Discovery and Translation of Arid-Land Microbiomes
A white paper to initiate a CALS/UA working group
Betsy Arnold, Associate Professor, SPLS
1. Rationale. Ensuring human health and sustainability in a rapidly changing world requires innovative
solutions that link fundamental research with novel applications. In the context of climate change, loss of soil
fertility, loss of arable land, decreasing biodiversity resources, and increased reliance on core crops by a
growing human population, the need is strong for new strategies to enhance crop plant resiliency,
productivity, and nutritional quality.
Breeding and plant biotechnology provide extremely important tools for plant enhancement, but do not take full
advantage of the immensely powerful and yet-understudied toolkit embodied by microbes, and the diverse
ways in which they interact with wild and domesticated plants. Recent advancements in microbial ecology,
genomics, crop science, bioinformatics, and computation indicate that characterizing and translating the
plant microbiome represents a powerful tool for rapid enhancement of crop plants.
Our organizing principle is that CALS has the expertise, infrastructure, and drive to make the UA a world
leader in fundamental and applied research on the microbiome of arid-land plants – and that in doing so, CALS
will contribute in globally innovative ways to resolve major challenges facing sustainability in Arizona, the
southwestern US, and worldwide.
2. Vision. One of the most profound insights of the past century is that no macroscopic organism exists in
nature in the absence of microbes. Numbering far beyond the subset that cause disease, the diverse
assemblage of microorganisms that occur within, around, and upon macroscopic organisms – that is, their
microbiome -- shapes all aspects of human health and sustainability. Microbiomes influence processes as
diverse as our development and digestion, the nutritive enhancement and release of our food, the uptake of
water by our crop plants, and the protection of diverse organisms against abiotic stress, aging, and disease.
Among the most accessible, important, and least-characterized microbiomes are those associated with
plants – the bacteria, fungi, archaea, protists, and viruses that occur in plant tissues, on plant surfaces, and
in soil. These diverse and often beneficial microbial communities represent genetic, biochemical, and
functional resources for crop improvement that are unmatched in terms of transformative potential.
Widespread evidence points to the importance of plant microbiomes in influencing plant productivity,
protecting plants against environmental stresses, and transferring phenotypic traits -- such as drought-, salt-,
or heat tolerance – rapidly and reliably from one host plant to another. Recent advances in microbial ecology
highlight the global uniqueness of Arizona’s plant-microbiome resources, and advances in informatics and
sequencing technologies now permit the rapid characterization and application of these resources in
innovative ways.
Here, we propose to establish a working group of CALS faculty with a shared interest in discovering and
translating arid-land plant microbiomes. We envisage our collaboration as having the potential to grow into a
Center that brings together microbiology, genomics, biotechnology, crop science, nutritional science,
bioengineering, plant ecology, bioinformatics, and cyberinfrastructure. The working group would be unique in
its attention to the microbiomes of wild and domesticated plants in arid, semi-arid, and marginal lands –
providing a unique and important toolbox for crop improvement in a rapidly changing world.
3. Objectives. From a basis as a working group to the potential emergence of a center of excellence, we will
catalyze existing research strengths in CALS to achieve four landmark aims:
(1) Characterize the diverse and understudied microbiome of native and human-used, arid-land
plants. Specifically, by synthesizing existing expertise in agricultural and wild settings, we will develop
a comprehensive, cross-cutting perspective on the structure and function of arid- and semi-arid-land
microbiomes. Focal research questions will include, but not be limited to: What microbial characteristics
are shared among drought-, salt-, and heat-adapted plants? What microbial symbionts enable growth of
wild relatives of crop plants in marginal lands? What genomic traits of plants facilitate microbial
enhancement? What is the relationship of microbiome taxonomy and function to yield and quality in
major crops for Arizona, the Southwest, and arid- and arid-transitioning lands worldwide?
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(2) Translate arid-land plant microbiomes for crop improvement in marginal, altered, and arid lands.
Through innovative development of biodiversity informatics, genetic resources, microbial collections,
and collaborations that leverage CALS infrastructure, we will test hypotheses regarding plant health and
sustainability based on predictions from microbiome surveys and genomic analyses.
(3) Link microbiome characteristics to nutritional aspects of food plants through novel collaborations
that will eventually interface across the majority of CALS units.
(4) Develop an infrastructure for intellectual and translational advancement of microbiome studies
on campus and beyond, with the long-term goal of fostering research innovation, discovery, translational technologies, education, extension, outreach, and the garnering of extramural funds.
4. Initial core research collaborators (CRC). In phase 1 (microbiome discovery and tool development), a
small group of highly collaborative and active researchers will work together on ‘proof of concept’ studies
using existing strengths and leveraging existing resources. The list is not exclusive of other core
collaborators, but we emphasize that the phase 1 team should be nimble, effective, and willing to work
rapidly toward our shared goal. We will work closely with Technology Transfer experts (e.g., Tod McCauley)
in phase 1 to clarify IP rights and opportunities/roadmaps for internal and external partnerships.
Dr. Betsy Arnold, Associate Professor, SPLS: fungal biodiversity, ecology
Dr. Dave Baltrus, Assistant Professor, SPLS: bacterial biodiversity, evolutionary biology
Dr. Rachel Gallery, Assistant Professor, SNRE: soil microbiome, microbial ecology
Dr. Bonnie Hurwitz, Assistant Professor, ABE: biodiversity informatics, iMicrobe
Dr. Eric Lyons, Assistant Professor, SPLS and iPlant: cyberinfrastructure, genomics
5. Potential collaborators: research, translation, application. Pending extramural funding and CALS
support, in phase 2 (implementation of predictive tools; microbiome application for crop improvement;
genomics) and phase 3 (nutritional enhancement and downstream partnerships) we anticipate expanding the
working group to include diverse research strengths from CALS and partner groups. Initially we propose inviting
collaboration by six additional CALS faculty whose expertise will enhance our research and translational
portfolio: Monica Schmidt (plant bioengineering for nutritional quality), Leslie Gunatilaka (natural products
chemistry), Mike Ottman (crop physiology), Jeff Fehmi (plant-soil ecology), Russ Monson (ecophysiology and
climate; potential NSF-STC leader), and Raina Maier (microbial ecology). In a phased process we then would
welcome diverse members of SPLS, SNRE, SWES, and related researchers from other units as research
partners or affiliates, including (but not limited to) Jean McClain (microbial ecology), Dennis Ray (crop science),
Mohammad Pessarakli and David Kopec (turfgrass management), Rod Wing (genomics; high-throughput
phenotyping), David Galbraith (technology implementation), Karen Schumaker (stress tolerance), Istvan Molnar
(natural products chemistry), Ursula Schuch (extension, horticulture), Barry Pryor (plant pathology), and Chieri
Kubota (controlled environment agriculture). We see connections with all of the core missions of CALS,
including extension, teaching, and research in many disciplines.
6. Funding opportunity roadmap. In addition to leveraging existing funding, including current support from
NSF, NIH, industry, CALS, and related sources, members of the working group’s CRC will strategically seek
support, both individually and together, from sources including the following (selected examples for 2014-15
shown here; * = led by CRC member).
UA Green Fund*
Tech Launch Arizona*
JGI/DOE*
NSF STC
NSF STC*
Human Frontiers*
NSF GoLife
US-Israel BARD/NIFA*
SIMBIO-U, microbial biodiversity and applications on campus, F14
Proof of concept: microbial symbionts for enzyme production, F14
Metagenome sequencing, arid land plants, F14; genome sequencing
Ecological genomics, F14
Fungal biodiversity (UC Berkeley, pending internal review), F14
Fungal-plant interactions, F14
Fungal biodiversity, S15
Arid land plant enhancement, F15
From fall 2015-on we will explore opportunities with industrial partners while growing toward federal and
private funding opportunities. Ultimately we will aim for successful funding applications, and where possible,
training grants, to NSF (microbial ecology, diversity, systematics), NIH (human microbiome responses to
food microbiomes; nutrition and allergen studies), USDA (crop microbiome, food safety, plant-pathogen
interactions), NASA (controlled environment manipulation of plant health via microbes) and DOE/JGI
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(genomics, metagenomics). Should the working group (WG) grow into a Center, it will provide ready access
to collaborators, shared vision, and an intellectual launching pad for novel research campus- and statewide.
Research
phase 3
Research
phase 2
Research
phase 1
Major aim
Education,
Working
group
outreach,
development
extension
7. Timeline.
Although we
intend the WG to have a
lasting impact, we anticipate
dynamic
changes
to
technology and
research
opportunities over coming
years. Therefore, we outline
only the first three years of
our vision. We anticipate
publication submission as
soon as spring 2015 by
participating labs, and funding
applications to begin as soon
as fall 2014 by WG members.
Specific aim
F14
Microbiome assessments (proof of concept)
Microbiome assessments (systematic, part 1)
Microbiome assessments (systematic, broad)
Establish roadmap for IP rights; engage tech transfer
Microbial/plant genome sequencing
Cyberinfrastructure pipeline/resources (part 1)
Integration of metadata, genomics, transcriptomics
Tool development for predictive translation
Plant enhancement (proof of concept)
Plant enhancement (systematic)
Assessment of nutrition outcomes (proof of concept)
Assessment of nutrition/enhancement interactions
Develop new funding opportunities
Sponsor seminar speakers
Participate in CALS RIC
Interface with cluster hires
Enhance CALS courses
Enhance CALS resources, collections
Engage citizen scientists, public, industry
Establish training opportunities at multiple levels
S15
F15
S16
F16
S17
8. Landmarks. Progress of
the WG will be assessed at
the conclusion of each halfyear interval. For F14, landmarks will include initiation of
the working group, microbiome assessments for the proof-of-concept stage, initiation of cyberinfrastructure
collaborations, submission of applications for funding, and contribution of strains and genetic resources to
CALS collections. For S15, our success will be reflected by submission of at least one manuscript for
publication; completion of the proof-of-concept for microbiome sampling and initial IP planning; initiation of
genome sequencing, pending support of F14 proposals; and initiation of plant enhancement studies at the
proof-of-concept stage. We anticipate sharing tools with the public through iPlant, participating in the CALS
RIC, expanding our CRC to include six additional collaborators, providing project overviews to CALS
instructors interested in describing our activities, and submitting additional proposals for extramural funding.
Thereafter, our major progress in each half-year increment will be reflected by activities as described above,
submission of publications and proposals, successful funding of research and outreach, establishment of
new partnerships with collaborators, increased enrollment in the working group’s/center’s activities, and
overall contributions to the major, emerging missions of CALS.
9. Request for initial support. The CRC has pledged to participate in proof-of-concept analyses needed to
isolate and sequence the bacterial and fungal microbiome of two wild, native species that flourish in marginal
lands and are related to crop plants of importance to Arizona. We will sample tissues/soil from related crop
plants simultaneously, with analysis pending extramural funding. The proposed work will generate a culture
library for plant/soil inoculation; create a novel Sanger- and Illumina sequence library; provide a much-needed
perspective on microbiome structure; beta-test existing cyberinfrastructure, provide the basis for predictive tool
development; enhance biodiversity collections; leverage existing funds; and train CALS students. We have
already negotiated a highly cost-effective quote from Argonne National Laboratories for Illumina sequencing.
We request the following to catalyze our vision: a calendar-year 0.5 FTE RA for a Ph.D. student
interested in biodiversity informatics, microbiome research, and translation of technology, who will work at
the interface of these five research groups, or a technician for the same period; and $15,000 in research
support, to be divided among the five core labs for material costs, sequencing, and/or undergrad support.
As one potential pathway to help meet CALS support ‘midway’, and as an alternative to requesting a
0.5 FTE RA per above, we have identified a potential Ph.D. student who has received an international,
four-year fellowship for graduate studies. Her fellowship will provide living expenses ($1200/ month) and
partially off-set tuition ($10,000/yr). If we proceed to work with her, we would request a partial tuition waiver
for three years and support for her insurance to cover the remainder of her expenses, and research
support per above for year 1. She is applying for admission to the PLS graduate program and has a fiveyear student visa. She could begin in January, but she is presently here and is available for training. We will
be happy to discuss details of this and all aspects of our proposed WG if this proposal is of interest to CALS
leadership.
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