Executive Summary

*General Comments*

*In general, the accomplishments of the work conducted fell within the
theme of the Manure & Byproduct Program. Projects were geared towards
finding value in manure while being protective of the environment. The
review team found that the ARS projects were comprehensive and relevant,
and that they addressed contemporary issues. The quality of the research
was high. Numerous publications in high quality peer-reviewed journals,
and several patents, provide evidence of the contributions ARS has made
in developing new technologies, protocols and procedures. The
accomplishments related to P Index, microbial component to SWAT models,
and reviews of N cycle are evidence of the solid contributions ARS
research has made to solving problems in these relatively mature
research areas. There was also good work in making progress in new areas
of research (i.e emissions, pathogens, and byproducts.)*

*The review panel commends ARS on bringing together a diverse group of
stakeholders as a review team.*

*Format of the Accomplishment Report*

*ARS needs to develop a mechanism to map the research needs, outputs and
outcomes of the action plan to the Accomplishment Report and vice versa.
The nature and quality of the Accomplishment Report does not provide
what is needed to truly evaluate the impact of the work. What is needed
is a synthesis report that discusses how deliverables and goals of the
Action Plan have been met. This synthesis should address why some
outputs and outcomes were not addressed (e.g. change in mandate, change
in personnel, earmarks). The Problem Area sections should provide a
discussion of the overarching accomplishments of the program followed by
abstracts of the products. One suggestion to facilitate this process
would be to have the annual stations reports tie back to the Action
Plan, specifically identifying the tasks and objectives.*

*Scope of work*

*Overall, the Accomplishment Report does not show that ARS is taking
advantage of the interdisciplinary capabilities it has to address
problems holistically and nationally. Furthermore, the national programs
need to work towards developing balance across species and pollutants.
The gap between functional information (how do we make it economical)
and technical information needs to be addressed*

*Relationship between accomplishments and stakeholder needs*

*The Accomplishment Report lacks evidence that stakeholder-related
outputs have been accomplished. Products, deliverables (surveys,
compendiums, fact sheets) appear to be seriously lacking. Perhaps there
is a need to either strengthen partnerships with cooperators or have
staff that can take research to application (e.g. fact sheets). It was
noted that a catalogue of projects would be very helpful to stakeholders
on an annual basis. The Review Panel was left wondering if there was a
disconnect between federal funding allocations and customer priorities,
as defined in the Action Plan.*

**National Program 206: Manure and Byproduct Utilization**

**Assessment Report Template**

**Component I: Atmospheric Emissions**

[Problem Area 1: Understanding the Biological, Chemical, and Physical
Mechanisms Affecting Emissions]{.underline}

[Problem Area 2: Emission Factors from Livestock Facilities]{.underline}

####### 

###### [Problem Area 3: Control Technologies and Strategies for Emissions]{.underline} 

[Problem Area 4: Atmospheric Fate and Transport to
Receptors]{.underline}

**Component II: Nutrient Management**

[Problem Area 1: Animal Feeding and Management]{.underline}

######### [Problem Area 2: Innovative Technology for Collection, Storage, and Treatment]{.underline} 

[Problem Area 3: Management Tools for Indexing and Evaluating Nutrient
Fate and Transport]{.underline}

[Problem Area 4: Farming Systems and Practices for Efficient and
Balanced Manure Nutrient Management]{.underline}

**Component III: Pathogens and Pharmaceutically Active Compounds (PACs)
Component**

####### 

######## [Problem Area 1: Methods Assessment and Development]{.underline} 

[Problem Area 2: Fate and Transport of Pathogens]{.underline}

####### 

[Problem Area 2a: Inactivation Rates and Transport Characteristics of
Pathogens from Animal Agriculture]{.underline}

####### 

######### [Problem Area 2b: Pathogen Indicators for Fate and Transport Research]{.underline} 

[Problem Area 2c: Biological Source Tracking]{.underline}

[Problem Area 2d: Bioaerosols]{.underline}

[Problem Area 2e: Modeling Fate and Transport of Manure-borne Pathogens
from "Pedon" to Watershed Scale]{.underline}

# [Problem Area 3: Pharmaceutically Active Compounds (PACs)]{.underline} 

[Problem Area 4: Holistic Treatment Technologies for Nutrients,
Pathogens and PACs]{.underline}

**Component IV: Byproducts**

[Problem Area 1: Phytoavailability and Bioavailability of Nutrients,
Trace Elements and Xenobiotics in Byproducts Considered for Beneficial
Use]{.underline}

[Problem Area 2: Protocols and Methodology Standards for Examination and
Approval of Byproducts for Beneficial Uses in Agriculture and
Horticulture]{.underline}

###### 

###### [Problem Area 3: Byproduct Utilization Technologies]{.underline} 

####### [Problem Area 4: Energy from Byproducts]{.underline} 

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####### **Component I: Atmospheric Emissions** 

####### 

[Problem Area 1: Understanding the Biological, Chemical, and Physical
Mechanisms Affecting Emissions]{.underline}

**Outputs/Products**

-   Scientific information regarding the microbial populations involved
    in emissions.

-   Information on the effect of animal diet and nutrition on emissions.

-   Decision support module for ammonia emissions from land applications
    of manure.

-   Decision support module for cattle feedlot surface management to
    influence emissions.

**Research needs.**

There is a need to provide information to extension educators, private
sector consultants, and emission scientists about the biological,
chemical, and physical mechanisms affecting emissions associated with
animal production agriculture. The *overall objective of this problem
area is to identify key emission control points spanning the range of
animal production from diet, through manure storage, and eventually to
manure application in order to better manage and predict emissions*.
Research within this objective needs to be *focused on the interrelating
roles of microorganisms and the physical and chemical environment*
controlling emissions. Furthermore, the *effect on nutrient and pathogen
issues of manipulations at key points* to control emissions must also be
determined.

#########  

***Review Team Rating: In the context of what we have been provided
across the report in its entirety,***

***Relevance: High***

***Impact: Indiscernible***

***Review Team Assessment:***

*We believe that research conducted under this problem area is of
fundamental nature and potentially of high impact. USDA-ARS engineers
and scientists from 10 states are cooperating with others from nearly 15
different entities to address this problem area.*

*The research on the microbial type, nature and activity impacting odor
emissions from liquid swine manure and poultry litter has generated new
scientific information and advanced understanding of biological
mechanisms affecting emissions and provided vital data and information
for developing odor control BMPs and treatment technologies to reduce
emission of noxious gases from liquid manure and poultry litter. Most
work has focused on ammonia emissions and considerable progress is made
on effects of biological and physicochemical relationships influencing
emission. This work needs to expand to other pollutants, different
animal species and manure management systems. There has been some
progress made on identification of emission control points but it did
not encompass a wide range of animal production systems.*

*Generally, there was good work done and published on physical factors
influencing emissions and measurement methods. The research is highly
relevant and data and information have a high probability to be
transferred to the field in the long-term. However, impact to end users
in the short and long-term is not discernible due to the lack of
information on deliverables and outcomes in the Accomplishment Report.
There is some evidence of use and application of ARS researchers'
findings by other stakeholders (e.g., USGS and O2 transfer equation) but
little information was provided regarding development of factsheets or
anything else that was implemented in the field. In one instance, it was
noted that an important deliverable in this problem area was a method to
assess how diet influences populations of Sulfur-reducing bacteria.
However, no explanation was provided if any Sulfur-reducing bacteria
populations' correlation to manure odor existed and if stakeholders
(including other scientists) are using this method. The ARS scientists
conducted research on predicting NH~3~ emissions from anaerobic lagoons,
but planned outputs listed a support module for NH~3~ emissions from
land application -- no information on this deliverable was provided in
the accomplishments report.*

*There was no evidence that the following outputs were produced:*

-   *Information on the effect of animal diet and nutrition on
    emissions.*

-   *Decision support module for ammonia emissions from land application
    of manure.*

-   *Decision support module for cattle feedlot surface management to
    influence emissions.*

*Generally, if the research led to a finding that leads to a
recommendation, then it should have been included in the impact
statement.*

[Problem Area 2: Emission Factors from Livestock Facilities]{.underline}

**Outputs/Products**

-   Fact sheets and guidelines on emission factors based on definable
    animal or input units that adequately represent regional climate,
    management input, and other factors.

-   New technologies to quantify emission factors based on improved
    technologies for concentration and flux measurement.

-   Comprehensive, relevant, science-based emission factors that
    represent a mass balance of the nutrient input.

-   Interaction among ARS scientists working on the underlying
    mechanisms of gas, particulate, and pathogen emissions and those
    addressing emission factors to develop process-based models of
    emissions.

**Research needs.**

The development of accurate emission factors will require surveys and
synthesis of current knowledge and information regarding emission
factors; evaluation of measurement tools, technologies, and sampling
methods used to quantify concentrations and emissions; evaluation of
field-based, scale-appropriate measurement of concentrations; and
estimation of fluxes across animal species, geographic regions, seasons,
climates, and management practices.

***Review Team Rating:***

***Relevance: High***

***Impact: Medium***

***Review Team Assessment:***

*ARS researchers from seven states and their cooperators have made
considerable advances in developing new methods, protocols and modeling
techniques to measure particulate and gaseous emission from AFOs, a very
important topic area. Whole farm emission factors have been developed
but mostly for ammonia, a non- regulated gas. Farm-scale emission
factors for PM, reactive VOCs and other GHG are also needed.
Additionally, there was no evidence of interaction with NAEMS
researchers in moving forward with long-term outputs ('addressing
emission factors to develop process-based models of emissions').*

*Considerable research was done on a new field sampling protocol for
odorants that involved solid- phase microextration and it correlated
well with traditional olfactometry. The new protocol provides rapid odor
sampling and evaluation as well as aids in the odor management from
livestock operations and wastewater treatment plants. However, it is not
clear how this valuable information is used/adopted by other scientists
and analytical laboratories.*

*Development, validation and use of a new dispersion model (BLS) to
determine air pollutants emissions are noteworthy. The report lacks
information on what was done to demonstrate that this is comparable or
worthy of EPA use, compared to current models such as AERMOD.*

*Research on pathogens emissions were listed in the Action Plan for this
problem area but not addressed (Interaction among ARS scientists working
on the underlying mechanisms of gas, particulate, and **pathogen**
emissions and those addressing emission factors to develop process-based
models of emissions.)*

*The Accomplishment Report for this problem area lacked information
regarding the following two important short-term deliverables and
outcome.*

-   *Fact sheets and guidelines on emission factors based on definable
    animal or input units that adequately represent regional climate,
    management input, and other factors.*

-   *Synthesis of current emission factors that can be applied to CAFO
    and animal production systems to assess the potential impacts of
    animal operations on air quality.*

###### [Problem Area 3: Control Technologies and Strategies for Emissions]{.underline} 

**Outputs/Products**

-   Database of information on gas formation and emissions based upon
    the current body of knowledge that can be used to identify potential
    control points for emissions.

-   BMP for manure storage and cleaning pen surfaces to reduce dust.

-   Control practices and strategies with associated decision support
    tools to reduce emissions of ammonia, greenhouse gases, VOCs, and
    odor that balance emission control, economic, and labor
    considerations.

**Research needs.**

Effective and reliable control strategies and technologies can be
developed through the application of scientific knowledge to various
components of animal production and manure storage and handling
processes. Research projects should aim to quantify the role of modified
animal diets; the microbial interactions that result in the production
of odor, VOCs, greenhouse gases and ammonia; chemical amendments and
inhibition of microbial interactions; and systems of treatment
technologies including improved manure handling and storage, all of
which will yield potential solutions to these problems. System analysis
approaches through mechanistic process models incorporating cross-media
and interactions with nutrients are needed to effectively reduce overall
emissions from agricultural operations.

***Review Team Rating:***

***Relevance: High***

***Impact: High***

***Review Team Assessment:***

*This is a new emphasis area for ARS, with ARS researchers from 12
states working to assess control strategies and developing and testing
technologies to reduce air pollutant emissions from AFOs. The focus was
clearly on ammonia with much less work conducted on other gases
identified in the project plan. Progress has been made in these areas:
management recommendations for pen surfaces to reduce dust and other
gases, BMPs to address pollutants, other innovative management practices
that can be accepted for cost-share programs and findings that have been
implemented by producers.*

*Work was conducted to assess litter additives, feeding strategies, cake
management, and alternative storage and treatment strategies, including
holistic strategies. In all cases, it is imperative that economics and
evaluation of unintended consequences be included as part of the
research plan. Further research in these areas with application to other
species is needed. System analysis approaches through mechanistic
process models incorporating cross-media and interactions with nutrients
are needed to effectively reduce overall emissions from agricultural
operations -- accomplishments in this area are not brought out in the
Accomplishment Report. We do recognize that it is still too early to
expect a complete systems analysis approach; however such an approach is
needed, and we expect this will come in the future.*

*A particular issue of importance that we wish to call to your attention
is the equal need by regulatory agencies and the industry to quantify
control efficiencies so that statutorily required cost analyses of
mitigation practices can be accurately performed. Additionally, control
efficiencies and quantification of effectiveness of mitigation practices
are being demanded by local jurisdictions when performing environmental
analyses of proposed projects. This type of output should be expanded in
future ARS studies.*

*A repeated comment throughout the evaluation performed by the panel was
concern about how and if the results of the work were being
disseminated. Much of the work appeared to be a single-station without
university partners. The alum work provides an indication of adoption by
industry, and information on economics is provided, which is important,
however, it appears that the research was conducted prior to this
project period.*

*The Action Plan called for a "database of information on gas formation
and emissions based on the current body of knowledge that can be used to
identify potential control points for emissions." Such a database was
not presented in the Accomplishment Report.*

[Problem Area 4: Atmospheric Fate and Transport to
Receptors]{.underline}

**Outputs/Products**

-   Transport potential of different gases, particulates, or pathogens
    through the atmosphere to receptor sites.

-   Standards and protocols for aerosol collection and analysis.

-   Transport models for gases, particulates, and pathogens capable of
    accurately predicting transport across complex terrain.

-   Assessment and prediction of the concentration of gases,
    particulates, and pathogens at receptor sites that can be linked
    with human and animal health assessments.

**Research needs.**

Much of the data needed to determine the atmospheric fate and transport
of gases, odorants, particulates and bioaerosols will come from research
in components 1 and 2 on processes and emissions factors, respectively.
Additional information on fate and transport is needed once these
substances are in the atmosphere. Transport models for gases,
particulates, and pathogens emitted from livestock facilities to
receptor sites are needed to assess the impact of livestock operations
on the environment. Current atmospheric transport models are limited by
a lack of understanding of the turbulent regime adjacent to the facility
or manure storage site and the movement of air across complex terrain
present in agricultural areas. Constituents in the atmosphere travel
differently because of size and interactions with air and there is a
need to quantify how these components change with distance traveled in
the atmosphere to provide more realistic estimates of the concentration
at the receptor site. Research is needed to develop improved atmospheric
transport models capable of estimating the movement of gases,
particulates, and pathogens from livestock facilities to downwind
receptor sites, quantify the micrometeorological conditions adjacent to
livestock buildings, manure storage, and manure application sites for
inclusion into transport models, and develop enhanced estimates of
gases, particulates, and pathogens at receptor sites for linkage with
human and animal health assessments.

***Review Team Rating:***

***Relevance: High***

***Impact: High***

***Review Team Assessment:***

*ARS researchers from seven states and their cooperators are conducting
this high impact research work. We note that the on going work on impact
of wind turbulence, wind speed variations and other meteorological
parameters on PM and gaseous plume emissions is needed and is a valuable
input to the air pollutants transport models. This work should include
PM speciation from AFOs to assess bioaerosol and ammonium transport from
source to receptor.*

*The work on the use of LiDAR to evaluate PM emissions from AFOs should
be compared to existing TSP, PM10 and PM2.5 samplers such as the tapered
element oscillating microbalance (TEOM) for continuous monitoring of PM
and cyclones for total suspended particles and equipped with PM10/PM2.5
heads. Sampler biases with this and other existing methods should also
be studied.*

*Research conducted on transport of PM and ammonia, and identification
of bioaerosol pathogens in transported and deposited materials from AFOs
is important. This work needs to be expanded to assess the fate and
transport of odors, GHG, and reactive VOCs from livestock and poultry
production sources to receptors such as residential area, schools etc.*

*The report lacked information on a number of important deliverables and
outcomes (such as the baseline data for different CAFO types, in
different geographical areas to help target effective use of resources
in evaluating and reducing potential health effects and guidelines for
protecting health of CAFO workers based on scientific observations)
listed in the Action Plan. However, the reviewers acknowledged that this
is an emerging area and these products and outcomes will be available in
the long-term. Based on the write up provided, it was not certain if the
findings have been shared with EPA or communicated to stakeholders.*

####### **Component II: Nutrient Management** 

####### 

*Overarching comments: This is one of the more mature components of the
program. A number of widely-used products have resulted from this
program over the years. A number of stations are involved in the
research area and there is evidence of cooperation among stations to
work towards a common vision.*

[Problem Area 1: Animal Feeding and Management]{.underline}

######### **Outputs/Products** 

######### 

-   Simple, reliable methods to determine bioavailability of feed
    nutrients and information on the bioavailability of nutrients in
    feeds for use in feed formulations.

-   Feed processing and ration formulation recommendations that balance
    animal production and environmental outcomes.

-   Methodologies that help identify the impacts of feeding regimes on
    manure nutrient composition, phytoavailability, and subsequent
    reactivity in the environment.

-   Data sets that help predict the effects of feeding strategies on
    animal production, farm profitability, and environmental outcomes.

**Research needs.**

Modifications are needed in animal feeding and management to increase
the proportion of dietary nutrients retained in the animal or animal
products and decrease the proportion of dietary nutrients excreted and
lost to the environment. Information is needed concerning the impact of
diet manipulation and animal management on animal production, health and
reproduction, manure composition, the availability of manure nutrients
to plants, and potential nutrient losses to the environment.

***Review Team Rating:***

***Relevance: Low to Med***

***Impact: Low to med***

***Review Team Assessment:***

*This is a very important topic area and is similar to work underway at
a number of universities. Patents have been issued and a number of the
featured studies show that there is decent cooperation with university
researchers and across stations. Their work represents good breadth in
research across species in the area of dietary impact on air emissions.*

*Considering the report of accomplishments provided to illustrate the
achievements during the reporting period, the work conducted does not
appear to be in line with the Action Plan nor does the work address
topics that are deemed highly relevant by the review panel. One example
of this, without wanting to single out any one project, is the research
with low phytate (LP) grains. As far back as 2003 it was evident that LP
grains would not be commercially available because of yield issues.
Therefore, while LP grains show environmental promise, it is difficult
to say that the work has had any impact on society; the impact of that
work was not conveyed in relevant terms.*

*Stakeholders are a vital part of this area of research as
implementation of the findings is dependent on producer 'buy in'.
Conveyance of research findings and means for implementation are
critical. The report lacked evidence that findings have been relayed to
industry. More veterinarians should be included as stakeholders for this
problem area as they have considerable influence over producer
decisions. Economics and animal performance measures need to be a key
part of the research conducted. This brings about the need to convey
findings in a manner that balances animal and economic considerations
with environmental benefit. The Accomplishments Report lacked
information related to economics and farm profitability.*

*Work related to the feed processing output was absent. No evidence of
development of a data set for use in predicting feeding strategy effects
was provided.*

######### [Problem Area 2: Innovative Technology for Collection, Storage, and Treatment]{.underline} 

**Outputs/Products**

-   Alternative technology to control runoff and improve water reuse in
    feedlots and at other AFOs.

-   Superior technologies to capture, transform, concentrate, and reuse
    nutrients in animal manures.

-   Refined constructed and natural treatment technologies to
    effectively manage nutrients.

-   New technologies to recycle or recover nutrients from lagoon sludge.

**Research needs.**

Innovative treatment technologies need to be developed and integrated
into systems to prevent off-farm release of nutrients. Technologies are
needed to control feedlot runoff, reuse water, and integrate these
practices into holistic management systems. A combination of new
biological, physical, and chemical treatment technologies are needed to
efficiently separate manure liquids and solids, to capture and
concentrate manure nutrients, and to treat lagoon sludge. New manure
application techniques to reduce nutrient losses to the atmosphere,
surface water, and groundwater need to be tested and developed. The
efficacy of current BMPs and treatment systems need to be quantified and
new ones developed. These technologies and systems will decrease the
potential for problems at farms and AFOs and improve the possibility for
transport of manure to where it can be used safely and beneficially,
thus protecting the environment and human and animal health.

***Review Team Rating:***

***Relevance: High***

***Impact: High***

***Review Team Assessment:***

*The achievements under this problem area were considered by the review
panel to be the result of a cohesive vision in responding to the Action
Plan, perhaps reflecting a mature program. Work conducted was broad in
scope and The Accomplishments Report illustrated a nice combination of
testing existing technologies with development of new technologies.
Multiple pollutants of interest were addressed.*

*As part of a mature program, economics should have been an integral
part of the work, through greater partnering with university or agency
economists. Evidence that findings have made their way to the general
public was lacking for many (most) of the projects described and is
essential for implementation and even further refinement of the
technology so that it will be adopted. Documentation of effectiveness of
all technologies should be relative to current practices used by the
appropriate stakeholders. Identification of technology limitations is as
essential as unveiling the positive attributes and should be considered
integral to the work.*

[Problem Area 3: Management Tools for Indexing and Evaluating Nutrient
Fate and Transport]{.underline}

**Outputs/Products**

-   Refined P Index

-   N Transport Index

-   Quick Tests for Determining Manure Nutrients

-   Refined Process Based Model for Organic Nutrient Management at
    Multiple Scales.

-   Decision Support System for Predicting N Availability from Manure

**Research needs.**

New tools are needed to evaluate manure nutrient availability. Research
is needed to develop "Quick Tests", which are appropriate for on-farm
use, particularly for plant-available N and bioactive P. Research is
needed to improve the P Index input parameters and validate the P Index
at the watershed scale. A Nitrogen Transport Index is needed to
determine the potential impacts of manure application on N transport to
air, rivers, and lakes. The impact of soil properties, climatic
variables, and manure composition on manure N availability must be
quantified so that manure N availability to crops can be accurately
predicted. Expanded knowledge is needed that quantifies the linkages
among C, N, and P cycling processes and incorporates this information
into process-based models. Decision support tools are needed that
incorporate all this information.

***Review Team Rating:***

***Relevance: Med***

***Impact: Med-High***

***Review Team Assessment:***

*Nutrient availability work is an important field of research as is the
development of rapid, low-cost field measurement techniques. The
Accomplishments Report highlighted a number of methods that were tested
over a range of nutrients. Over time, the program has produced a number
of products that have widespread adoption or have been incorporated into
widely-used models. The review panel saw evidence of strong
collaboration across stations, sharing a common vision and mission to
evaluate a problem at the national level.*

*However, within the current project period, other than the P Index
(which was monumental and largely developed prior to this Action Plan
period) and the P loss model, the review panel did not see much evidence
of products that are available to the industry right now; rather, the
report was primarily a listing of methods still under development. The
Decision Support System, the Process-based Model, and the quick tests
were identified as outputs and are much needed in the public domain but
there was no evidence that they are actually available.*

*As methods and quick tests are developed it will be essential that
costs and time savings, relative to traditional methods, be well
documented and disseminated.*

[Problem Area 4: Farming Systems and Practices for Efficient and
Balanced Manure Nutrient Management]{.underline}

**Outputs/Products**

-   Effective and environmentally sound nutrient management plans for
    nutrient-balanced livestock and crop production systems.

-   BMPs for manure nutrients that are specific to livestock and crop
    producers' goals and reflect the sensitivity of the watershed to
    nutrient loading.

-   Improved manure application equipment that increases nutrient use
    efficiency.

-   Alternative management systems for nutrient use and pathogen
    transport reduction at farm/watershed scales.

**Research needs.**

Customers need BMPs, e.g., tillage and cropping systems, application
timing, and application equipment for efficient use of manure nutrients.
These BMPs and their associated nutrient management plans must be
economically viable, environmentally sound, and evaluated at field,
farm, and watershed scales. New application methods and associated
equipment need to be developed. Alternative systems of manure
utilization are needed where land application is not a viable practice.
To be adopted, these practices (both land and non-land based) should be
effective, efficient, and fit into crop production systems used by the
producer.

***Review Team Rating:***

***Relevance: High***

***Impact: High***

***Review Team Assessment:***

*As a problem area within a mature component, the accomplishments within
this area were evidenced by strong impact statements in addition to
outputs (review articles, books, publication in a nutrition trade
journal). The demonstration of findings as part of the program
deliverables, is critical and a means of ensuring adoption which may be
quick in this area if demonstrated appropriately. Cost-share
opportunities to aid in adoption may follow as well and ARS scientists
should be working with agencies to develop these opportunities.
Partnering with Extension in portions of the program helps to achieve
implementation and improve the overall impact of the component.*

*This problem area addresses important topics and ARS is the best-suited
entity to conduct long-term fertilization studies so it is encouraged
that this remains a strong aspect of the program. Outputs have included
updates on fertilizer recommendations, an important deliverable.*

*The work focused on broiler litter applications with some limited dairy
work. There was a clear geographic focus in the NE and SE, in addition
to a species focus. Research incorporating cattle and swine manure is
needed and would strengthen this program area.*

####### 

####### 

####### **Component III: Pathogens and Pharmaceutically Active Compounds (PACs)** 

####### 

*Taking from the Action Plan, "...The logical structure of the program
is to determine better what organisms and PACs are present, determine
how they are disseminated and survive in both the on-site and off-site
environment, quantify this behavior (e.g., with models), and develop
treatment methods for pathogen and PAC control that are compatible with
nutrient and other management objectives." Research conducted in this
component does address each of these steps, and individual research
projects are of high quality, resulting in publication in peer-reviewed
reports in significant journals. The Pathogens Problem Areas 1-3 appear
more focused on basic research than the PAC Problem Area. Most Pathogens
projects focus on a single organism, under relatively constrained
conditions or geographies, and do not appear to take advantage of ARS
interdisciplinary potential, or ability to address a wide array of
agricultural environments across the country. Several of the other
Components appear to be expecting contributions from the Pathogens
Component, as "pathogens" are included in the proposed outputs and
benefits for several "non-Pathogens and PACs" Problem Areas. However, it
does not appear that there was a concerted or focused effort to provide
data needed for these other Components. Pathogens Problem Areas 2a and
2e exemplify ARS capabilities to conduct agriculturally-relevant fate
and transport studies, and to take basic information to more
practical/applied products through development of model components and
subroutines that have generated user interest and application. The PAC
problem area also produced particularly useful information by
addressing, for example, whether poultry litter application at levels
based on N, affected hormone load in soil and water. The other Pathogens
Problem Areas would benefit from projects more focused along similar
lines, targeting agricultural practices and technologies.*

######## [Problem Area 1: Methods Assessment and Development]{.underline} 

**Outputs/Products**

-   A compendium of current methods.

-   A set of validated methods for specific pathogens and matrices.

**Research needs.**

There is a need for scientists to rigorously evaluate current and new
methods and then communicate their observations and findings to other
scientists conducting related research to minimize duplication of
effort. Specifically, it would be useful to evaluate methods with
respect to (1) selectivity, (2), sensitivity, (3) quantitativeness, (4)
analysis time, and (5) cost. These methods need to be tested in all
relevant matrices -- soil, manure and biosolids, wastewater, air and
water. New methods need to be developed when current methods are
lacking.

All the ARS units conducting pathogen research necessarily utilize one
or more detection methods depending on the mix of pathogens, matrices,
and research goals. Consequently, all units will contribute, either by
actively developing or optimizing new methods, or by validating
previously existing methods.

***Review Team Rating:***

***Relevance: Low to Med***

***Impact: Low***

***Review Team Assessment:***

*The report in this problem area suffers from an inexplicable failure to
link to the stated outputs/products (as listed above) or to the stated
target pathogens in the Action Plan. Developing reliable, validated
methods for even the five target pathogens in agricultural matrices
would be, as the Action Plan explains, a significant research challenge.
Only a few ARS locations appear dedicated to this task, and the proposed
compendium of methods (many developed by non-ARS researchers) seems to
be a critical first step in focusing ARS methods development on critical
areas for agricultural applications, and in efficiently moving from
basic research to actual applications such as solving manure management
problems or developing models. However, the proposed compendium of
methods appears not to have been worked on at all. Methods for two
target pathogens (and two non-target pathogens) were developed. The new
methods developed are of high quality, and the pathogens not stated to
be targets in the Action Plan are nevertheless of great significance to
agriculture or even human health. Hence, these are fundamental
contributions to the overall goals of this Component, but result in what
appears to be an unfocused and perhaps arbitrary program.*

*The E. coli O157:H7 quantitative real-time PCR was used in
field/watershed studies, and exemplifies the direction this problem area
should take from basic methods development to application to real-world
issues and conditions.*

[Problem Area 2: Fate and Transport of Pathogens]{.underline}

**Research needs.**

Information is needed on pathogen inactivation and die-off as well as
their potential for regrowth as functions of environmental conditions
(e.g., temperature, moisture, etc.) during all stages of waste
management. These stages include deposition, collection, storage,
handling, treatment, utilization and application. This information
should be linked to pathogen movement in air and water. The
determination of their transport characteristics needs to address
variables such as soil type and vegetative cover. In addition, a better
understanding of the connection between the pathogens and indicator
organisms is needed, if, for example, regulated total maximum daily
loads (TMDLs) for indicator organisms are to be meaningful measurements
of surface water impairment.

Because fate and transport of pathogens from animal agriculture is a
complex and multifaceted area of research, five sub-problem areas and
groups will be established to concentrate on a particular aspect of
pathogen fate and transport:

1.  

[Problem Area 2a: Inactivation Rates and Transport Characteristics of
Pathogens from Animal Agriculture]{.underline}

**Outputs/Products**

-   Data sets on inactivation rates for Salmonella, E. coli 0157:H7,
    Campylobacter, Cryptosporidium parvum, and fecal indicator bacteria.

-   Data sets on transport parameters on Salmonella, E. coli 0157:H7,
    Campylobacter and C. parvum relative to fecal indicator bacteria.

-   Data on the ability of various pathogens to contaminate or infect
    various crops.

-   Knowledge of pathogen persistence, inactivation rates, and transport
    parameters that will be useful to producers, managers of watersheds,
    regulators, decision makers, and developers of predictive models.

**Research needs.**

An improved and more extensive data set on the survival of particular
pathogens is needed. Pathogens such E. coli 0157:H7, Salmonella spp.,
the protozoan parasite Cryptosporidium parvu and viruses will have
different die-off rates under the same environmental conditions. These
die-off rates need to be determined and compared with those of the
indicator organisms that are used to monitor the presence of pathogens
from animal agriculture. Rates of die-off for pathogens need to be
carried out under controlled laboratory conditions as well as under
variable field conditions in both soil and water. In addition to these
survival studies, transport studies need to be designed. Small-scale
plot studies that involve rain simulation in conjunction with small
watershed scale studies need to be undertaken in which both particular
pathogens and indicator organisms are measured. The objectives of this
research will be to:

1.  1\. Develop a data set of die-off rates for particular pathogens and
    indicator organisms for controlled environmental conditions as well
    as field conditions in different seasons.

    2\. Determine the transport characteristics of the pathogens and
    indicator organisms at plot and watershed scales.

    3\. Develop survival and transport datasets that can be readily used
    by modelers and decision makers who make recommendations for BMPs.

***Review Team Rating:***

***Relevance: High***

***Impact: High***

***Review Team Assessment:***

*This problem area constitutes high quality research on fate and
transport of E. coli O157:H7, Campylobacter jejuni in groundwater
(particularly with respect to generic E. coli as an indicator),
Cryptosporidium parvum in soil (field plots), and of several
microorganisms with respect to manure particulates and P runoff (as a
predictor). The work is focused on the target pathogens from the Action
Plan, and on major transport pathways, and generally with applied focus.
The survival of E. coli O157:H7 was assessed in different environmental
samples using the methods developed under Problem Area 1, which the
review team found particularly commendable. Cryptosporidium parvum
oocysts were tested for survival and infectivity following placement in
various soils under various cropping regimes. Likewise, studies
demonstrating that manure affects/facilitates pathogen transport and
that organic P may be a reasonable surrogate for some pathogen transport
are major contributions, and demonstrate the need for applied,
field-relevant research of this type. These are particular examples of
the kind of field-oriented, practical studies where ARS research can
make a major contribution. Overall, this work has great potential
impact. However, there is no evidence in the report that any products of
immediate value to users, such as improved treatment technologies or
BMPs, have been developed based on the fundamental research conducted.
We appreciate that this is a new field, and acknowledge the importance
of the fundamental contributions reported. Datasets and new knowledge
listed as outputs/products were achieved, but linkage to users in ARS
(e.g., modelers, those testing technologies or BMPs), and rapid
dissemination to users outside of ARS should be developed.*

######### 

######### [Problem Area 2b: Pathogen Indicators for Fate and Transport Research]{.underline} 

**Outputs/Products**

-   Database of indicators and their properties (e.g., which indicators
    work well for which pathogens and their strengths and weaknesses).

-   Database from fate and transport studies that have used a common set
    of indicators at laboratory to watershed scales.

**Research needs.**

There is a need for more indicators and more appropriate indicators.
More indicators are needed because of the variety of pathogens present
in manure and some other byproducts. Bacteria, protozoans, fungi, and
viruses are all present. In addition, within each genus there are
differences in their properties, such as the capability to form spores
resistant to environmental factors leading to their death. These
indicators for each class of organism also then need to more
appropriately mimic the properties and behavior, such as attachment,
survival and regrowth in soil, water and air, of actual pathogens.
Research on this topic has three primary objectives:

1.  1\. Identification of improved indicators.

    2\. Testing of their traits and behavior (survivability, transport,
    etc.) relative to current indicators and pathogens.

    3\. Development of a robust data set of indicators and their
    properties for use in models and to inform policies.

All ARS researchers conducting fate and transport studies will use the
same indicators to help develop this robust dataset. Many ARS scientists
also will be cooperating with scientists at other agencies and
universities. We will cooperate with end-users, such as extension, state
agency offices, NRCS, USEPA, industry, etc. to put the information into
formats that are most readily useable for their organizations so that
the expected outcomes are quickly achieved.

***Review Team Rating:***

***Relevance: Low***

***Impact: Low***

***Review Team Assessment:***

*The report for this Problem Area, like that for Problem Area 1, suffers
from a lack of information. Only one study is mentioned --- a 9-month
watershed study of E. coli and virulence marker genes. However, the two
reports cited in this section pertain to groundwater studies. A
comparison of E. coli and Campylobacter survival and transport in porous
media (cited first in Problem Area 2a) did address the Problem 2b topic
area, and concluded, as have many other non-ARS studies, and as was
predicated in the research needs section above, that current indicators
are not adequate predictors of many pathogens.*

*The research in this area was minimum and far out of line with the
proposed outputs/products. Specifically, no steps were made toward
identification of any new or improved indicators for pathogen fate and
transport.*

[Problem Area 2c: Biological Source Tracking]{.underline}

**Outputs/Products**

-   Database/whitepaper of microbial source tracking "case studies,"
    including microorganisms/ecosystem(s) involved, and a critical
    assessment of studies with respect to the four key assumptions.

-   Testing innovative technologies such as DNA micro-array based
    approaches and other technologies with the potential to reduce cost
    and improve efficiencies.

-   Following organisms from excretion through environmental sample.

-   A model system in which all four assumptions are met with respect to
    a specific candidate source tracking organism, thus resulting in a
    defined system(s) where microbiological source tracking may be
    applied to identify sources of environmental contamination. This
    model may vary for a given organism and may reflect different animal
    production systems and/or different ecosystems.

**Research needs.**

All four key assumptions must be validated on the basis of sound science
for biological source tracking to be accepted as a valid environmental
method. *\[The four assumptions from the Action Plan were: For any
pathogen in question, the following points need to be answered: (1) host
specificity, (2) geographic stability of clonal composition, (3)
temporal stability of clonal composition, and (4) clones isolated from
the environment must correspond to those of the fecal source (secondary
vs. primary host).\]*Each animal species (swine, beef, dairy, etc), with
their attendant pathogen(s), operating under different production and
environmental conditions need to be investigated to address the above
four assumptions. Scientific methodology such as the following are just
some of the identifiable research areas (1) valid sampling methods
regarding production system/geographical location, (2) statistical
validation of sampling methodologies, (3) validation of detection
methods, (4) robust DNA fingerprinting techniques to establish clonal
relationships, (5) knowledge of environmental stability of pathogens,
and (6) knowledge of pathogen transmission pathways. Results for these
efforts will thus define future high priority research topics.
Alternatively, the lack of adequate technologies may indicate either the
futility of this endeavor or cost-ineffectiveness of conducting
biological source tracking at this time.

***Review Team Rating:***

***Relevance: High***

***Impact: Med***

***Review Team Assessment:***

*The review team rating reflects the commitment that microbial source
tracking (MST) is indeed an important topic area, and at least one of
the reported products (PCR primers for E. coli O157:H7 and related
serotypes) has the potential to contribute to this rapidly-evolving area
of research. However, the report was not available at the time of the
review team assessment. A second summary in this Problem Area
highlighted a watershed study that was not clearly addressed by either
of the cited reports. However, to the extent that this is a
collaboration with other ARS scientists studying other aspects (e.g.,
nutrients, BMPs) of the Santa Ana River Watershed, it is to be
commended. Overall, the impact of this Problem Area is diminished
because the newest MST methods were minimally applied, field application
was minimal, and it is not clear how soon products from this Problem
Area could be usefully employed in agricultural systems. The ability to
follow organisms from excretion through environmental samples would be
the goal (as per output three above) but little seems to have been
achieved with respect to this goal.*

Two studies and the first and fourth outputs/products address
library-based MST. ARS research contributed 1) to assessment of
library-based MST; 2) to demonstration that this approach has numerous
weaknesses, and; 3) to publication of the Microbial Source Tracking
Guide document that outlines these limitations. The Microbial Source
Tracking Guide document satisfies the first output listed for this
Problem Area. ARS research contributed to demonstrating that the
fundamental assumptions about the validity of library-based microbial
source tracking are not met under all circumstances. Based on these
limitations already, the fourth output/product would no longer be a
target for further study, although it was an appropriate target given
the state of microbial source tracking science when the Action Plan was
written.

[Problem Area 2d: Bioaerosols]{.underline}

###### **Outputs/Products** 

###### 

-   Bioaerosol sampling and detection protocols.

-   Database of baseline information relating to bioaerosol contaminant
    fate and transport by various livestock management practices.

-   Development or modification of management practices to reduce
    bioaerosols.

# **Research needs.** 

# 

# Since no standard protocols exist, methods suitable for the collection and detection of bioaerosol contaminants are needed. Establishment of methods to collect bioaerosols generated by livestock production practices will include (1) evaluation of bioaerosol collection equipment to efficiently recover bioaerosol contaminants from different livestock production practices; (2) evaluation of the manner in which to collect (location of bioaerosol collection equipment, air collection rate, etc.) bioaerosol contaminants to achieve a representative sample under different environmental conditions; and (3) definition of the physical and chemical parameters (weather conditions, wastewater and biosolids characteristics, etc.) that should be evaluated simultaneously to develop an understanding of fate and transport of manure-borne biological contaminants in air. Following methods assessment, baseline information needs to be collected to enhance our understanding of the (1) types and concentrations of biological contaminants in bioaerosols generated by various livestock production practices; (2) fate (survival or persistence) of biological contaminants in bioaerosols generated by different management practices and under various weather conditions; and (3) distance that contaminants travel from the bioaerosol source. These data can then be used to modify currently available, or establish new, bioaerosol transport models. 

Identification of effective bioaerosol collection protocols and
microbial contaminant detection methods will be important products of
this work. This work also will provide baseline data concerning
manure-borne contaminants in bioaerosols generated by different
livestock production environments. This information will be used to
identify current or develop new strategies for reducing bioaerosol
generation by various livestock production practices and to develop
bioaerosol transport models. Bioaerosol transport models will enhance
our understanding of the fate of biological contaminants and the ability
of these contaminants to reach water or food supplies under given
environmental and livestock management conditions. Baseline information
gained by the above research needs will provide critical information to
those conducting risk assessments for evaluating human and animal health
risks of bioaerosols generated by various livestock production
practices. The development of tools and treatment strategies for
bioaerosols will be advanced in collaboration with the NP 206
Atmospheric Emissions Component.

***Review Team Rating:***

***Relevance: Med***

***Impacts: Low***

***Review Team Assessment:***

*Research in this Problem Area does not seem consistent with the stated
goals (outputs/products) or the research needs. The need for new
validated methods for bioaerosol research was highlighted, but new
validated methods for collecting bioaerosols were not, apparently,
addressed. Nevertheless, the impact statement for this brief section
indicated that bioaerosols are not an off-site problem. The studies
conducted of particulates and endotoxins, or of bacterial pathogens with
respect to manure or biosolids application, add to the small database of
information on bioaerosols (output/product 2). However, the organisms
considered are not those expected to survive UV, and it is not clear why
those targets, as opposed to other more durable organisms or indicators
such a coliphage, were not addressed. Likewise, the focus seems to have
been on biosolids, but center pivot irrigation or spray guns might seem
other important (unaddressed) targets. The other outputs/products do not
appear to have been addressed and there is no evidence that findings
have been communicated to regulatory agencies. A significant effort on
output 1 would allow streamlining of research, and an ability to target
research to those practices or situations where information is needed
for better decision making.*

[Problem Area 2e: Modeling Fate and Transport of Manure-borne Pathogens
from "Pedon" to Watershed Scale]{.underline}

#  

# **Outputs/Products** 

# 

-   A set of pathogen transport submodels to use at different scales
    with water and solute transport and erosion models for determination
    of pathogen fate and transport.

####### Decision-support tools at pedon, hillslope, and watershed scales that will inform policies and assist in the development of better BMPs. 

**Research needs.**

There is a need for reliable models at different scales. Proper models
and parameters have to be found to simulate behavior of pathogens such
as attachment; survival; and regrowth in soil, water, and air. At the
pedon scale, models are needed to evaluate the potential for pathogen
transport through soil to groundwater. Models of pathogen transport and
partitioning between runoff and infiltration need to be developed at the
hillslope scale to assess the potential for pathogen contamination of
surface water sources and the mitigation efficiency of various
management practices. Watershed-scale modeling needs to more precisely
identify and establish relationships between parameters of models and
environmental factors affecting pathogen transport. Model flexibility
needs to be achieved to incorporate specific fate and transport
characteristics of the various pathogen genera. Research on this topic
has three primary objectives at each of the three scales:

1.  1\. Identification of dominant processes and the development of
    appropriate models.

    2\. Development of appropriate data sets to refine and test the
    models.

    3\. Development of user-friendly tools for the efficient use of
    models in decision support and regulation development.

All ARS researchers conducting pathogen fate and transport studies will
contribute their data and expertise to achieve objectives 1 and 2. Many
ARS scientists also will be cooperating with scientists at other
agencies and universities. Objective 3 requires close cooperation with
users and a partnership with software developers.

To maximize the usability of proposed models, potential model users will
be involved at all stages of the model development process, including
model design, model evaluation, and model integration.

#  

***Review Team Rating:***

***Relevance: High***

***Impact: High***

***Review Team Assessment:***

*This is a Problem Area in which ARS has made and continues to make
outstanding contributions. The need to model transport through
vegetative filter strips was a new, potentially valuable effort. Adding
the microbial component to SWAT is an important contribution, as
previous versions have not dealt well with microbial transport. It is
also clear that some of the fundamental research from other problem
areas is informing the models, as factors such as regrowth, or the
influence of manure itself on transport, are being incorporated.
Likewise, the subroutine for E. coli release from manure is an important
contribution to any fate and transport model. To the extent that these
models develop decision-support tools, this research addresses the
research needs and outputs/products identified above. Research into
colloid transport and basic research on bacteria transport in
unsaturated porous media is of very high quality, but is far more basic
research. Most of these latter experiments were done under very
controlled, laboratory conditions, and the contrasting findings that
manure influences transport, argue for the need for more realistic
experimental evaluations. Likewise, worst-case scenarios (e.g.,
event-based transport) are not necessarily captured by this basic
research, nor by models for e.g., vegetated filter strips if significant
rainfall causes failure of filtration. Nevertheless data that were
developed in this research will contribute to development of more
sophisticated fate and transport modeling, and the research conducted
directly addresses the outputs/products and stated research needs.*

# 

# [Problem Area 3: Pharmaceutically Active Compounds (PACs)]{.underline} 

###### **Outputs/Products** 

###### 

-   Detection methods

-   Baseline information concerning the fate and dissemination of
    hormones, antibiotics, degradates, and antibiotic- resistant
    bacteria in manure and manure impacted environments.

**Research needs.**

To accurately determine the exposure risks associated with hormones,
antibiotics, degradation byproducts, and antibiotic-resistant bacteria
derived from animal wastes, the following research needs to be
conducted: (1) evaluation of current or development of new methods for
the detection of manure and biosolid borne hormones, antibiotics,
degradation byproducts and antibiotic resistant bacteria from
environmental samples; (2) determination of the presence, persistence,
and transport of these agents in manure, soil, water, and air; (3)
determination of the presence, development, survival, and transport of
antibiotic-resistant bacterial populations in manure, soil and water,
and air; (4) development of tools (e.g., computer models) to predict the
fate of hormones, antibiotics, and antibiotic-resistant bacterial
populations under different management practices and environmental
conditions. Concurrent research is needed to develop treatment
strategies and BMPs for manure and wastewater to minimize the occurrence
and environmental dissemination of PACs and antibiotic-resistant
bacteria.

#########  

This work also will stimulate the development of treatment and
management practices that reduce these contaminants in livestock
productions systems. In the long-term, this work will result in
protocols and guidelines for protection of the environment and human
health. Data collected during these studies are needed for those
conducting risk assessments (e.g., EPA, CDC) concerning the human and
animal health risks related to antibiotics and endocrine disrupting
chemicals associated with livestock manure management practices. The
development of tools and treatment strategies for PACs and
antibiotic-resistant bacteria will be advanced in collaboration with
other NP 206 Components, such as Atmospheric Emissions.

***Review Team Rating:***

***Relevance: High***

***Impact: High***

***Review Team Assessment:***

*Given that the stated research needs and outputs/products were to
develop fundamental information, ARS has forwarded the research in this
area. The researchers studied selected hormones, as well as antibiotics,
that would be expected to be present in several agricultural settings.
Evaluating hormones in poultry litter applied to the land at prescribed
agronomic rates (based on N) had practical applications and is highly
relevant. The impact was high because the information has already been
communicated to the producers. However, the review team noted that there
are a number of variables that might contribute to the levels of
hormones in runoff, so multiple facility evaluations would expand the
impact of this research. ARS research could take advantage of multiple
facilities across the country to accomplish this broader scope of
research.*

*This work was targeted towards practical applications that work in the
field. This problem area is producing the information that is needed
right now to decide what the potential issues are and what work needs to
be done. Technologies (nanofiltration, TMAL activator) were developed
with potential for use by others, and the influence of agricultural or
treatment practices (composting, constructed wetlands, anaerobic lagoon)
on hormones or antibiotics was addressed.*

[Problem Area 4: Holistic Treatment Technologies for Nutrients,
Pathogens and PACs]{.underline}

**Outputs/Products**

-   A database detailing survival and persistence of pathogens in
    different treatment systems including the effects of how climate and
    other variables effects survival and persistence.

-   Identification of critical pathogen and PAC control points of these
    treatment systems.

-   Models and decision support tools that incorporate critical pathogen
    and PAC control points.

-   Treatment system design modifications based on the database
    information.

**Research needs.**

Reduction of manure-borne contaminants needs to be investigated in both
currently used and newly developed treatment systems. This research
begins with a determination of the influence of various diets and
management systems on pathogen and PAC levels and transmissibility. The
survival and persistence of pathogens contained in various types of
animal waste products (manure, poultry litter, dairy and swine
effluents, etc.) as they pass through collection, storage, treatment and
application systems must be determined. This will require knowledge of
how different ecosystem variables (geographical, climatic, etc.) affect
survival and persistence of various pathogen/waste combinations.

A publicly available relational database similar to that of ComBase,
which estimates the behavior of different pathogenic bacteria in various
food environmental conditions, will be established. Predictive models
that can be queried will be made available on the web to influence
control point decisions made by producers and/or other agencies
regarding management systems for manure by-products.

***Review Team Rating:***

***Relevance: High***

***Impact: Medium***

***Review Team Assessment:***

*There was a significant gap between the work done and the original
outputs described in the Action Plan. This problem area is focused on
impacting many of the problems associated with manure management at
once. This need was raised in previous problem areas and is particularly
difficult because of the multi-disciplinary nature of the work. Work was
conducted on the actual application of tools and technology; however,
the stated goals seem much more long-term (or more comprehensive) than
the actual accomplishments. The demonstration that a multi-step aerobic
treatment system effectively eliminated Salmonella (and had other
benefits in the nutrients and emissions areas) is particularly
noteworthy and exemplifies the type of concerted, focused, holistic
research on practical solutions that ARS can contribute. These findings
need to be better/more widely communicated to increase the impact of
this work. Likewise, the research demonstrating that VTA can be used to
control pathogens is useful information, but there is no indication that
this information has been communicated to producers. Research into use
of phage to control Salmonella is an interesting approach, but
technology application would be several years down the road. In the
future, more research into other BMPs (e.g., riparian buffers) would be
useful. Likewise, in this Problem Area, different ARS locations have
researched individual pathogens in different scenarios, but there would
be greater impact if samples were analyzed for multiple pathogens to
provide more broadly applicable information about pathogens and manure
management.*

####### **Component IV: Byproducts** 

####### 

*[General Comments]{.underline}:*

*The research under this component strongly supports the mission of the
Manure and Byproduct Utilization National Program. The research into
applications of byproducts supports the goal of capturing the value of
manure and other byproducts, and the research into risk supports the
goal that byproducts only be used in a manner that does not degrade
environmental quality or threaten human and animal health. The outputs
of the research under this component will often be directly applicable
to decisions about the appropriateness of using byproducts in a variety
of applications. As the research under this component progresses, it
will be important to consider opportunities to communicate with state
regulators so the results can contribute to approval of use of specific
byproducts in specific applications.*

*Appropriately, the outputs of the research were directly applicable to
the needs of many of the stakeholders, not focused only on one or two
stakeholder groups. Because of the multiple stakeholders involved in the
use of municipal, industrial and agricultural byproducts, it will be
important for ARS researchers to find opportunities to coordinate with
stakeholders, including extension agents, state environmental agencies,
and USEPA researchers and regulators.*

*It is unclear whether there is a clear prioritization of byproducts or
organization of study efforts. While this was not a specific goal
described in the action plan, a clearer statement of priorities could
increase the impact of the research in all four problem areas.*

*In some cases the discussions and research presented on remediation
were not clearly related to the objectives of this component. More than
one study presented neither included agricultural byproducts in the
remediation techniques being research nor focused on the remediation of
land that would be used in agricultural or horticultural applications.
ARS researchers clearly have the expertise to contribute significantly
to research in the area of site remediation, so future action plans
could benefit from identifying remediation as its own component.
Alternatively, the scope of this component could be expanded to include
remediation.*

*While cost to the end-user was not generally quantified, the use of
cost-effectiveness as an over-arching criterion/desired impact was
beneficial in providing a context and scope for this component.
Estimation of cost savings and other benefits would have been useful in
describing the impacts of the research projects. Additionally,
quantified benefits (agricultural, environmental, or economic) are
essential for the adoption of byproduct utilization.*

[Problem Area 1: Phytoavailability and Bioavailability of Nutrients,
Trace Elements and Xenobiotics in Byproducts Considered for Beneficial
Use]{.underline}

######## **Outputs/Products** 

######## 

-   Analysis of nutrients, trace elements and xenobiotics in byproducts
    being considered for beneficial use.

-   Characterization of potential transfers to plants and livestock, and
    bioavailability of nutrients, trace elements and xenobiotics in
    byproducts.

-   Identification of management practices needed to allow beneficial
    use of byproducts while protecting the environment.

-   Assessment of byproducts as feed ingredients.

**Research needs.**

Research is needed to characterize the risk and benefits to soil
fertility, soil biology, plant production, food safety and the
environment when byproducts are used on land. Nutrients, trace elements,
or xenobiotics, in manure or byproducts may be a concern to generators,
users, and regulators until the fate and potential of these constituents
to cause adverse effects can be clarified. Alternatively, byproducts can
act as biocontrol agents or liming agents or overcome important physical
constraints in manufactured soils and media. Overall objectives include
(1) laboratory evaluation, field tests and demonstrations to obtain
information for support of state permits for wider beneficial use of
many byproducts; (2) characterization of nutrient, trace element or
xenobiotic bioavailability to plants, to grazing animals that would
ingest byproducts or amended soils, and to animals that would ingest the
crops produced on amended soils; (3) in the case of feeding byproducts
from the ethanol industry, better characterization of the feeding value,
identification of effective ways to utilize these byproducts as
livestock feeds without causing environmental concerns, identification
of better methods to assess the bioavailability of nutrients to
livestock, and identification of methods to improve the consistency and
feeding-value of these byproducts.

***Review Team Rating:***

***Relevance: Med***

***Impact: High***

***Review Team Assessment:***

*The data produced in the assessment of spent foundry sand is highly
relevant to this problem area, and the methodology used in that research
can be applied to other byproducts. The quality of research was also
very high. The breadth of the materials studied under this problem area
was somewhat narrow. While that is to be expected in this relatively new
area of research, the desired outputs and outcomes stated in the action
plan were not limited to any one or two byproducts.*

*The work directly addressed the outputs in the action plan regarding
xenobiotics and trace elements in byproducts. More research is needed to
address some of the questions and stated outputs/outcomes in this
problem area. Specifically, research into nutrients, particularly
bioavailability of nutrients, is still needed. Additionally, research
that could be used to quantify the economic and environmental benefits
of byproduct applications could increase the impact of this problem
area.*

***Comments on specific research:***

*The research into phytoavailability of cadmium is valuable for
decisions being made about the use of biosolids in various types of land
applications; however, the link to agricultural and horticultural
applications was unclear.*

*While the research on phytoextraction of cadmium was of high quality
and potentially high impact, it was not clear how it fit into the
objectives of the Byproduct Component. If there is the potential for
highly contaminated land to be reclaimed and used for crop/livestock
production, that could be a separate problem area or component. More
information is needed to determine what could be done with the
byproducts from the phytoremediation (i.e., the biomass containing
hundreds or thousands of parts per million of Cd). Additionally, a
clearer explanation of how this research supports the objectives in the
action plan would help in determining the relevance of this work in the
context of this problem area.*

[Problem Area 2: Protocols and Methodology Standards for Examination and
Approval of Byproducts for Beneficial Uses in Agriculture and
Horticulture]{.underline}

**Outputs/Products**

-   Generic test models or analyses.

-   Decision trees for state, city, or local agencies.

-   Guidelines on beneficial uses.

**Research needs.**

Many regulators are reluctant to approve byproducts for land
application, soil manufacturing and other agricultural and horticultural
uses because of a lack of knowledge of interactions with soil, nutrient
bioavailability, groundwater impacts, and impacts on other soil-related
functions and processes. The development of a process to examine and
approve byproducts based on sound science will simultaneously ensure
environmental protection, improve soil quality and function, and derive
economic benefits to both byproduct generators and the agricultural
community. Accurate and cost-effective methods of byproduct evaluation
must be established. The specific research goals are to (1) identify
agricultural, municipal, and industrial byproducts amenable to
beneficial use in agriculture and horticulture; (2) develop a generic
framework by which byproducts of different origin and constituents can
be evaluated; (3) identify analytical methods that can accurately
identify and quantify byproduct constituents using proper QA/QC; (4)
develop a Decision Tree to help stakeholders determine which evaluation
methodologies are appropriate for matching byproducts with intended
uses\--then develop a "branching" evaluation protocol that proposes
analyses that could ultimately be carried out in independent
laboratories and universities; (5) characterize a number of different
byproducts using the generic framework to demonstrate to stakeholders
that the proposed framework yields comparable and reproducible data; and
(6) develop model sampling protocols for byproducts, taking into account
differences in uniformity of generation.

***Review Team Rating:***

***Relevance: High***

***Impact: Med***

***Review Team Assessment:***

*The foundry sands risk assessment provides valuable information about
potential methodologies that can be used to evaluate byproducts for
beneficial use. It is unclear from the accomplishments report whether
ARS is collaborating with federal or state environmental agencies on
this assessment and/or the development of a standard protocol. Such
collaborations are taking place and will likely increase the impact of
this work.*

*While this work is highly relevant and has the potential for high
impact, the stated research needs and desired outputs/outcomes were not
specifically addressed. If the risk assessment that is projected to be
released in 2008 provides a detailed description of the methodology
used, it could serve as the basis for a protocol. Any such protocol will
be helpful for generators of byproducts, users of byproducts and state
regulators in making decisions about reuse. Additionally, other
byproducts beyond foundry sands could be assessed in order to validate
the methodology as an assessment protocol or decision tree for state,
city or local agencies.*

###### [Problem Area 3: Byproduct Utilization Technologies]{.underline} 

######## **Outputs/Products** 

######## 

-   New and improved systems to capture, concentrate, and reuse
    nutrients from manures and other organic byproducts.

-   Guidelines for using byproducts to stabilize or sequester nutrients
    in manures and soils.

-   Treatment methods for byproducts that yield biomass that can be used
    as a horticultural amendment.

-   Procedures to use manure, compost, and byproducts to remediate and
    improve soils and to formulate manufactured soils.

-   Knowledge of the effects of manure and byproducts on the ecology of
    fungi in soil and their use as biocontrol materials that promote
    plant health and product quality.

**Research needs.**

Technologically sound methods are needed for utilizing byproducts that
will be characterized as beneficial. This includes blending, composting,
and amending byproducts as well as developing land application and
management techniques that will improve soil quality, water quality, and
plant growth. Specific sub-areas of research include development of
application technologies, measurement of fate and transport of byproduct
components, measurement of treatment efficacy and controlling processes,
identification of beneficial properties, and cost-benefit evaluations.
The overall objective is to utilize agricultural, municipal, and
industrial byproducts in a cost-effective and environmentally sound
manner.

***Review Team Rating:***

***Relevance: High***

***Impact: High***

***Review Team Assessment:***

*The research in this problem area was highly relevant. The diversity of
information clearly illustrated the opportunities for utilization of
byproducts and the need for continued research in the areas covered by
this component of the Manure and Byproducts Utilization National
Program. A clear organization/prioritization of which byproducts should
be evaluated for potential beneficial use opportunities might have
increased the impact of the work. Quantification and discussion of the
economic aspects of byproduct utilization, especially cost savings for
byproduct users would be highly beneficial, and more research under this
problem area into potential utilization of agricultural byproducts in
non-agricultural applications could significantly benefit generators of
agricultural byproducts.*

*There was a clear link between the research and the stated outputs.
However, some work appears to pre-date the project cycle. One article,
the Pb remediation guidance, was not relevant to topic because no
byproducts were used in the remediation study.*

*The impact of this work would have been higher if there was some
acknowledgment of the implications of the uses studied. Nutrient
management and trace metal contamination are potential complicating
factors that may need to be mitigated in some cases in order for the
proposed uses to be viable. While the implications of the use of
byproducts was not the focus of this problem area, it is important to
identify any limitations to a use that might result from the need to
manage nutrients or contaminants and any areas in which potential
negative impacts need to be investigated. As fundamental research, the
projects are relevant and useful but cost evaluation and implication
evaluation need to be explored.*

***Comments on specific research:***

*The research into remediation of metal toxic soils and urban runoff is
highly relevant. While the overall volume of manure and byproducts that
can be used in remediation applications is small relative to the volumes
produced annually, the combined benefits of reusing a waste and
remediating a contaminated site have the potential for significant
impact. However, there was not sufficient research presented in the
Accomplishments Report to support the unqualified statement that the
byproduct mixtures "fully remediated metal toxic mine wastes and smelter
contaminated soils."*

*Research into organic byproducts as horticultural potting media
supports the desired output to use byproducts to formulate manufactured
soil. It is clear that the potential impacts are high. The
accomplishment report should acknowledge that there are implications of
use of wood residue.*

*The research on FGD gypsum demonstrated that there are many
agricultural benefits that can be derived from the use of this material.
It should be noted that FGD gypsum contains metals that are released in
coal combustion, and because of this some regulators are concerned about
approving its use in agricultural applications. States environmental
regulators have the authority to approve the use, so proving that there
is a benefit is only the first step. More holistic assessment of overall
effects is needed.*

[Problem Area 4: Energy from Byproducts]{.underline}

########  

######## **Outputs/Products** 

######## 

-   Specific cost-effective conversion strategies for by-products
    depending on source, location, and composition.

-   Identification of additional by-products, which may have
    applications as animal feeds and/or soil amendments.

**Research needs.**

The overall research objectives are (1) to identify agricultural
byproducts suitable for conversion to energy; and (2) to develop
specific, cost-effective environmentally acceptable technologies to make
the energy conversion and to use residues formed during energy
production. A number of research activities need to be performed to
accomplish these goals. The composition of byproduct feedstocks needs to
be determined so that there suitability for conversion to energy via
biological (e.g., fermentation, anaerobic digestion) and/or
physical-chemical methods (e.g., gasification, direct burning) can be
assessed, and the nature of residues formed during processing are
identified. Specific conversion technologies need to be developed that
are customized to individual feedstocks; additional co-products will
need to be identified and developed; and economic evaluations of the
overall processes conducted to determine the potential for commercial
development.

The research is largely being conducted under National Program 307,
Bioenergy and Energy Alternatives. The research program focuses on
developing alternate energy sources and increasing the use of
agricultural crops as feedstocks for biofuels. ARS researchers in NP-307
would be expected to contribute technologies for the conversion of
byproducts to energy as an element of their existing research projects.

***Review Team Rating:***

***Relevance: High***

***Impact: Indiscernible***

***Review Team Assessment:***

*The research into potential uses of byproducts from energy production
technologies is and will continue to be highly relevant. In order for
energy production efforts to be well-coordinated, research into the
energy value of byproducts should be part of the energy production
national program.*

*The impact of this work has the potential to be high. The stated output
"specific cost-effective conversion strategies," implied that some cost
evaluation would be performed. Such evaluations would have increased the
impact of the work in this problem area. The impact also could have been
improved by evaluating how farm management practices influence quality
of byproduct for re-use. More emphasis on nature and use of residues and
clear characterizations of energy potential is needed in order to meet
the objectives stated in the action plan.*

*Combustion of chicken litter to produce activated carbon has the
potential to be a viable use of this byproduct. The research into
thermochemical conversion technologies and into the use of residues from
ethanol production for feed were highly relevant.*