JBEI July 2020 Highlights

1. Life-cycle greenhouse gas emissions and
human health trade-offs of organic waste
management strategies
Background
• Organic waste poses a challenge in terms of the cost of disposal, which
can cost over $100/tonne in some regions, and fugitive emissions of
short-lived climate pollutants once they are placed in landfills
• Tradeoffs between different waste-to-energy, landfilling, and composting
strategies involve numerous complex emissions sources
Approach
• Develop a set of scenarios to compare strategies for converting organic
waste to energy
• Leverage newly-collected operational and emissions data from a
commercial-scale dry anaerobic digestion facility in San Jose, CA and a
composting facility in Gilroy, CA
• Build a complete life-cycle inventory model for greenhouse gas and key
air pollutant emissions
• Utilize two integrated assessment models to convert air pollutant
emissions into PM2.5-related human health damages
Outcomes and Impacts
• Converting organic waste to energy has greenhouse gas impacts similar
to composting, and considerably better than landfilling
• Emissions from composting raw organics or solid residuals left over after
energy generation are dominated by NH3 after adjusting for relative
impacts on human health
• Results suggest that nitrogen-rich wastes can post health risks if
composted in some regions of the U.S., and enclosed processes for
converting these wastes to bioenergy is preferable
Nordahl et al. (2020) Environ. Sci. Technol., doi: 10.1021/acs.est.0c00364
Life-Cycle Greenhouse Gas Emissions for all Scenarios
Life-cycle social costs of different organic waste
management options as calculated in two different
reduced-form public health cost tools (EASIUR and AP3)

2. Background
• Identification and characterization of key enzymes
associated with cell wall biosynthesis and
modification is fundamental to gain insights into
cell wall dynamics
• However, it is a challenge that activity assays of
glycosyltransferases are very low throughput and
acceptor substrates are generally not available.
Shao et al. (2020) Plant Method, doi.org/10.1186/s13007-020-00641-1
Approach
• We optimized and validated microscale
thermophoresis (MST) to achieve high throughput
screening for glycosyltransferase substrates
• This method was optimized to allow the
determination of substrate binding affinity without
purification of the target protein from the cell lysate
Outcomes and Impacts
• Proof of concept with pectin β-1,4-
galactosyltransferase validated the capability to
screen both nucleotide-sugar donor substrates and
acceptor substrates
• The application was expanded to members of
glycosyltransferase family GT61 in sorghum for
substrate screening, which will narrow down their in
vivo function and help to select candidates for
further studies and engineering
Microscale thermophoresis as a powerful tool for
screening glycosyltransferases involved in cell wall
biosynthesis
β-1,4-galactosyltransferase AtGALS1 validated the capability to screen both donor
substrates and acceptor substrates. Acceptor substrates can bind only after a
conformational change in the protein is induced by the presence of UDP.
The GT61 family is expanded in grasses and most members have no known
function. We are systematically testing the substrate specificity. The figure shows
an example of a protein binding UDP-Arabinofuranose (Kd = 1.9 µM) suggesting that
it is a xylan arabinofuranosyltransferase..
Workflow of substrate screening using Microscale Thermophoresis. Proteins are
expressed transiently in tobacco as YFP fusions and tested without purification.
Express in N. BenthamianaClone the gene with
YFP florescence tag
Extract Microsome Microscale
Thermophoresis

3. Background
• Agrobacterium fabrum ARqua1 is a hybrid of Agrobacterium fabrum C58C that is used by many plant researchers to
generate transgenic roots to assist in the study of desirable traits for bioenergy crops
Thompson et al. (2020) Microbiol Resour Announc, doi:10.1128/MRA.00506-20
Approach
• The ARqua1 strain was obtained from the laboratory of Maria Harrison at the Boyce Thompson Institute at Cornell
University
• Illumina library preparation and sequencing were performed by the Vincent J. Coates Genomics Sequencing Laboratory
Outcomes and Impacts
• The assembly resulted in 19 contigs of >2,000 bp (N50, 379,426 bp; L50, 4), constituting a genome with a total size of
5,680,458 bp, a GC content of 59.06%, and an average read coverage of 1,118X
• Contigs were annotated via the Prokaryotic Genome Annotation Pipeline (PGAP)
• This whole-genome sequencing project has been deposited in NCBI GenBank under the accession no.
JABCPX000000000, and the Illumina short-read data have been deposited in the SRA under the accession no.
SRX5372558
Draft genome sequence of
Agrobacterium fabrum ARqua1

4. Sorghum biomass production in the continental
United States and its potential impacts on soil
organic carbon and nitrous oxide emissions
Background
• National scale projections of bioenergy crop yields and
their environmental impacts are essential to identify
appropriate locations to place bioenergy crops and ensure
sustainable land use strategies
Approach
• We used the process-based Daily Century (DAYCENT)
model with site-specific environmental data to simulate
sorghum biomass yield, soil organic carbon (SOC) change,
and nitrous oxide emissions across cultivated lands in the
continental United States (US)
Gautam et al. (2020) GCB-Bioenergy, doi: 10.1111/gcbb.12736
Outcomes and Impacts
• Our results suggest 10.2 million ha of cultivated lands in the
Southern and Lower Midwestern US will produce >10 Mg ha-
1 yr-1 biomass sorghum with net carbon sequestration under
rainfed conditions
• Methodology developed in this study to upscale field scale
process model to national scale provides future opportunity
to explore other candidate bioenergy crops
• Our high resolution national-scale spatially explicit results are
critical inputs for robust life-cycle assessment of bioenergy
production systems and land- use-based climate change
mitigation strategies

5. Competition for iron limits microbial growth
among model rhizobial community microbes
Background
• Diverse microbial communities form on plant roots, but how
communities assemble remains unclear
• Many microbes have the capacity to modify their environment
by sequestering rare elements or secrete secondary
metabolites – is this a rare or common phenomenon?
• Do microbes compete with each other under nutrient-limiting
or nutrient rich conditions?
Eng et al. (2020) Frontiers in Microbiology, doi.org/10.3389/fmicb.2020.01742
Approach
• Characterized pairwise interactions between representative
members of a model microbial community under different
growth conditions
• Identified different potential interactions, such as colony formation
changes or growth inhibition
• Validated detected interactions related to growth inhibition
using a sensitized transposon mutant library generated in P putida
KT2440
Outcomes and Impacts
• Identified rare microbe-microbe interactions: out of thirty seven
(37) pairwise interactions, one microbe inhibited the growth of a
second microbe in three (3) cases – morphology changes were
more common
• Validated growth inhibition was through a secreted molecule that
did not require direct cell contact
• Exposure of the growth inhibitor to the sensitized transposon
library of P. putida identified iron-sequestration as a strong
candidate
• Supplementation of iron to the media prevented the onset of
microbial competition, validating our findings
Supported by
LBL-LDRD