Embed Size (px)
Citation preview
A REPORT FROM THE AMERICAN ACADEMY OF MICROBIOLOGY
RESEARCH OPPORTUNITIES IN
FOOD & AGRICULTUREMICROBIOLOGY
Copyright © 2005American Academy of Microbiology1752 N Street, N.W.Washington, DC 20036http://www.asm.org
This report is based on a colloquium, sponsored by the American Academy of Microbiology, held March 12-14, 2005, in Washington, DC.
The American Academy of Microbiology is the honorificleadership group of the American Society for Microbiology.The mission of the American Academy of Microbiology is to recognize scientific excellence and foster knowledgeand understanding in the microbiological sciences. TheAcademy strives to include underrepresented scientists in all its activities.
The opinions expressed in this report are those solely of the colloquium participants and may not necessarilyreflect the official positions of the American Society for Microbiology.
MICHAEL DOYLE LEE-ANN JAYKUS MATTHEW METZ
A REPORT FROM THE AMERICAN ACADEMY OF MICROBIOLOGY
RESEARCH OPPORTUNITIES IN
FOOD & AGRICULTUREMICROBIOLOGY
BOARD OF GOVERNORS, AMER ICAN ACADEMY OF M ICROB IOLOGY
R. John Collier, Ph.D. (Chair)Harvard Medical School
Kenneth I. Berns, M.D., Ph.D.University of Florida Genetics Institute
Arnold L. Demain, Ph.D.Drew University
E. Peter Greenberg, Ph.D.University of Washington
Carol A. Gross, Ph.D.University of California, San Francisco
J. Michael Miller, Ph.D.Centers for Disease Control and Prevention
Stephen A. Morse, Ph.D.Centers for Disease Control and Prevention
Harriet L. Robinson, Ph.D.Emory University
George F. Sprague, Jr., Ph.D.University of Oregon
David A. Stahl, Ph.D.University of Washington
Judy A. Wall,University of Missouri
COLLOQU IUM STEER ING COMMI T TEE
Michael Doyle, Ph.D., (Co-Chair)University of Georgia
Lee-Ann Jaykus, Ph.D. (Co-Chair)North Carolina State University
Charles Rice, Ph.D.Kansas State University
Sue Tolin, Ph.D.Virginia Tech University
Anne Vidaver, Ph.D.University of Nebraska
Carol A. Colgan,Director, American Academy of Microbiology
COLLOQU IUM PART IC IPANTS
Thomas E. Besser, D.V.M., Ph.D.Washington State University
Michael Doyle, Ph.D.University of Georgia
Paul Hall, Ph.D.Kraft Food of North America
Craig Hedberg, Ph.D.University of Minnesota
Lee-Ann Jaykus, Ph.D.North Carolina State University
Vivek Kapur, Ph.D.University of Minnesota
Todd Klaenhammer, Ph.D.North Carolina State University
Jan Leach, Ph.D.Colorado State University
Harley W. Moon, Ph.D.Iowa State University
Cindy Nakatsu, Ph.D.Purdue University
Donald Nuss, Ph.D.University of Maryland Biotechnology Institute
Charles Rice, Ph.D.Kansas State University
John L. Sherwood, Ph.D.University of Georgia
William Sischo, Ph.D.University of California, Davis
Trevor V. Suslow, Ph.D.University of California, Davis
Sue Tolin, Ph.D.Virginia Tech University
Anne Vidaver, Ph.D.University of Nebraska
Paul White, Ph.D.Kansas State University
FOOD & AGRICULTURE 1
E X E C U T I V E
SUMMARYThis report presents a wealth of research opportunities infood and agriculture microbiology. The backdrop forthese research opportunities is a world of microorganismsteeming with threats and benefits to abundant, healthyfood and associated environments. Threats come frommicrobial pathogens that perpetrate a wide range of plantand animal diseases, destroying agricultural productivity.The constant spread and evolution of agriculturalpathogens provides a continually renewed source of chal-lenges to productivity and food safety. Pathogenscontinue to cause harm once food has left the farm, caus-ing spoilage, and in some cases poisoning and diseasesof humans and animals. New vulnerabilities are generatedfor agriculture by global movement of agricultural prod-ucts, trading policies, industrial agricultural practices, andthe potential for malicious releases of pathogens by“bioterrorists.” In addition to the threats, benefits alsocome from the many microorganisms associated with, orintroduced into, our food supply where they serve impor-tant roles in bioprocessing, fermentation, or as probiotics.
Science and technology emerging from microbiologyresearch can help meet these challenges to food andagriculture. Knowledge of microbial pathogens will leadto tools for surveillance and disease prevention. Benefi-cial microbes may find uses in protecting agriculture,preserving food, enhancing the value of food productsand providing general benefits to health and well being.Complex interactions among microbes and agriculturalsystems must be better understood to facilitate the opti-mal use of beneficial microorganisms and maximalcontrol of pathogens.
Opportunities in microbiology research are the gate-way to sustaining and improving agriculture and foodproduction, quality, and safety. Multidisciplinary researchmust be undertaken to capitalize on advances in differ-ent disciplines, such as genomics, nanotechnology, andcomputational biology. Research into the interactions ofanimal and plant hosts with pathogens and beneficialmicrobes is essential to preventing disease and encour-aging mutualistic interactions. On a more holistic scale,interactions occurring among organisms within a micro-bial community require study so that a healthy balancebetween the highly managed ecosystems of industrialagriculture and the unmanaged ecosystems of the natu-ral environment can be achieved. Finally, research is
critical to determine why pathogens continue to emergeand where and how newly developed technologiesshould be put to use.
Barriers to seizing these research opportunities mustbe overcome. The lagging priority of food and agricul-ture research will be reversed as funding programs andresearch institutions recognize its importance andimprove resources, infrastructure, and incentives accord-ingly. Endeavors, such as long-term research projectsand the banking of diverse microbial specimens, requiresupport so that a foundation of future innovation anddiscovery is established and sustained. A decline in thenumber of young scientists entering the fields of foodand agriculture research will have to be reversed withfunding and fellowship opportunities to provide a highlytrained core that will carry out the research of the future.Regulatory hurdles impose stringent processes forresearch on certain organisms, but are viewed as out ofstep with actual hazards and must be revised consistentwith scientific assessment of risk. Changes that areneeded will have to be advocated by scientists, researchinstitutions, professional societies, non-governmentalinstitutions, and companies that are committed to foodand agriculture.
This report offers recommendations for research prior-ities and identifies barriers to a strong food andagriculture research agenda.
BACKGROUNDMicrobes permeate the entire food and agriculturalprocess. While the most visible role of agriculture isprobably that of producing and delivering food, microbi-ology is critical to other agricultural sectors as well, e.g.,for production of energy and for bioremediation of agri-cultural wastes. Some microorganisms are a constantsource of trouble for agricultural endeavors, while othersare an integral part of successful food production. Micro-bial influences on food and agriculture have producedboth advancements and disasters that have punctuatedhuman history. Some examples of microbe-driven out-comes set the stage for describing how important it is toseize research opportunities in food and agriculturemicrobiology.
MICROBES ON THE FARM & IN OUR FOOD
In the fall of 1844 a horde of hungry microbes, whosename Phytopthora infestans was earned from the dam-age they were about to cause, lurked in the soil ofWestern Europe. This pathogen causes a disease knownas Potato Late Blight, and over the next several yearsthey spread to the fields of Ireland where subsistencefarmers were completely reliant on growing potatoes.Devastation of the Irish potato crop led to a terriblefamine where almost one million people died and morethan twice that many fled their country in abject poverty.A new variant of this blight emerged in the United Statesin the 1980s, causing serious losses and even bankruptcyfor modern potato growers.
The relationship of microbes to the human food sup-ply also includes many examples of organisms thatpreserve rather than destroy. Early Mediterranean soci-eties discovered that fermentation could be used to helpcreate yogurt and cheese from dairy products. Theseproducts were flavorful, safe, and could be stored forextended periods of time. Different types of bacteria andfungi are now known to be involved in fermentationprocesses. For example, fermentation of sugars inextracts from grain or grape juice produces alcohol thatserves as a preservative and provides its own addedvalue. The ancient Egyptians are frequently credited withinventing beer.
Every category of microorganism has members thatimpact food and agriculture. These include bacteria, sin-gle-cell organisms without special compartments for
storing their genes; fungi, which can be single- or multi-cellular, and like plants and animals store their morecomplex genomes in a compartment called a nucleus;and viruses, which are little more than an infectious set ofgenes that must operate inside a host cell to reproduce.Among all of these different organisms there are thosethat benefit agriculture and food, enhancing productivityor nutrition through their interactions with plants andanimals. Some microorganisms provide benefit by virtueof their ability to harm other organisms that would causedamage or spoilage if not disrupted. Agriculture andfood are prey to many microorganisms that, in the courseof their life cycles, destroy crops, animals, and foodstuffs.Some of these microbial pathogens create toxins or areinfectious enough to cause disease in humans exposedto the products they have tainted.
MICROBIOLOGY RESEARCH IN FOOD& AGR ICULTURE
The wide-ranging impact that microbes have on agricul-ture and food has always been, and is expected to remain,a challenge. To eat and survive, humans have answeredthis challenge with ingenuity. Answers sometimes begin asempirical approaches to problems, like the early develop-ment of fermentation. Such solutions are subject toimprovement and refinement through scientific study anddiscovery. The better the understanding of the livingorganisms involved in the agriculture and food chain, thebetter equipped people are to steer the course of theseinteractions in our favor.
Basic research is a critical driver for innovation in agri-culture and food. For example, despite centuries ofusing fermentation to ward off spoilage, people stillfound their wine and beer spoiling over time. In the mid1800s Louis Pasteur was embroiled in a scientific con-flict, disputing the favored belief at the time thatmicroorganisms could appear through “spontaneousgeneration” in nutrient broth. To disprove this contem-porary view, Pasteur devised a method for heatsterilizing broth and keeping it sealed off from contami-nation. Lengthy demonstrations that the treatmentprevented any growth of microorganisms, however, didnot win his theory immediate acceptance in the intellec-tual community. The French navy, then struggling todeal with spoilage on its ships and eruptions of mutinydue to shortages of wine, was ready to perform a largescale test of the principle. “Pasteurization” provedeffective, and a basic research problem led to a funda-mental technological advancement.
2
REAPING BENEFITS FROM RESEARCH
Technological advancements do not always find immedi-ate or the most opportune applications. In the case ofpasteurization, the technology was shown to effectivelyrid milk of dangerous pathogens before the end of the19th century. Despite promotion of the benefits of pas-teurization, it was adopted very slowly due to reluctantproducers and suspicious consumers. Milk remainedresponsible for one quarter of all food borne illnessthroughout the first third of the 20th century in the
United States. Wide scale use of pasteurization now pro-vides the invisible benefit of a much safer food supply. Inanother example, the new technology of genetic modifi-cation or engineering has led indirectly to decreases inmycotoxins produced by fungi in some growing crops.These toxins are highly detrimental to animals andhumans, including being implicated in several cancers.
On the opposite end of the spectrum, some tech-nologies experience rapid and extensive adoptionbefore their impact is sufficiently understood. Extensiveuse of antibiotics in livestock and poultry production
came into practice to protect large popula-tions of closely quartered animals from
infection, and for its poorly under-stood growth-promoting effect.
The practice is associatedwith the appearance
of some strains of
antibiotic resistant microbial pathogens. Furthermore,this practice may provide a pool of resistance genes thatcan be transferred among organisms in both the gut ofanimals and the production environment.
The contribution of research towards providing a plen-tiful, healthy, and safe food supply reaches beyond thecycle of basic research and applied science. Research isalso required after development of a technology todirect its prudent or appropriate use. For example,research predicted the selection of antibiotic resistant
microbes in agriculture, but did not predict the potentialconsequences of changing the formulation and process-ing methods for feed used in British cattle production.Most scientists believe that the origin of bovine spongi-form encephalopathy, the so-called “Mad Cow” disease,was the supplementation of cattle feed with animal pro-tein derived from other ruminants. This resulted in adisease caused by a replicating protein that was propa-gated through British cattle herds and was subsequentlyepidemiologically linked to a deadly neurological condi-tion in humans. Assurances of the safety of the meatsupply were provided without scientific backing as ananimal epidemic gained momentum. As of 2003, therehave been over 180,000 confirmed diagnoses of BSE inBritish cattle and the most recent 2005 statistics cite over100 confirmed deaths from variant Creutzfeldt-Jakob dis-ease, the human form of the disease believed to belinked to BSE.
In an endeavor such as food production and distribu-tion, tension is always present between technologicaladvances and avoidance of unintended consequences.This tension can be heightened when disasters, such asthe Mad Cow episode in Britain, are amplified by poli-cies made without sufficient scientific understanding.Even with scientific understanding of benefits and risks, atechnology may be scuttled by lingering mistrust or poorpublic understanding of complex issues. This is part ofwhat caused the slow adoption of pasteurization, andstill has the adoption of food irradiation mostly ham-strung in the United States. Irradiation, proven fordecades to destroy pathogens in spices and food andprotect against spoilage, lacks a confidence-inspiring
“M ILK REMA INED RESPONS IBLE FOR ONE QUARTER OF ALL
FOOD BORNE I LLNESS THROUGHOUT THE F IRST TH IRD OF THE
20TH CENTURY IN THE UN I TED STATES .”
FOOD & AGRICULTURE 3
name and popular understanding. Similarly, the use ofmodern molecular biology to add genes into crops, ani-mals, or microbes, creating so-called GeneticallyModified Organisms (GMOs), has met with a cool recep-tion in many parts of the globe. Despite their benefits interms of production, reduced pesticide use, and now arecord of safe use after one decade, there remains ran-corous dispute about the potential risks of GMOs.Government-sponsored research and oversight, with rea-sonable transparency in some countries, has enabledcommercialization of several crops. Use of rigorous sci-ence to study risks and weigh them against the benefitsof any new technology has not yet been convincingenough to diffuse the tension that interrupts progress.
Nineteen scientists with expertise in areas rangingfrom plant pathology to food microbiology to microbialecology were brought together for a two-and-a-half-daycolloquium to examine the future of food and agriculturemicrobiology. Their deliberations and conclusions arecaptured in this report.
M I C R O B I O L O G I C A L
CHALLENGES TO F O O D & A G R I C U LT U R E
An abundant and healthy food supply is expected fromour agricultural systems. Fulfilling this demand is a com-plicated process involving plant cultivation, animalhusbandry, soil and water management, harvesting, pro-cessing, storage, and transport. At each step themicrobial world presents obstacles to success.
MICROB IAL D ISEASE
Disease-causing microbes continually assault the animalsand crops that humans raise for food. These unwelcomeguests make their living off of our agriculture as well.Each animal or plant that we raise is host to an assort-ment of bacterial, viral, and fungal pathogens. One ofthe more famous examples of viral diseases in animals,Foot and Mouth Disease, infects cloven hoofed animalssuch as cattle and sheep. It is extremely contagious andpersists in susceptible animals in the wild and in hus-bandry. The severe blisters and cankers caused by thevirus are usually not deadly, but the lifespan and produc-tivity of infected animals is severely reduced. The diseaseis dreaded globally as a problem for trade because it canbe spread easily, not only by sick animals, but by meatproducts and even on clothing.
The most virulent diseases are crippling or deadly toagriculture, draining or even annihilating a crop harvestor animal population. Some of these diseases have con-sequences for humans reaching beyond their impact onthe availability or expense of our food. Pathogensknown as “zoonotic” are those that can be transmittedfrom animals to humans and include transmission viavectors (i.e., insects, rodents), food, or water that havebecome contaminated from these animal sources. Themost notorious contemporary example is Anthrax. Thissoil dwelling bacterium can kill cattle and other herdanimals that encounter it while grazing. It is also knownto cause skin lesions, gastrointestinal infection, and seri-ous systemic disease in people exposed to infectedanimals. This bacterium has some choice properties as apotential biological weapon, including deadly toxins itproduces while growing in the warm tissues of an animalhost. In the fall of 2001, illnesses and deaths resultedfrom letters containing special preparations of Anthraxspores, which infected individuals who had contact withthe contaminated mail.
4
Plant diseases also impact humans. Most significantly,fungi leave behind toxins poisonous to people and ani-mals that eat them, as well as to the host plant. Asunlikely as it seems, there is some evidence that plantpathogens can also be infectious to people. The great-est number of documented cases so far are pathologiesfound in the immune compromised, but an increasingnumber are associated with apparently healthy humans.However, this is a neglected field of study, and it is notknown how widespread or important such infectionsmight be and with what types of syndromes these agentsmight be associated.
Fungal, bacterial, and viral pathogens are problems inany system where dense populations of the same kind ofplants or animals are being cultivated for food. This princi-ple extends beyond fields and pastures, to areas likeponds or net-cages, where aquaculture is performed, and
caves, where mushrooms are grown. Diseases that assailagriculture can also be more complicated than an infectionby a single pathogen; polymicrobial diseases result fromthe compound effects of multiple pathogens actingtogether. Diseases of this kind can be more difficult to pre-dict, diagnose, and respond to than those caused by oneorganism alone.
MICROB IAL PATHOGENS MOV ING & MORPH ING
Pathogens have a variety of ways to invade agriculturalplants, animals, and products, such as sliced meats andcheeses. Vector transmission, seed and aerial dispersion,environmental persistence, and living on alternate, oftenperennial hosts are some of the ways that pathogens canbreak into an agricultural setting. Vector transmissionoccurs when another organism, such as an insect, carriesthe pathogen from an infected host and inoculates ahealthy host. For example, the glassy-winged sharp-shooter can suck sap from a grape vine infected withPierces’ Disease, and be able to transmit the disease-causing bacteria to other healthy vines for several days.Infected plants rapidly show complete loss of productiv-ity. Vector transmission, seed and aerial dispersion,
environmental persistence, and living on alternate, oftenperennial hosts are some of the ways that pathogens canbreak into an agricultural setting. The spores of theAnthrax bacterium mentioned above can remain viablein the soil for decades until one finds its way into thenutrient rich, warm setting of a skin scratch or the lung ofa mammal. Some pathogens are not able to survive longwithout a host, but are able to linger on what are called“alternate hosts.” This allows the pathogen to last over awinter or for several years, with the alternate host provid-ing a reservoir of infectious material upon reappearanceof the susceptible agricultural host and the right condi-tions for infection.
Agricultural pathogens not only have diverse ways ofinfecting plants and animals, but also have ways to over-come host defenses directed against them. The sheerenormity of microbial populations provides them with
an evolutionary advantage. In vast microbial populationswhich replicate very quickly, variations in geneticmakeup become statistically more probable when com-pared to slower growing plant and animal populations.Genetic variation allows for the emergence ofpathogens that are no longer recognizable to theimmune system of a host, or that have improved mecha-nisms for inflicting disease. Foot and Mouth disease oflivestock comes in about 80 different “serotypes”around the world; each one is serologically different. Ananimal resistant to one serotype through vaccination orexposure will still have an immune system that is unpre-pared for most of the other serotypes.
Evolution frequently produces pathogens resistant topesticides and antibiotics through genetic routes morecomplex than simple mutation. For example, the prob-lem of antibiotic resistant bacteria is driven by theswapping of genetic material between organisms. Genescan be transferred on mobile pieces of DNA, or shuttledfrom one cell to another by plasmids or bacteria-infect-ing viruses called bacteriophages. Not recognized byopponents of GMOs, microbial pests of agriculture andpublic health readily take advantage of “natural” genetransfer or genetic engineering for survival and spread.
FOOD & AGRICULTURE 5
“FOOT AND MOUTH D ISEASE OF L IVESTOCK COMES IN ABOUT
80 D IFFERENT “SEROTYPES” AROUND THE WORLD; EACH ONE
IS SEROLOG ICALLY D I FFERENT.”
Viruses are capable of even greater wholesale shuf-fling of genetic material. Virus genomes reproduceinside of a host cell. Co-infection of a cell with differentviruses allows the opportunity for a broad array of hybridgenomes to result. These new “hybrid” variants are usu-ally inactive, but occasional variants gain properties, suchas increased virulence, enhanced infectivity, or alteredhost range or vector specificity. A frightening agriculturalexample of this phenomenon is Avian Influenza. In 1918,a pandemic flu emerged that decimated cities and coun-tries around the world. Today, with high density poultryproduction and many people in close contact with flocks,zoonotic episodes of Avian Influenza are being reported.Experts are concerned that it is only a matter of timebefore another highly virulent pandemic strain of humaninfluenza evolves, perhaps this time of avian origin.
MICROBES ROTT ING & PO ISON INGTHE FOOD SUPPLY
Microbial interference with an abundant and healthy foodsupply continues once plant and animal products leavethe farm. Since pathogens can be part of the normal gas-trointestinal flora of many animals, they are difficult, if notimpossible, to completely eradicate and may contaminateour food supply. Bacteria such as Salmonella, Campy-lobacter, and certain strains of Escherichia coli, as well asenteropathogenic viruses, can persist, and some bacteriawill multiply. If not killed before the food is eaten, thesemicrobes can cause serious illness. There are an estimated76 million incidents of foodborne illness in the United
States each year. This is despite all of the advancements infood handling and processing hygiene, such as pasteur-ization, already in practice. Pathogens can also reach thefood supply through contaminated water, transmissionbetween infected animals, using animal manure as fertil-izer, and even from contaminated or infected foodhandlers. Some contaminated seafood acquires viruses,for example, from contaminated harvest waters.
Illness due to microbes is also caused by toxins leftbehind in food as a consequence of microbial growth.Fungi, such as those in the genus Fusarium andAspergillus, grow well on grains and other crops. Asthey grow, they produce toxic substances called myco-toxins. These toxins remain in edible tissues, or canaccumulate after harvest if the fungus continues grow-ing, and are poisonous to humans and animals that eatthem. The toxins cause a variety of damaging effects onthe nervous, digestive, immune and vascular systems.Some are also highly carcinogenic, including one of themost potent cancer causing chemicals known, aflatoxin.The most potent neurotoxin known causes Botulism,and is a product of a bacterium that grows in food in theabsence of oxygen.
Even without directly causing human disease,microbes can have a chilling effect on the efficiency andcost of food production. Most people are familiar withvegetables left too long in the refrigerator drawer whichare transformed into black puddles of mush. Thisspoilage is caused by bacteria and/or fungi that eat, orrot, the food. The process of spoilage erodes the quality
6
and availability of our food supply at every step in thefood production, processing, transportation, and market-ing chain. Its costs are borne by producers, shippers,processors and consumers.
PRACT ICES THAT INCREASE THEM ICROB IAL THREAT TO FOOD &AGR ICULTURE
A newly realized threat to agricultural production andfood safety is the purposeful use of disease and dam-age-causing organisms. Whether thought of as“bioterrorism” or simply malicious sabotage, this is a realthreat derived from the microbial world. The systems wehave in place to detect and deal with the broad array ofdiseases and toxins discussed above now must take intoaccount human-made versions of the threats as well.
Many elements of the modern world interact with themicrobial world to create new problems. Regional andinternational shipment of agricultural products meansthat pathogens do not necessarily require natural disper-sion. Although some pathogens, such as soybean rust,can be transported by wind, others that might notspread so easily by natural forces can arrive by plane orboat. Stiff trade restrictions are established to preventthe entry and spread of certain diseases, but theserestrictions are only as good as the inspection anddetection measures used. Foot and Mouth Disease is anotable example. Countries that are free of FMD prohibitimport of any meat products from countries not consid-ered free of the disease. However, because of limitationsto current detection methods, countries that vaccinateagainst the disease are automatically treated as thoughthey have infectious animals. Countries that are able tooperate without using vaccine have privileged access tocertain markets, but at the cost of having completely vul-nerable herds if the disease were introduced. Manymicrobiological issues are thus serious international agri-cultural trade issues and often are a reason for blockingtrade of certain commodities.
Modern, intensive agricultural practices provideadvancements in efficiency and product uniformity, butalso bear some elements contributing to their owndemise. Overuse of antibiotics and pesticides can selectfor resistance in the microorganisms that they target.Many of these chemicals are also pollutants, contaminat-ing the environment and perhaps reaching people ororganisms that were never their intended targets. Heavyuse of fertilizers feeds nutrients into waterways, fuelingmicrobial growth that can kill fish and other wildlife. And
animal manure, used as a fertilizer, can contaminatewater sources used for animal and plant production, pro-viding a source of foodborne pathogens if not appliedusing best management practices.
In the drive for uniformity, intensive agriculture, suchas planting row upon row of genetically identical crops,or raising large herds or flocks with little genetic diver-sity in close quarters, may result in expansivepopulations of vulnerable hosts upon the emergence ofpathogens that are newly resistant to pesticides, vac-cines, or other critical barriers.
FOOD & AGRICULTURE 7
FOOT & MOUTH D ISEASE & TRADE BARR IERS
Trade in cattle, sheep, goats, and pigs is
controlled based on a variety of animal
diseases, one of the most important
being Foot and Mouth Disease (FMD).
Countries that have the status “FMD-free
where vaccination is not practiced” are,
with few exceptions, the more economi-
cally advanced nations or those that have
insignificant livestock operations. Coun-
tries with this status are entitled to
exclude products from others, but at a
perilous price. The unvaccinated herds
are vulnerable to the highly infectious
disease. An outbreak in 2001 in Great
Britain led to the slaughter of over 6 mil-
lion animals in order to eradicate the
disease (without using vaccine) and
return the country to its FMD-free status.
MEET ING CHALLENGES W I TH
MICROBIOLOGICALSCIENCE & TECHNOLOGY
The microbial world is not just a source of endless prob-lems for food and agriculture. Some of the solutions todisease and spoilage lie in the application of microbiol-ogy. Solutions to non microbe-derived problems mayalso be provided through microbiology. An ever growinghuman population is demanding more food, and is alsousing more energy and creating more waste. Food andagriculture microbiology can present opportunities toaddress some of these problems. Furthermore, some ofthe solutions to agricultural problems, such as soil salin-ization and drought, may lie with microbes.
UNDERSTAND ING M ICROB IALPATHOGENS & COMBAT ING THEM
Better understanding of the microorganisms that causedisease and spoilage in agriculture and food will lead tobetter ways of controlling them. Pesticides are neededthat are more environmentally friendly and that haveadded barriers to the production of resistance. Improvedvaccines and immunomodulators are needed to makeimmunization of herds and flocks against pathogensmore effective. Advances in these areas are dependenton knowing more about the “enemy,” i.e., microbes thatcause the diseases.
It also pays to know about the enemies of one’s ene-mies. Pathogens that attack crops and animals frequentlyhave competitors and pathogens of their own. Harness-ing the capabilities of these antagonists is an approachcalled biological control. Through biological control, rel-atively harmless microorganisms (or their metabolicproducts) that inhibit or kill a harmful organism are massproduced and applied to food or crops as a protectivemeasure. Large scale production of biological controlorganisms is a difficult process, and their performance ina field setting is often unpredictable as a match witheach local ecosytem’s conditions is needed. Neverthe-less, genetic engineering of biological control organismsis a possible way to overcome these shortcomings. Asbiological control using GMOs is more difficult to clearthrough regulatory and political hurdles due to the cur-rent climate, little work is in progress.
A strategy of containment and destruction is requiredin instances whereby plant and animal diseases cannot
be controlled by selective breeding, pesticides, vac-cines, drugs, or biological control. The approach ofquarantining and then depopulating possibly infectedplants and animals becomes more expensive and dev-astating with increased disease spread. This isillustrated by the expense of destroying millions ofchickens during the 2003-04 outbreaks of AvianInfluenza, and by the 2001 FMD outbreak in GreatBritain. The appearance of citrus canker in Florida hasrequired extensive cutting of citrus trees, even in urbanareas, at the cost of millions of dollars. Reducing theselosses relies upon the ability to detect and react quicklyto the appearance of a pathogen.
SURVE ILLANCE FOR M ICROB IALPATHOGENS
Improved surveillance of, and response to, disease out-breaks relies on a variety of technologies. Accuratemodels of pathogen spread are required to preventcostly overestimates of pathogen dispersion, or under-estimates that render control measures incomplete orineffective. Better coordination and networking betweenthe different entities handling surveillance operationsand the standardization of detection technologies willfacilitate more rapid, thorough response to outbreaks.
8
Ideally, surveillance networks should also be capable oftracing the cause of an outbreak to its point of origin.Knowledge of how incidents were initiated is critical toinstituting changes that will prevent future incidents.Under ideal circumstances, surveillance networks shouldbe capable of distinguishing among incidents caused bynatural, accidental, and purposeful release of patho-genic organisms. This would require a much greaterknowledge of microbial communities than we presentlyhave, as well as forensic capabilities. Robust systems fordisease surveillance advance the capability of respond-ing to microbiological threats, thereby reducingdamage. This is the case in preemptive actions againstsome agricultural diseases. For example, planting ofcertain genotypes of wheat in North America is guidedeach year by a forecasting system that observes whatwheat rust virulence types are appearing to the South,and then recommending what available resistancegenotypes will fare best in the upcoming planting sea-son. Surveillance is also applied to respond as early aspossible to outbreaks such as Avian Influenza. Anotherform of surveillance is routinely applied when we moni-tor for contaminants in the food supply. For example,grains are screened for mycotoxin contamination, andraw meats are sometimes tested for the presence ofenteropathogenic bacteria.
Successful surveillance depends on accurate, fast, andpractical detection technologies. Most immediately,there is a need for diagnostics that can test for multipleorganisms in a single test, a concept termed multiplex-ing. In addition, diagnostic tests must be robust enoughto be applied to complex sample materials, such as soil,food, and fecal material. The complexity of these mate-rials can cause so-called matrix effects, severelyhindering the sensitivity and specificity of a diagnostictest that would otherwise perform perfectly whenapplied to a pristine sample matrix, such as a pure cul-ture of the target organism.
Other needed improvements to diagnostics are onesthat enable them to be more widely accessible for useand more widely relied upon. Improving the accuracyand versatility, as described above, will help accomplish
this. Standardization of tests nationally and internation-ally will be a challenge. The technologies need to bemore portable and more rapid, enabling field samplingand real time analysis. Diagnostics should be made lessexpensive so they can be used more frequently and byprograms with restricted budgets. Finally, diagnostictechnologies must contribute useable information toinform risk management. Wrong information in a practi-cal sense can consist of more than a simple false-positiveresult; information can also be useless if the test correctlydetects the presence of the target organism, but it isdead, or not present at levels of concern. To help resolvethese issues, it is necessary for diagnostic tests to bemade more quantitative. Along similar lines, test speci-ficity needs to be refined so that we are detecting thepresence of pathogenic variants of microorganisms.There are many cases where diagnostic specificity to thespecies level is insufficient to accurately reflect riskbecause different strains within a species can differ sig-nificantly in their pathogenic characteristics.
The versatility and ruggedness that is needed fromdiagnostic technologies is also dependent on improvingmethodologies for handling specimens before testing.Improved methods for the pre-analytical processing ofspecimens are required. Means of cultivating organisms
that have previously been non-culturable will improvediagnostic capabilities, although knowledge of microbialgenomics will enable identification of many non-cultur-able micro-organisms as well as viruses.
PRESERV ING FOOD & ENHANC INGI TS VALUE
A major point of inefficiency in food production will beimproved with reductions in post-harvest spoilage. Find-ing ways to slow or even prevent microbial spoilage willprovide one set of solutions to this problem. Inactivationof spoilage-causing microbes is only one way to preservefood. Better understanding the spoilage process itself willopen opportunities to alternatives to spoilage control,such as the biocontrol option. A time honored example
FOOD & AGRICULTURE 9
“… SURVE ILLANCE NETWORKS SHOULD BE CAPABLE OF
DISTINGUISHING AMONG INCIDENTS CAUSED BY NATURE, ACCIDENTAL,
AND PURPOSEFUL RELEASE OF PATHOGEN IC ORGAN ISMS.”
of this principle is in the production of yogurt. The bacte-ria that grow in milk to generate yogurt convert thenutrients into byproducts that make the food environ-ment much less amenable to the growth of spoilageorganisms, thereby extending the shelf life of the food.
Beneficial microbes cultivated in food can provideadded value far beyond delay or prevention of spoilage.Many of these microbes have “probiotic” properties thatcan help exclude disease-causing organisms and preventinfections. Probiotic properties of beneficial microbesare thought to be derived in part from competitive exclu-sion of pathogenic microbial species. However, thephenomenon is complex and may include other ele-ments, such as the release of compounds antagonistic topathogens or stimulation of the host immune system.Deepening understanding of the nature of such probi-otic effects and elucidated ways that these can bestrengthened will allow scientists to capitalize further onthe beneficial effects of these microbes.
The presence of beneficial microbes in agriculture andfood holds the possibility of generating added value toproducts. Some microbes have properties that conveynutritional enhancement to food. For example, yeast is asource of B-complex vitamins. There is also speculationthat interactions between plants and certain microbescan stimulate enhanced production of compounds withpharmaceutical properties. This possibility may provideopportunities to generate health-promoting foods withso-called nutraceutical properties.
A HELP ING HAND IN AGR ICULTUREFROM M ICROBES
Other interactions with beneficial microbes can be ofdirect benefit to agricultural plants and animals. A classicexample of mutualism in action is the partnershipbetween legumes and bacteria called Rhizobia. The bac-teria take up residence in plant roots, receiving nutrients.In exchange, they fix nitrogen from the air into a formthat the plants can use, replacing a need for nitrogen-containing fertilizer. There are other cases of microbeshelping a host organism scavenge essential nutrients, orfend off pathogens. In the intestinal tract of ruminants, acomplex mixture of bacteria enables the animal toextract sufficient nutrients from a diet of grasses.
Even the best-recognized and most-studied forms ofmutualism are not understood well enough to be effec-tively controlled or expanded to cover hosts previouslyunknown to benefit from a particular interaction. Scien-
tists have been unsuccessful in getting Rhizobia to forma mutualistic relationship with wheat roots, for instance.For the few classic examples of mutualism in agriculturalsystems, there are likely to be many more interactionstaking place in obscurity. Study of interactions betweenorganisms that boost agricultural success is a field richwith opportunities. More knowledge of microbial ecol-ogy and mutualistic interactions will pave the way foradvances that enhance agricultural organisms’ nutrientuse, pathogen resistance, and hardiness.
Microbial ecology will likely be found to have impactson agricultural systems beyond those currently recog-nized. Complex interactions between plants and theconsortia of microbes found in soil probably extendbeyond resisting pathogens and scavenging nutrients.Properly tuned interactions could help improve droughtresistance and salt tolerance of plants and have othergrowth-promoting activities. Understanding and manag-ing microbial ecology will have major benefits forstressed agricultural systems.
The massive scale of human agricultural and food pro-duction enterprises brings with it an array of problemsthat microbiology can help address. Any technologicaladvances that increase resistance to pathogens or nutri-ent scavenging will also contribute to reduced use ofpesticides and fertilizers. This represents a correspon-ding reduction in pollutants. Other pollutants are a directconsequence of agricultural production itself, rather thanproduction practices. Waste produced by animals, par-ticularly when produced in high densities, frequentlyrepresents a serious environmental and health hazard.Animal manure is typically accumulated in bulk and someof the material is used as fertilizer on agricultural fields.Technology to harness microbes for digestion of animalwaste could alleviate some of the environmental andhealth hazards generated by large-scale animal rearingoperations. Microbes may also be harnessed for theremediation of agricultural chemicals or for mitigatinggreenhouse gases.
Microbial digestion, another form of fermentation,can be harnessed to produce alternative fuels. Fermen-tation of animal wastes can create flammable gases,such as methane. Devising bioreactors that efficientlyconvert animal waste on a large scale would help elimi-nate an environmental and health hazard, while alsosatisfying growing energy needs. Fermentativeprocesses also produce fuels, such as ethanol from plantmaterial. The inefficiency of this type of fermentation forfuel production has kept it from being widely adopted.Improvements in fuel generating technology would
10
allow the gradual replacement of highly polluting fossilfuels with more environmentally friendly fuel sources.However, continued removal of plant waste from fieldsmay have unintended effects, such as altering the com-position and characteristics of the soil, affectingmicrobial populations and subsequent plant growth.Thus, this practice needs to be examined and followedover multiple years to monitor its effects.
M I C R O B I O L O G Y R E S E A R C H
OPPORTUNITIES T O A D V A N C E F O O D &
A G R I C U L T U R E
The previous lineup of microbiology-related problemsconfronting agriculture and food, followed byapproaches to solving these problems, provides anempirical appreciation of the value of agriculture andfood research. There have been attempts to measurethis value. Estimates of the return on investment in agri-cultural research, based on a purely economic level,range from approximately 30-60%. This means that forevery dollar invested in agricultural research, there is anannual net flow of return to society of 30 to 60 cents.However, many of the benefits of research in agricultureand food microbiology carry over into other importantareas, such as public health and economic development.These returns have not yet been estimated.
PROGRESS THROUGHMULT ID ISC IPL INARY RESEARCH
Food and agriculture microbiology research intersectswith many other fields. This overlap is evident in theresearch opportunities associated with multidisciplinaryresearch. For example, the need for improved detectiontechnologies will be addressed by research that combinessuch diverse fields as microbiology, molecular biology, sta-tistics, and engineering. Multidisciplinary researchapproaches will also lead the way in developing bettertools to model the behavior of microbiological hazards,and successful application of massive amounts of biologi-cal information to the management of the living systemsthat comprise agriculture.
Assays and detectors used in surveillance for agricul-tural diseases and human pathogens in food have thepotential to be improved as a result of several types ofmultidisciplinary research. One approach that is rapidlyimproving detection technology is the combination ofmicrofluidic engineering and molecular biology. Devicesarising from the marriage of these fields will be inexpen-sive to operate, portable, and rapid. The combination ofgenetically engineered microorganisms and opticaldevices is facilitating the creation of biosensors in which aliving microbe is actually the interface that detects tar-geted microbes or toxins.
FOOD & AGRICULTURE 11
ETHANOL FUEL FROMCELLULOSE
For many years, ethanol fuel has been
available as a supplement to gasoline
used for transportation. Ethanol can
replace up to 85% of the gasoline volume
and still be used to efficiently power
vehicles. However, the fermentation of
grain has been used for ethanol produc-
tion until recently. Because the value of
crop material as food far exceeds its
value for ethanol production, this has not
been a cost-effective use of grain. New
fermentation technologies have been
developed that produce ethanol from
cellulose-based plant materials left over
after food is harvested. Cellulose is bro-
ken down into sugars during a primary
fermentation step, followed by a second-
ary fermentation to produce ethanol. The
result is a clean burning fuel created from
agricultural waste, putting otherwise dis-
carded energy to use.
The ability to predict pathogen spread and persist-ence is being boosted by multidisciplinary research.Combining Global Information Systems (GIS) tools,mathematical modeling, and microbial physiology, it isnow possible to simulate microbial behavior in the envi-ronment. This will enable integration of climateinformation and biology to predict or track microbial dis-persion or viability upon release into the environment.Improving predictive capability is the key to predicting,recognizing, and containing outbreaks and enablingintervention efforts to be properly and efficiently appliedin a timely manner.
Application of massive computing power to the han-dling and analysis of biological information has expandedour understanding of many biological systems andprocesses in ways not imagined previously. Computa-tional analysis of genetic, protein, and metabolic data hasspawned new approaches to studying complex, net-worked events that take place within living organisms togive rise to particular phenotypes. Genomics, pro-teomics, and metabolomics rely on microscopic handling
of molecular samples (e.g., microarrays) to generate enor-mous data sets that measure the state of genes, proteins,or metabolic products in an organism. As computingadvances allow processing of ever increasing amounts ofdata and nanotechnology improves the ability to pre-cisely handle and detect molecular samples, genomic,proteomic, and metabolomic studies will becomeincreasingly effective. These kinds of analyses will enablediscoveries that can advance agricultural efficiency andfood quality and safety. The power of these analyses iscurrently expanding to enable study of the interactionsbetween diverse microbial species and the interactionsbetween microbes and their environments.
MULT I -ORGAN ISM B IOLOGY –INTERACT IONS BETWEEN HOSTS ,PATHOGENS & MUTUAL ISTS
An exciting and relevant area in food and agriculturemicrobiology is the study of disease and infection. Agri-cultural productivity and food safety can be improved bydisruption of pathogen inflicted disease in plants and ani-mals. Traditional studies of pathogen virulence and hostrange continue to contribute to our understanding of dis-ease processes. Breeding of disease resistance intoplants and animals, for example, remains an importanteffort to continue. Creation of improved vaccines isanother area where sustaining the pursuit of previouslysuccessful approaches can continue to reap benefits.Many vaccines could be improved by increasing theirbreadth of immunogenic activity, facilitating the ability todifferentiate vaccinated animals from disease carriers,and increasing the duration of immunity that is conferred.
Beyond traditional methods of combating pathogens,research into the disease process itself and the role ofinnate host resistance will open new insights into thecomplex set of interactions between hosts andpathogens associated with food and agricultural systems.Budding areas of research, such as the use ofimmunomodulators to fortify host innate immunityagainst pathogens, will contribute to this end. Research isrevealing that, in many cases, a critical part of the diseaseprocess occurs when pathogens disrupt immuneresponses in the host. As multi-organism genomic, pro-teomic, and metabolomic studies reveal precisely howpathogens attack a host, subsequent studies can investi-gate immunomodulation as a way to interfere with theinfection process of specific pathogens.
Organisms that are participating in complex biologicalinteractions represent a hugely underexploited pool of
12
interventions to prevent disease through efforts such asimmunological fortification, production of antibiotics/pro-biotics, and other mechanisms. Current investigation andknowledge of probiotics scratches the surface of this areaof research, and even in this area, specific knowledge islacking about what interactions occur between microbesand the host and how those interactions can be capital-ized upon to prevent disease. For example, beneficialorganisms may contribute to the prevention of disease byproducing substances that interfere with successful colo-nization or infection by a pathogen in a host, and/or thebeneficial organisms may exclude pathogens by compet-ing for resources while not damaging the host. Pastmethodological restraints have limited our ability tounderstand complex host-microbe interactions. However,functional genomics, proteomics, and metabolomicapproaches can all be harnessed to answer basic sciencequestions about these interactions. In so doing, probioticapproaches can be refined, providing public health bene-fits and enhancing the sustainability of agriculture. This isone area where agriculture may come face-to-face withhuman and animal clinical medicine.
Another related phenomenon where microorganismsprotect against pathogens is biological control. Manymicroorganisms can actively antagonize or kill the organ-
isms that damage or cause disease in our agriculturalcrops and animals. A famous example is the soil bac-terium Bacillus thuringiensis (Bt) that producesinsect-killing toxins. Microbiology research has extracteda wide range of toxin specificities from different strains ofBt and enabled these toxins to be expressed directly ingenetically modified crops, providing the plants withtheir own protective compounds. Continued researchwill undoubtedly produce more discoveries from this bio-control organism. Many other biological control options,such as fungi and viruses that are pathogenic to a widevariety of specific agricultural pests, are largely unex-plored and may be exploited for protection of crops andanimals. Genetic engineering of biocontrol organismshas promise for ensuring their effectiveness in targeted,large scale use against pests.
MICROB IAL ECOLOGY & HEALTHYAGR ICULTURAL SYSTEMS
The role of beneficial organisms in promoting the healthof agricultural plants and animals extends beyond com-bating pathogens. Research into how beneficialmicroorganisms can promote growth, improve stress tol-erance, and aid in the uptake of nutrients are researchareas ripe for discovery and innovation. Research intothese complex and often delicate interactions betweendifferent organisms should ultimately pay off by reveal-ing ways to assure that agriculture can become heartierand less environmentally taxing.
The same communities of microbes that benefit agri-cultural health and efficiency are likely to be disturbed bysome of the practices of industrialized agriculture. Oneway to fortify agriculture against disease and stress is tosupplement systems with probiotic and biocontrolorganisms, but a complementary and sometimes alterna-tive approach is to protect beneficial organisms that mayalready be present in the environment. Research inmicrobial ecology will help to determine how to preservea balance in microbial communities that favors agricul-ture. Heavy pesticide and fertilizer use, in particular, aretwo practices that should be studied using a holistic or
integrated approach to determine their impact on micro-bial ecology within the context of tradeoffs between risksand benefits. More knowledge in this area will helpdetermine optimal tradeoffs such that the benefits of useoutweigh the disruption caused by chemical inputs intoour agricultural systems.
Microbial communities are both vulnerable to, andcontribute to, removal of pollutants. Research into howmultiple organisms work in partnership to degradecomplex molecules is essential to increase options fordealing with the byproducts of industrialized agricul-ture. Understanding this aspect of microbial ecologymay also lead to improvements in waste disposal andenergy generation through fermentation, as well asbioremediation.
FOOD & AGRICULTURE 13
“RESEARCH IN M ICROB IAL ECOLOGY W ILL HELP TO DETERM INE
HOW TO PRESERVE A BALANCE IN M ICROB IAL COMMUN I T I ES
THAT FAVORS AGR ICULTURE .”
Organisms that cannot currently be cultivated in alaboratory setting are likely to be pivotal in advances inprobiotics, biocontrol, and microbial ecology. Researchefforts targeted on identification of these previouslyuncharacterized organisms, whether through new culti-vation methods or by indirect detection approachesmade possible by genomic knowledge, will strengthenour ability to use beneficial organisms effectively.
MAK ING THE BEST USE OFAGR ICULTURAL TECHNOLOGY
Research offers opportunities for understanding morecompletely the impacts of technologies that are alreadyused in agriculture and food production. Questionsremain concerning if genetically modified organismsinteract differently in the environment as compared totheir non-engineered counterparts. Whether or not thereare negative impacts associated with the use of GMOsneeds to be considered and balanced within the broadercontext of sustained use and potential benefits.
Increased attention to food hygiene, which hasoccurred in the developed world over the last century,has dramatically reduced incidence of foodborne infec-tion. However the void of microbially-based immunestimulation has been proposed as a culprit in weakeningimmune systems in animals and people. Further researchinto this area will determine whether this is a real phe-nomenon and, if so, how to balance tradeoffs between amicrobiologically safer food supply and maintaining ahealthy immune system throughout life.
Food and agriculture microbiology research providespotential solutions to problems that cut across manyfields. The scientific principles and the implications offood and agricultural research are increasingly linked topublic health and the environment, topics that histori-cally have received more public attention. For example,interventions against Avian Influenza, which has beendevastating poultry production, may also prevent dis-semination of another human influenza epidemic.Providing biologically-based alternatives for protectionof crops and animals against pathogens will help reducepesticide and antibiotic use, both of which have publichealth and environmental implications.
OVERCOMING BARR IERS TO SUCCESSFUL
A G R I C U LT U RA L & F O O D
M I CROB I O LOG Y R ESEARCH
Despite the need for continued advances in agricultureand food microbiology, and the proven track record ofagricultural research, research support for these fieldsover the last few decades has been lean and is, in fact,decreasing. Reversing the decline in funding andrecognition of the value of agricultural researchrequires fundamental changes, in addition to an infu-sion of financial support. The major barriers toadvancing agriculture and food research are institu-tional and perception based.
PUTT ING FOOD & AGR ICULTUREM ICROB IOLOGY IN THE SPOTL IGHT
The profile and priority of agricultural research needs tobe raised. Designated research centers of excellence,similar to those in the biomedical and defense arenas,would make strides in this respect. There are numerousinstitutions that provide a backbone of exceptional sci-entific work for U.S. agriculture, but their programs run inaging facilities and with limited financial resources.Within U.S. research institutions, agriculture is too oftena subordinate priority. One way to reverse this would beto raise the institutional overhead rate that is currentlyallowed on USDA grants from its uniquely low level to alevel on par with that provided by other funding agen-cies, such as the National Science Foundation (NSF) orthe National Institutes of Health (NIH). With limited over-head capital, administrators and investigators arerestricted in their efforts to build strong programs andrecruit personnel to pursue state-of-the-art agriculturalresearch. Increases in overall research expenditures forU.S. Department of Agriculture (USDA) programs wouldthen be needed to maintain even the current level ofdirect funds for research.
A healthy agricultural research community depends onan influx of young scientific talent. Trouble recruiting andmaintaining graduate students is impacting programsand will ultimately affect the field. Several measures canbe taken to alleviate this problem. A program of presti-gious and remunerative fellowships for graduatestudents and postdoctoral fellows would provide some
14
FOOD & AGRICULTURE 15
needed recruiting leverage. Internships involving indus-try, non-governmental organizations (NGOs), andgovernment agencies would have mutually beneficialvalue. Such internships would infuse awareness and tech-nical knowledge of agricultural science to institutionsand provide the visiting scientists with networking andtraining opportunities. The recent security-motivatedtightening of immigration procedures has limited accessof the U.S. scientific community to international talent.Making the U.S. more accessible to legitimate interna-tional students and scientists again would help allscientific endeavors, including invigorating the base forrevival of agricultural science.
Funding for agriculture and food research is essentialto fulfilling any of the potential benefits that have beenproposed. Because of the shallow profit margin in agri-culture and food, it is to be expected thatindustry/commodity funding for research in these areaswill be minimal, and when it does occur, it is usuallyfocused on short-term payoffs. Such sources of fundingtraditionally have provided no indirect costs, further per-petuating the declining research facility infrastructure.Therefore, basic research on high priority agriculture andfood problems is deeply dependent on governmentsources to provide sufficient funding. Currently the
National Research Initiative of the USDA explicitly favors“translational research,” i.e., those projects with thepromise of providing near-term, technological productsor advances. By nature, many agriculture and foodresearch endeavors are long-term, but competitive fund-ing for long-term projects is more or less unavailable. Anexpansion of research priorities to emphasize basic andlong-term research and dedicated funding to back thisexpansion will help revive agricultural research.
RESEARCH PR IOR I T I ES W I TH REACH
Long-term agricultural research projects are the onlyway to obtain scientific answers to many questions inareas such as microbial ecology and epidemiology.Unfortunately, the formula-funded land grant universitysystem once could support such long-term research, butfunds have diminished to the point that this is no longer
possible, even though the land facilities are still thereunder university ownership. One mechanism for over-coming barriers to long-term research in agriculturewould be through projects like the Long-Term Ecologi-cal Research (LTER) stations. Sustained study ofparticular agriculture and food science problems is alsohampered by certain institutionalized incentive struc-tures. Tenure evaluation procedures draw heavily onpublication records of individuals, but long-term proj-ects may be incomplete and unpublished by the time oftenure or promotion review. It is also the case thatresearch grants generally demand a structure that prom-ises completion of a project within two or three, and atmost, five years. Allowing for longer project duration,including sustained funding, and evaluation of produc-tivity based on alternative measures, would makelong-term research a more viable scientific pursuit.
Collections of microbial specimens are an essentialasset to agriculture and food microbiology research.Availability of specimens for initiation and verification ofresearch can be assured only if the resources and expert-ise are maintained to properly curate collections ofmicrobes. In the same way that institutions and fundingagencies determine the viability of long-term research,their commitment of resources and recognition to the
maintenance of microbe collections will determinewhether this asset is sustained or lost.
With multidisciplinary research at the center of manyneeded advances in food and agriculture research, someof the disincentives to this type of work should be lifted.Institutions frequently fail to recognize the effortrequired to coordinate across different research groupsand disciplines to make a project run successfully. Themany-author publications that result from this type ofwork are also not as highly regarded as ones wherecredit is less widely distributed or—in a view that is notnecessarily justified—less diluted.
The research community is also responsible for somebarriers to more successful food and agriculture science.Compartmentalization between fields of research andindustrial practice prevent effective cross-fertilizationand sharing of lessons learned. Divisions also stand in
“LONG -TERM AGR ICULTURAL RESEARCH PROJECTS ARE THE ONLY
WAY TO OBTA IN SC IENT I F IC ANSWERS.”
16
the way of greater multidisciplinary efforts. Researchopportunities will expand as scientists become moreaware and more engaged across fields dealing withmicrobiology, veterinary and human medicine, plant dis-eases (pathology), epidemiology, statistics andmathematical modeling, environmental sciences, andengineering, to name a few.
PAV ING THE WAY FOR ESSENT IALRESEARCH
Various regulations present obstacles to researchbecause they are inappropriately stringent or lacking indiscrimination. For example, listing certain pathogenspecies as “select agents” dramatically increases theexpense and legal liability of working with these microor-ganisms. In many cases, agents that are on the selectagent lists are already prevalent in the environment, andtheir study in a laboratory represents no extraordinarysafety or security risk. For example, soybean rust recentlyreached and spread throughout the southeastern UnitedStates, creating the potential to cause havoc with grow-ers in the current growing season. But because of thepathogen’s select agent rating before its arrival into thecountry, there was a scarcity of research at a time whenstudies of the pathogen were urgently needed. Fortu-nately, the action by USDA to remove it from the selectagent list will permit a greater number of researchers towork with the organism and monitor its progress acrossthe soybean fields of the country. Regulations that aremore science-based and flexible will allow essential sci-entific investigation to proceed. For the cases for whichthe select agent regulation remains sensible, it is impor-tant that funding programs allow investigators to budgetfor the biosafety and security measures that are legallyrequired to work with these organisms. These require-ments are becoming necessary for many non-selectagent plant pathogens as well and must be met for basicresearch to continue.
Basic research is stifled by a number of forces in theresearch funding arena. The push for applied results in ashort timescale as seen in the USDA’s National ResearchInitiative is one such force. While understandable thatagencies are under pressure to demonstrate an immedi-ate payoff from research supported by taxpayers, thisultimately drains the scientific foundation of innovation.If every grant is charged with generating specific,applied solutions to problems that are most politicallycompelling at the time, there will not be time orresources for the occasional unexpected but remarkablediscovery. This phenomenon is currently at its worst in
the area of biodefense research. In fact, biologicalresearch funding programs are currently skewed in favorof supporting proposals with a biodefense spin, and theagricultural arena is no exception.
The product-oriented leaning of research funding pro-grams also spills over to discourage proposals that arenot stoked with preliminary data. This puts innovativebut perhaps “high-risk” proposals at a funding disadvan-tage because they are seen as exploratory or speculativerather than hypothesis-driven. It also puts younger inves-tigators at a disadvantage.
FOOD & AGR ICULTURE ADVOCACY
Successful institution of the changes necessary to revital-ize food and agriculture research must be influenced byvarious players. Consumers, commodity groups, and legis-lators need to be persuaded of the importance of foodand agriculture microbiology research, particularly basicresearch. Organizations whose members are part of thisresearch community include the American Society forMicrobiology, the American Phytopathological Society,the Institute of Food Technologists, the Council on Agri-cultural Science and Technology, and the NationalAssociation of State Universities and Land-Grant Colleges.
More successful communication of the benefits offood and agricultural microbiological research is critical.Interested organizations and academic institutions cancontribute by training some of their scientists in speakingto and writing for the lay public. They can further con-tribute by training educators of non-scientists to be ableto convey basic scientific literacy. As scientific informa-tion can reach and be understood by the public, factsbecome more likely to be used for decision making. Thiswill be of benefit to many arenas, including those thatimpact food quality and safety, public health, and envi-ronmental protection. It will also encourage the public tobe a more informed participant in decisions regardingfood and agriculture technology, rather than being eithercomplacent or frenzied by rumor and conjecture.
Building awareness of the critical value of a broad, basicresearch agenda in food and agriculture microbiology isan important step to overcoming obstacles that have infact hindered the progress of these disciplines.
RECOMMENDATIONSRESEARCH AGENDA
• Study the impact of production and processing prac-tices on microorganism evolution, persistence, andantibiotic/pesticide resistance as they affect agricul-tural animals, plants, and environments.
• Apply systems biology approaches to understandingcommunities of microorganisms within agriculturalhosts, food matrices, and production/processingenvironments.
• Develop more sophisticated understanding of thenature, specificity and adaptation of microorganismsto food environments, hosts (human/animal/plant),and host responses to both pathogenic and benefi-cial microbes.
• Use a comparative pathobiology approach to under-stand the importance of pathogens that cross fromanimals or plants to humans and what characteristicsenable their pathogenicity to multiple hosts.
• Develop microbial technologies that can be applied inagricultural contexts for reduction of inputs, bioreme-diation of pollution, conversion of biomass, andconverting wastes to fuel.
• Pursue multidisciplinary strategies for developingknowledge and technologies to solve food and agri-culture problems.
REBU ILD ING THE FOUNDAT ION FORTECHNOLOGY USE & RESEARCH
• Coordinate development and standardize use of diag-nostic tests across agricultural production, foodprocessing, and public health systems to provide afoundation for integrated surveillance systems.
• Provide, through integrated educational initiatives, sci-entifically trained professionals who will serve the foodand agricultural communities.
• Facilitate implementation of systems approaches,long-term projects, and multidisciplinary research infood and agricultural microbiology.
REFERENCES & B IBL IOGRAPHY
Fiehn, O. 2001. Combining genomics, metabolome analyis, andbiochemical modelling to understand metabolic networks.Comparative and Functional Genomics. 2:155-168.
Harmon, PF, MT Momol, JJ Marois, H Dankers, and CL Harmon.2005. Asian soybean rust caused by Phakopsora pachyrhizi onsoybean and kudzu in Florida. Online. Plant Health Progressdoi:10.1094/PHP-2005-0613-01-RS.
Institute of Food Technologists. 2002. Emerging microbiologicalfood safety issues: implications for control in the 21st century.
National Research Council. 2000. National Research Initiative:A Vital Competitive Grants Program in Food, Fiber, and Nat-ural-Resources Research. National Academy Press,Washington, DC.
Schumann, GL. 1991. Plant Diseases: Their Biology and SocialImpact. American Phytopathologial Society, St. Paul, MN.
http://www.dh.gov.uk/PublicationsAndStatistics/PressReleases/PressReleasesNotices/fs/en?CONTENT_ID=4112474&chk=tbjtJp
http://www.fsis.usda.gov/Fact_Sheets/Bovine_Spongiform_Encephalopathy_BSE/index.asp
http://www.plantmanagementnetwork.org/infocenter/topic/soybeanrust/
FOOD & AGRICULTURE 17
