1. Office of Biological and Environmental Research
Prospects for carbon-negative biomanufacturing
Background/Objective
• There is frequent confusion in the literature about what qualifies as a
carbon negative bioproduct
• Microbial production processes can replace many petrochemicals
Approach
This article quantifies the total carbon removal potential for bio-based
chemicals and differentiates between carbon removal and GHG mitigation.
Results
Polymers are by far the largest opportunity for stable carbon storage in
bioproducts (besides building materials). But carbon sequestration potential
would be modest (~3% of energy-related GHG emissions) if all polymers are
bio-based and landfilled at end-of-life.
Significance/Impacts
The downsides of perpetuating linear supply chains outweigh the modest
carbon removal potential. Novel bioproducts need to be designed for recycling.
Scown, C. D. (2022) Trends in Biotechnology. DOI: 10.1016/j.tibtech.2022.09.004

2. Office of Biological and Environmental Research
Cell wall ester modifications and volatile emission
signatures of plant response to abiotic stress
Background/Objective
• Plants emit volatile organic compounds (VOCs), including methanol
(MeOH) and acetic acid (AA), especially in response to stresses
such as drought.
• We hypothesized that MeOH/AA are derived from cell wall esters.
Approach
• We tested the metabolic connection between leaf free acetylation and
cell wall polysaccharide acetylation using a 13C2-acetate labeling
method in poplar.
• We also collected real time MeOH and AA leaf gas exchange data.
Results Temperature sensitive emissions of MeOH/AA were detected,
but drought led to suppression of MeOH and enhancement of AA
• Increased AA likely due to activation of aerobic fermentation.
Significance/Impacts
• The AA/MeOH emission ratio could be used as an atmospheric
signal to determine the health of plants at the ecosystem level
Jardine, KJ., et al. Plant, Cell & Env, 10.1111/pce.14464
Real-time branch emissions of VOCs together with transpiration (E, mmol m−2 s−1) and net
photosynthesis (Anet, µmol m−2 s−1) fluxes during a 10-day drought experiment. A branch
enclosure was installed on a potted poplar tree and water withheld for the 10-day duration.
Daily branch flux patterns of (a) Methanol (MeOH), Acetic Acid (AA), AA/MeOH
emission ratio, (b) Aerobic fermentation intermediates (acetaldehyde, ethanol, acetone) (c)
CO2 and H2O and the photosynthetic product isoprene. Shaded areas represent the nigh-
time where the grow light was switched off

3. Office of Biological and Environmental Research
Substrate-Dependent Cellulose Saccharification Efficiency and LPMO
Activity of Cellic CTec2 and a Cellulolytic Secretome from Thermoascus
aurantiacus and the Impact of H2O2-Producing Glucose Oxidase
Background/Objective
• Understanding and improving the efficiency of enzymatic saccharification of
lignocellulosic biomass will promote the use of this renewable material.
Significance/Impacts
• These results underpin the potential of the T. aurantiacus secretome for
hydrolysis of lignin-poor substrates
Ostby, H., et al. ACS Sustainable Chemistry and Engineering, doi.org/10.1021/acssuschemeng.2c03341
Approach
• We have studied how saccharification could be optimized, focusing on the
role of lytic polysaccharide monooxygenases (LPMOs).
Results
• Comparison of an LPMO-rich secretome from Thermoascus aurantiacus with
Cellic CTec2 showed that saccharification of sulfite-pulped spruce (lignin-poor)
at 60 °C with the secretome was as efficient as saccharification with Cellic
CTec2 at 50 °C (Figure 1).
• Reactions with steam-exploded birch highlighted a strong impact of the
feedstock on enzyme performance. In this case, the reaction with Cellic CTec2
at 50 °C was clearly most efficient.
Figure 1. Saccharification of lignin-poor sulfite-pulped spruce by T.
aurantiacus (T.a.) secretome and Cellic CTec2.

4. Office of Biological and Environmental Research
Background/Objective
• Cultivated microbiomes are a source of microbes and enzymes for
biomass deconstruction.
• These microbiomes provide a unique resource to guide the design of
synthetic microbial communities.
Approach
• To assess comparative microbiome performance, parallel microbiomes
were cultivated on sorghum (Figure 1).
Results
• Network reconstructions from metatranscriptomics demonstrated that the
microbiomes proceeded through enzyme-linked successive stages.
• Cellulose-degrading Actinobacteria differentiated the performance of these
microbiomes.
Significance/Impacts
• Subtle differences in community composition and strain variation may lead to
significant differences in performance.
Tom, L, et al. Microbiome, doi.org/10.1186/s40168-022-01377-x
Figure 1. Development of parallel microbiomes growing
on sorghum
Low-abundance populations distinguish microbiome
performance in plant cell wall deconstruction

5. Office of Biological and Environmental Research
JBEI Enabled Publications

6. Office of Biological and Environmental Research
Permeability-Engineered Compartmentalization Enables
In Vitro Reconstitution of Sustained Synthetic Biology
Systems
Background/Objective
• Biological compartments rely on dynamically controlled permeability for matter exchange and complex cellular
activities.
• The ability to engineer compartment permeability is crucial for in vitro systems.
Approach
We developed a facile strategy to build permeability-configurable compartments using microfluidics
Results
• A compartmentalized cell-free protein synthesis system
sustains multicycle protein production.
• The bacteria-enclosing compartments possess near-perfect
phage resistance and enhanced environmental fitness.
Significance/Impacts This method will enable green
bioproduction, environmental sensing, and bacteria-based
therapeutics
Li et al. (2022) Adv Sci (Weinh). doi: 10.1002/advs.202203652
www.advancedsciencenews.com www.advancedscience.com
Figure 1. Schematic of the permeability-engineered compartmentalization strategy. PeCS compartmentalizes open in vitro molecular and cell-based
systems in micrometer-sized, layered hydrogel-based compartments. The compartments own configurability in selective permeability, architecture, ma-
terials, and functionalization. The compartmentalized systems allow biological reactions and activities to execute in a sustained manner due to engi-
neered passive transport. For a reconstituted molecular system, the selective permeability of compartments can be tuned to achieve desired transport of
biomolecules such as protein and DNA while allowing constant input of reactants and energy, enabling sustained biosynthesis. Reconstituted cell-based
systems can protect the encapsulated cells from competitors and predators and support the cells’ growth and functioning, thereby enhancing the fitness
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7. Office of Biological and Environmental Research
Tracing Carbon Metabolism in Soil with
Stable Isotope Metabolomics
Background
• Carbon (C) metabolism in soil remains poorly described due to the
inherent difficulty of tracking microbial metabolites produced by complex
soil communities
Approach
• Examined community metabolism of nine common C sources in soil by
tracking the 13C enrichment dynamics of metabolites using SIP-
metabolomics.
Results
• 13C-metabolite profiles varied more by C source than by incubation time
• The variation corresponded with difference in the metabolically-active
microbial population composition
Significance
• Among the first studies of SIP-metabolomics in soil systems
• Demonstrates the fate of C in soils is influenced by differences in
metabolism of C sources supplied to soils
Wilhelm R.C., et al. Appl Environ Microbiol. doi: 10.1128/aem.00839-22