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Food & Agriculture Microbiology: Research Opportunities in
Food & Agriculture Microbiology: Research Opportunities in
RESEARCH OPPORTUNITIES IN
FOOD & AGRICULTURE
MICROBIOLOGY
Copyright © 2005
American Academy of Microbiology
1752 N Street, N.W.
Washington, DC 20036
http://www.asm.org
RESEARCH OPPORTUNITIES IN
FOOD & AGRICULTURE
MICROBIOLOGY
2
REAPING BENEFITS FROM RESEARCH antibiotic resistant microbial pathogens. Furthermore,
this practice may provide a pool of resistance genes that
Technological advancements do not always find immedi- can be transferred among organisms in both the gut of
ate or the most opportune applications. In the case of animals and the production environment.
pasteurization, the technology was shown to effectively
rid milk of dangerous pathogens before the end of the The contribution of research towards providing a plen-
19th century. Despite promotion of the benefits of pas- tiful, healthy, and safe food supply reaches beyond the
teurization, it was adopted very slowly due to reluctant cycle of basic research and applied science. Research is
producers and suspicious consumers. Milk remained also required after development of a technology to
responsible for one quarter of all food borne illness direct its prudent or appropriate use. For example,
throughout the first third of the 20th century in the research predicted the selection of antibiotic resistant
United States. Wide scale use of pasteurization now pro- microbes in agriculture, but did not predict the potential
vides the invisible benefit of a much safer food supply. In consequences of changing the formulation and process-
another example, the new technology of genetic modifi- ing methods for feed used in British cattle production.
cation or engineering has led indirectly to decreases in Most scientists believe that the origin of bovine spongi-
mycotoxins produced by fungi in some growing crops. form encephalopathy, the so-called “Mad Cow” disease,
These toxins are highly detrimental to animals and was the supplementation of cattle feed with animal pro-
humans, including being implicated in several cancers. tein derived from other ruminants. This resulted in a
disease caused by a replicating protein that was propa-
On the opposite end of the spectrum, some tech- gated through British cattle herds and was subsequently
nologies experience rapid and extensive adoption epidemiologically linked to a deadly neurological condi-
before their impact is sufficiently understood. Extensive tion in humans. Assurances of the safety of the meat
use of antibiotics in livestock and poultry production supply were provided without scientific backing as an
came into practice to protect large popula- animal epidemic gained momentum. As of 2003, there
tions of closely quartered animals from have been over 180,000 confirmed diagnoses of BSE in
infection, and for its poorly under- British cattle and the most recent 2005 statistics cite over
stood growth-promoting effect. 100 confirmed deaths from variant Creutzfeldt-Jakob dis-
The practice is associated ease, the human form of the disease believed to be
with the appearance linked to BSE.
of some strains of
In an endeavor such as food production and distribu-
tion, tension is always present between technological
advances and avoidance of unintended consequences.
This tension can be heightened when disasters, such as
the Mad Cow episode in Britain, are amplified by poli-
cies made without sufficient scientific understanding.
Even with scientific understanding of benefits and risks, a
technology may be scuttled by lingering mistrust or poor
public understanding of complex issues. This is part of
what caused the slow adoption of pasteurization, and
still has the adoption of food irradiation mostly ham-
strung in the United States. Irradiation, proven for
decades to destroy pathogens in spices and food and
protect against spoilage, lacks a confidence-inspiring
4
Plant diseases also impact humans. Most significantly, environmental persistence, and living on alternate, often
fungi leave behind toxins poisonous to people and ani- perennial hosts are some of the ways that pathogens can
mals that eat them, as well as to the host plant. As break into an agricultural setting. The spores of the
unlikely as it seems, there is some evidence that plant Anthrax bacterium mentioned above can remain viable
pathogens can also be infectious to people. The great- in the soil for decades until one finds its way into the
est number of documented cases so far are pathologies nutrient rich, warm setting of a skin scratch or the lung of
found in the immune compromised, but an increasing a mammal. Some pathogens are not able to survive long
number are associated with apparently healthy humans. without a host, but are able to linger on what are called
However, this is a neglected field of study, and it is not “alternate hosts.” This allows the pathogen to last over a
known how widespread or important such infections winter or for several years, with the alternate host provid-
might be and with what types of syndromes these agents ing a reservoir of infectious material upon reappearance
might be associated. of the susceptible agricultural host and the right condi-
tions for infection.
Fungal, bacterial, and viral pathogens are problems in
any system where dense populations of the same kind of Agricultural pathogens not only have diverse ways of
plants or animals are being cultivated for food. This princi- infecting plants and animals, but also have ways to over-
ple extends beyond fields and pastures, to areas like come host defenses directed against them. The sheer
ponds or net-cages, where aquaculture is performed, and enormity of microbial populations provides them with
caves, where mushrooms are grown. Diseases that assail an evolutionary advantage. In vast microbial populations
agriculture can also be more complicated than an infection which replicate very quickly, variations in genetic
by a single pathogen; polymicrobial diseases result from makeup become statistically more probable when com-
the compound effects of multiple pathogens acting pared to slower growing plant and animal populations.
together. Diseases of this kind can be more difficult to pre- Genetic variation allows for the emergence of
dict, diagnose, and respond to than those caused by one pathogens that are no longer recognizable to the
organism alone. immune system of a host, or that have improved mecha-
nisms for inflicting disease. Foot and Mouth disease of
livestock comes in about 80 different “serotypes”
M I C R O B I A L PAT H O G E N S M O V I N G around the world; each one is serologically different. An
& MORPHING animal resistant to one serotype through vaccination or
exposure will still have an immune system that is unpre-
Pathogens have a variety of ways to invade agricultural pared for most of the other serotypes.
plants, animals, and products, such as sliced meats and
cheeses. Vector transmission, seed and aerial dispersion, Evolution frequently produces pathogens resistant to
environmental persistence, and living on alternate, often pesticides and antibiotics through genetic routes more
perennial hosts are some of the ways that pathogens can complex than simple mutation. For example, the prob-
break into an agricultural setting. Vector transmission lem of antibiotic resistant bacteria is driven by the
occurs when another organism, such as an insect, carries swapping of genetic material between organisms. Genes
the pathogen from an infected host and inoculates a can be transferred on mobile pieces of DNA, or shuttled
healthy host. For example, the glassy-winged sharp- from one cell to another by plasmids or bacteria-infect-
shooter can suck sap from a grape vine infected with ing viruses called bacteriophages. Not recognized by
Pierces’ Disease, and be able to transmit the disease- opponents of GMOs, microbial pests of agriculture and
causing bacteria to other healthy vines for several days. public health readily take advantage of “natural” gene
Infected plants rapidly show complete loss of productiv- transfer or genetic engineering for survival and spread.
ity. Vector transmission, seed and aerial dispersion,
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and availability of our food supply at every step in the animal manure, used as a fertilizer, can contaminate
food production, processing, transportation, and market- water sources used for animal and plant production, pro-
ing chain. Its costs are borne by producers, shippers, viding a source of foodborne pathogens if not applied
processors and consumers. using best management practices.
Modern, intensive agricultural practices provide disease (without using vaccine) and
advancements in efficiency and product uniformity, but return the country to its FMD-free status.
also bear some elements contributing to their own
demise. Overuse of antibiotics and pesticides can select
for resistance in the microorganisms that they target.
Many of these chemicals are also pollutants, contaminat-
ing the environment and perhaps reaching people or
organisms that were never their intended targets. Heavy
use of fertilizers feeds nutrients into waterways, fueling
microbial growth that can kill fish and other wildlife. And
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Ideally, surveillance networks should also be capable of this. Standardization of tests nationally and internation-
tracing the cause of an outbreak to its point of origin. ally will be a challenge. The technologies need to be
Knowledge of how incidents were initiated is critical to more portable and more rapid, enabling field sampling
instituting changes that will prevent future incidents. and real time analysis. Diagnostics should be made less
Under ideal circumstances, surveillance networks should expensive so they can be used more frequently and by
be capable of distinguishing among incidents caused by programs with restricted budgets. Finally, diagnostic
natural, accidental, and purposeful release of patho- technologies must contribute useable information to
genic organisms. This would require a much greater inform risk management. Wrong information in a practi-
knowledge of microbial communities than we presently cal sense can consist of more than a simple false-positive
have, as well as forensic capabilities. Robust systems for result; information can also be useless if the test correctly
disease surveillance advance the capability of respond- detects the presence of the target organism, but it is
ing to microbiological threats, thereby reducing dead, or not present at levels of concern. To help resolve
damage. This is the case in preemptive actions against these issues, it is necessary for diagnostic tests to be
some agricultural diseases. For example, planting of made more quantitative. Along similar lines, test speci-
certain genotypes of wheat in North America is guided ficity needs to be refined so that we are detecting the
each year by a forecasting system that observes what presence of pathogenic variants of microorganisms.
wheat rust virulence types are appearing to the South, There are many cases where diagnostic specificity to the
and then recommending what available resistance species level is insufficient to accurately reflect risk
genotypes will fare best in the upcoming planting sea- because different strains within a species can differ sig-
son. Surveillance is also applied to respond as early as nificantly in their pathogenic characteristics.
possible to outbreaks such as Avian Influenza. Another
form of surveillance is routinely applied when we moni- The versatility and ruggedness that is needed from
tor for contaminants in the food supply. For example, diagnostic technologies is also dependent on improving
grains are screened for mycotoxin contamination, and methodologies for handling specimens before testing.
raw meats are sometimes tested for the presence of Improved methods for the pre-analytical processing of
enteropathogenic bacteria. specimens are required. Means of cultivating organisms
“ … S U R V E I L L A N C E N E T W O R K S S H O U L D B E C A PA B L E O F
DISTINGUISHING AMONG INCIDENTS CAUSED BY NATURE, ACCIDENTAL,
A N D P U R P O S E F U L R E L E A S E O F PAT H O G E N I C O R G A N I S M S . ”
Successful surveillance depends on accurate, fast, and that have previously been non-culturable will improve
practical detection technologies. Most immediately, diagnostic capabilities, although knowledge of microbial
there is a need for diagnostics that can test for multiple genomics will enable identification of many non-cultur-
organisms in a single test, a concept termed multiplex- able micro-organisms as well as viruses.
ing. In addition, diagnostic tests must be robust enough
to be applied to complex sample materials, such as soil,
food, and fecal material. The complexity of these mate- PRESERVING FOOD & ENHANCING
rials can cause so-called matrix effects, severely I T S VA L U E
hindering the sensitivity and specificity of a diagnostic
test that would otherwise perform perfectly when A major point of inefficiency in food production will be
applied to a pristine sample matrix, such as a pure cul- improved with reductions in post-harvest spoilage. Find-
ture of the target organism. ing ways to slow or even prevent microbial spoilage will
provide one set of solutions to this problem. Inactivation
Other needed improvements to diagnostics are ones of spoilage-causing microbes is only one way to preserve
that enable them to be more widely accessible for use food. Better understanding the spoilage process itself will
and more widely relied upon. Improving the accuracy open opportunities to alternatives to spoilage control,
and versatility, as described above, will help accomplish such as the biocontrol option. A time honored example
10
allow the gradual replacement of highly polluting fossil MICROBIOLOGY RESEARCH
fuels with more environmentally friendly fuel sources.
However, continued removal of plant waste from fields
may have unintended effects, such as altering the com-
OPPORTUNITIES
position and characteristics of the soil, affecting TO ADVANCE FOOD &
microbial populations and subsequent plant growth.
Thus, this practice needs to be examined and followed AG R I C U LT U R E
over multiple years to monitor its effects.
The previous lineup of microbiology-related problems
confronting agriculture and food, followed by
approaches to solving these problems, provides an
empirical appreciation of the value of agriculture and
food research. There have been attempts to measure
ETHANOL FUEL FROM this value. Estimates of the return on investment in agri-
CELLULOSE cultural research, based on a purely economic level,
range from approximately 30-60%. This means that for
For many years, ethanol fuel has been every dollar invested in agricultural research, there is an
annual net flow of return to society of 30 to 60 cents.
available as a supplement to gasoline However, many of the benefits of research in agriculture
used for transportation. Ethanol can and food microbiology carry over into other important
areas, such as public health and economic development.
replace up to 85% of the gasoline volume These returns have not yet been estimated.
and still be used to efficiently power
vehicles. However, the fermentation of
PROGRESS THROUGH
grain has been used for ethanol produc- M U LT I D I S C I P L I N A R Y R E S E A R C H
tion until recently. Because the value of
Food and agriculture microbiology research intersects
crop material as food far exceeds its with many other fields. This overlap is evident in the
research opportunities associated with multidisciplinary
value for ethanol production, this has not
research. For example, the need for improved detection
been a cost-effective use of grain. New technologies will be addressed by research that combines
fermentation technologies have been such diverse fields as microbiology, molecular biology, sta-
tistics, and engineering. Multidisciplinary research
developed that produce ethanol from approaches will also lead the way in developing better
cellulose-based plant materials left over tools to model the behavior of microbiological hazards,
and successful application of massive amounts of biologi-
after food is harvested. Cellulose is bro- cal information to the management of the living systems
ken down into sugars during a primary that comprise agriculture.
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interventions to prevent disease through efforts such as M I C R O B I A L E C O L O G Y & H E A LT H Y
immunological fortification, production of antibiotics/pro- A G R I C U LT U RA L S Y S T E M S
biotics, and other mechanisms. Current investigation and
knowledge of probiotics scratches the surface of this area The role of beneficial organisms in promoting the health
of research, and even in this area, specific knowledge is of agricultural plants and animals extends beyond com-
lacking about what interactions occur between microbes bating pathogens. Research into how beneficial
and the host and how those interactions can be capital- microorganisms can promote growth, improve stress tol-
ized upon to prevent disease. For example, beneficial erance, and aid in the uptake of nutrients are research
organisms may contribute to the prevention of disease by areas ripe for discovery and innovation. Research into
producing substances that interfere with successful colo- these complex and often delicate interactions between
nization or infection by a pathogen in a host, and/or the different organisms should ultimately pay off by reveal-
beneficial organisms may exclude pathogens by compet- ing ways to assure that agriculture can become heartier
ing for resources while not damaging the host. Past and less environmentally taxing.
methodological restraints have limited our ability to
understand complex host-microbe interactions. However, The same communities of microbes that benefit agri-
functional genomics, proteomics, and metabolomic cultural health and efficiency are likely to be disturbed by
approaches can all be harnessed to answer basic science some of the practices of industrialized agriculture. One
questions about these interactions. In so doing, probiotic way to fortify agriculture against disease and stress is to
approaches can be refined, providing public health bene- supplement systems with probiotic and biocontrol
fits and enhancing the sustainability of agriculture. This is organisms, but a complementary and sometimes alterna-
one area where agriculture may come face-to-face with tive approach is to protect beneficial organisms that may
human and animal clinical medicine. already be present in the environment. Research in
microbial ecology will help to determine how to preserve
Another related phenomenon where microorganisms a balance in microbial communities that favors agricul-
protect against pathogens is biological control. Many ture. Heavy pesticide and fertilizer use, in particular, are
microorganisms can actively antagonize or kill the organ- two practices that should be studied using a holistic or
isms that damage or cause disease in our agricultural integrated approach to determine their impact on micro-
crops and animals. A famous example is the soil bac- bial ecology within the context of tradeoffs between risks
terium Bacillus thuringiensis (Bt) that produces and benefits. More knowledge in this area will help
insect-killing toxins. Microbiology research has extracted determine optimal tradeoffs such that the benefits of use
a wide range of toxin specificities from different strains of outweigh the disruption caused by chemical inputs into
Bt and enabled these toxins to be expressed directly in our agricultural systems.
genetically modified crops, providing the plants with
their own protective compounds. Continued research Microbial communities are both vulnerable to, and
will undoubtedly produce more discoveries from this bio- contribute to, removal of pollutants. Research into how
control organism. Many other biological control options, multiple organisms work in partnership to degrade
such as fungi and viruses that are pathogenic to a wide complex molecules is essential to increase options for
variety of specific agricultural pests, are largely unex- dealing with the byproducts of industrialized agricul-
plored and may be exploited for protection of crops and ture. Understanding this aspect of microbial ecology
animals. Genetic engineering of biocontrol organisms may also lead to improvements in waste disposal and
has promise for ensuring their effectiveness in targeted, energy generation through fermentation, as well as
large scale use against pests. bioremediation.
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needed recruiting leverage. Internships involving indus- possible, even though the land facilities are still there
try, non-governmental organizations (NGOs), and under university ownership. One mechanism for over-
government agencies would have mutually beneficial coming barriers to long-term research in agriculture
value. Such internships would infuse awareness and tech- would be through projects like the Long-Term Ecologi-
nical knowledge of agricultural science to institutions cal Research (LTER) stations. Sustained study of
and provide the visiting scientists with networking and particular agriculture and food science problems is also
training opportunities. The recent security-motivated hampered by certain institutionalized incentive struc-
tightening of immigration procedures has limited access tures. Tenure evaluation procedures draw heavily on
of the U.S. scientific community to international talent. publication records of individuals, but long-term proj-
Making the U.S. more accessible to legitimate interna- ects may be incomplete and unpublished by the time of
tional students and scientists again would help all tenure or promotion review. It is also the case that
scientific endeavors, including invigorating the base for research grants generally demand a structure that prom-
revival of agricultural science. ises completion of a project within two or three, and at
most, five years. Allowing for longer project duration,
Funding for agriculture and food research is essential including sustained funding, and evaluation of produc-
to fulfilling any of the potential benefits that have been tivity based on alternative measures, would make
proposed. Because of the shallow profit margin in agri- long-term research a more viable scientific pursuit.
culture and food, it is to be expected that
industry/commodity funding for research in these areas Collections of microbial specimens are an essential
will be minimal, and when it does occur, it is usually asset to agriculture and food microbiology research.
focused on short-term payoffs. Such sources of funding Availability of specimens for initiation and verification of
traditionally have provided no indirect costs, further per- research can be assured only if the resources and expert-
petuating the declining research facility infrastructure. ise are maintained to properly curate collections of
Therefore, basic research on high priority agriculture and microbes. In the same way that institutions and funding
food problems is deeply dependent on government agencies determine the viability of long-term research,
sources to provide sufficient funding. Currently the their commitment of resources and recognition to the
“ L O N G -T E R M A G R I C U LT U RA L R E S E A R C H P R O J E C T S A R E T H E O N LY
W A Y T O O B TA I N S C I E N T I F I C A N S W E R S . ”
National Research Initiative of the USDA explicitly favors maintenance of microbe collections will determine
“translational research,” i.e., those projects with the whether this asset is sustained or lost.
promise of providing near-term, technological products
or advances. By nature, many agriculture and food With multidisciplinary research at the center of many
research endeavors are long-term, but competitive fund- needed advances in food and agriculture research, some
ing for long-term projects is more or less unavailable. An of the disincentives to this type of work should be lifted.
expansion of research priorities to emphasize basic and Institutions frequently fail to recognize the effort
long-term research and dedicated funding to back this required to coordinate across different research groups
expansion will help revive agricultural research. and disciplines to make a project run successfully. The
many-author publications that result from this type of
work are also not as highly regarded as ones where
RESEARCH PRIORITIES WITH REACH credit is less widely distributed or—in a view that is not
necessarily justified—less diluted.
Long-term agricultural research projects are the only
way to obtain scientific answers to many questions in The research community is also responsible for some
areas such as microbial ecology and epidemiology. barriers to more successful food and agriculture science.
Unfortunately, the formula-funded land grant university Compartmentalization between fields of research and
system once could support such long-term research, but industrial practice prevent effective cross-fertilization
funds have diminished to the point that this is no longer and sharing of lessons learned. Divisions also stand in
16
RECOMMENDATIONS
RESEARCH AGENDA R E B U I L D I N G T H E F O U N D AT I O N F O R
TECHNOLOGY USE & RESEARCH
• Study the impact of production and processing prac-
tices on microorganism evolution, persistence, and • Coordinate development and standardize use of diag-
antibiotic/pesticide resistance as they affect agricul- nostic tests across agricultural production, food
tural animals, plants, and environments. processing, and public health systems to provide a
foundation for integrated surveillance systems.
• Apply systems biology approaches to understanding
communities of microorganisms within agricultural • Provide, through integrated educational initiatives, sci-
hosts, food matrices, and production/processing entifically trained professionals who will serve the food
environments. and agricultural communities.
http://www.dh.gov.uk/PublicationsAndStatistics/PressReleases/P
ressReleasesNotices/fs/en?CONTENT_ID=4112474&chk=tbjtJp
http://www.fsis.usda.gov/Fact_Sheets/Bovine_Spongiform_Enc
ephalopathy_BSE/index.asp
http://www.plantmanagementnetwork.org/infocenter/topic/so
ybeanrust/