
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 ...
NOAH FIERER
www.colorado.edu/eeb/EEBprojects/.../researchdescrippage.ht...
We are combining molecular analyses of microbial communities (both metagenomic and small subunit rRNA surveys) with techniques to assess microbial ...
[PDF]
Metagenomic analysis of soil microbial communities - doiSerbia
www.doiserbia.nb.rs/ft.aspx?id=0354-46641003559D
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
en.wikipedia.org/wiki/Metagenomics
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 ...
www.nature.com/nmeth/journal/v9/n8/.../nmeth.2066.html?...
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 ...
[PDF]
METAGENOMIC ANALYSIS OF SOIL MICROBIAL COMMUNITIES ...
archonline.bio.bg.ac.rs/.../!ABS%2062.3%20-%207%20djokic...
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 ...
www.ploscompbiol.org/.../info%3Adoi%2F10.1371%2Fjourn...
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 ...
www.natureasia.com/en/research/highlight/7033
Jun 11, 2012 – Home»Research highlights»Assessing microbial diversity ... of large microbial communities is reported online this week in Nature Methods.

4)
communication between soil bacteria
https://www.google.com/search?q=communication+between+soil+bacteria+2012+article&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en-US:official&client=firefox-a

Scholarly articles for communication between soil bacteria 2012 article
… : communication between bacteria and their hosts - Hughes - Cited by 143
http://scholar.google.com/scholar_url?hl=en&q=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667375/&sa=X&scisig=AAGBfm0v28ruZYJYOhGE90jrZHou605XJg&oi=scholarr

Root exudation and rhizosphere biology - Walker - Cited by 381
http://scholar.google.com/scholar_url?hl=en&q=http://www.ziektefaq.info/pdf/exudation/2.pdf&sa=X&scisig=AAGBfm2BrbNas7U0KhEpiPR_qg88ktlDkw&oi=scholarr

Interactions of bacteria, protozoa and plants leading to … - Clarholm - Cited by 385
http://scholar.google.com/scholar_url?hl=en&q=http://www.sciencedirect.com/science/article/pii/0038071785901130&sa=X&scisig=AAGBfm2CU6Nx0WGkcDQ9bJNxZ9ZHWVcp8w&oi=scholarr

5)

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

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

http://newscenter.lbl.gov/news-releases/2011/05/05/community-soil-microbes/

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.

-Allison

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

-Allison

6)

Inter-kingdom signalling: communication between bacteria and their hosts
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667375/

Abstract

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.

7)

Update on Root Exudation and Rhizosphere Biology
Root Exudation and Rhizosphere Biology1
Travis S. Walker, Harsh Pal Bais, Erich Grotewold, and Jorge M. Vivanco*
http://www.ziektefaq.info/pdf/exudation/2.pdf


8)
[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
http://www.sciencedirect.com/science/article/pii/0038071785901130
"Abstract

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."







  • [permaculture] UD researchers show how beneficial soil bacteria can boost plant immunity & other related articles on soil life, venaurafarm, 09/17/2012

Archive powered by MHonArc 2.6.24.

Top of Page