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DOE OSTI2020

Fabricated ecosystem workshop: bridging laboratory to field science. Workshop report.

Lawrence Berkeley National Laboratory (Berkeley Lab) scientists held a workshop at the DOE BER Genomic Sciences PI meeting on the use of Fabricated Ecosystems in Washington D.C. on February 25th, 2020. Ecosystem fabrication is an approach to creating controlled microbial, soil and plant ecologies within a laboratory setting that enable discovery and dissection of environmental variables, activities, and interactions. At Berkeley Lab, we are developing two systems which span spatial and temporal scales — the EcoFAB and the EcoPOD. The participants of the workshop discussed the potential applications and challenges of using fabricated ecosystems as tools to tackle BER-relevant scientific questions. Specifically, they identified (1) research challenges that would benefit from ready access to this infrastructure (2) identified and prioritized technical challenges that currently limit these systems and (3) discussed how to use them to bridge the gap between lab and field research. To ensure that the fabricated ecosystems , in particular the larger-scale EcoPODs, are of use to as much of the BER community as possible, the workshop participants made the following recommendations: 1. Produce publicly available datasets for a set of control variables. Use for benchmarking, and assessing reproducibility between systems. 2. Implement data standards. 3. Develop/leverage nano/micro sensors and in situ root imaging. 4. Encourage the development of interdisciplinary teams to develop EcoPOD experiments. 5. Develop fabricated ecosystems with size and complexity that sits between the EcoFAB and EcoPOD to accelerate use and access.

42 ENGINEERING↗

DOE OSTI2023

Genetic control of photoprotection and photosystem II operating efficiency in plants

Summary Photoprotection against excess light via nonphotochemical quenching (NPQ) is indispensable for plant survival. However, slow NPQ relaxation under low light conditions can decrease yield of field‐grown crops up to 40%. Using semi‐high‐throughput assay, we quantified the kinetics of NPQ and photosystem II operating efficiency (ΦPSII) in a replicated field trial of more than 700 maize ( Zea mays ) genotypes across 2 yr. Parametrized kinetics data were used to conduct genome‐wide association studies. For six candidate genes involved in NPQ and ΦPSII kinetics in maize the loss of function alleles of orthologous genes in Arabidopsis ( Arabidopsis thaliana ) were characterized: two thioredoxin genes, and genes encoding a transporter in the chloroplast envelope, an initiator of chloroplast movement, a putative regulator of cell elongation and stomatal patterning, and a protein involved in plant energy homeostasis. Since maize and Arabidopsis are distantly related, we propose that genes involved in photoprotection and PSII function are conserved across vascular plants. The genes and naturally occurring functional alleles identified here considerably expand the toolbox to achieving a sustainable increase in crop productivity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A Mesorhizobium japonicum quorum sensing circuit that involves three linked genes and an unusual acyl-homoserine lactone signal

ABSTRACT Members of the genus Mesorhizobium, which are core components of the rhizosphere and specific symbionts of legume plants, possess genes for acyl-homoserine lactone (AHL) quorum sensing (QS). Here we show Mesorhizobium japonicum MAFF 303099 (formerly M. loti ) synthesizes and responds to N -[(2 E , 4 E )-2,4-dodecadienoyl] homoserine lactone (2 E, 4 E- C 12:2 -HSL). We show that the 2 E, 4 E- C 12:2 -HSL QS circuit involves one of four luxR-luxI -type genes found in the sequenced genome of MAFF 303099. We refer to this circuit, which appears to be conserved among Mesorhizobium species, as R1-I1. We show that two other Mesorhizobium strains also produce 2 E, 4 E- C 12:2 -HSL. The 2 E, 4 E- C 12:2 -HSL is unique among known AHLs in its arrangement of two trans double bonds. The R1 response to 2 E, 4 E- C 12:2 -HSL is extremely selective in comparison with other LuxR homologs, and the trans double bonds appear critical for R1 signal recognition. Most well-studied LuxI-like proteins use S -adenosylmethionine and an acyl-acyl carrier protein as substrates for synthesis of AHLs. Others that form a subgroup of LuxI-type proteins use acyl-coenzyme A substrates rather than acyl-acyl carrier proteins. I1 clusters with the acyl-coenzyme A-type AHL synthases. We show that a gene linked to the I1 AHL synthase is involved in the production of the QS signal. The discovery of the unique I1 product enforces the view that further study of acyl-coenzyme A-dependent LuxI homologs will expand our knowledge of AHL diversity. The involvement of an additional enzyme in AHL generation leads us to consider this system a three-component QS circuit. IMPORTANCE We report a Mesorhizobium japonicum quorum sensing (QS) system involving a novel acyl-homoserine lactone (AHL) signal. This system is known to be involved in root nodule symbiosis with host plants. The chemistry of the newly described QS signal indicated that there may be a dedicated cellular enzyme involved in its synthesis in addition to the types known for production of other AHLs. Indeed, we report that an additional gene is required for synthesis of the unique signal, and we propose that this is a three-component QS circuit as opposed to the canonical two-component AHL QS circuits. The signaling system is exquisitely selective. The selectivity may be important when this species resides in the complex microbial communities around host plants and may make this system useful in various synthetic biology applications of QS circuits.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Intraspecific variability in plant and soil chemical properties in a common garden plantation of the energy crop Populus

Optimizing crops for synergistic soil carbon (C) sequestration can enhance CO 2 removal in food and bioenergy production systems. Yet, in bioenergy systems, we lack an understanding of how intraspecies variation in plant traits correlates with variation in soil biogeochemistry. This knowledge gap is exacerbated by both the heterogeneity and difficulty of measuring belowground traits. Here, we provide initial observations of C and nutrients in soil and root and stem tissues from a common garden field site of diverse, natural variant, Populus trichocarpa genotypes—established for aboveground biomass-to-biofuels research. Our goal was to explore the value of such field sites for evaluating genotype-specific effects on soil C, which ultimately informs the potential for optimizing bioenergy systems for both aboveground productivity and belowground C storage. To do this, we investigated variation in chemical traits at the scale of individual trees and genotypes and we explored correlations among stem, root, and soil samples. We observed substantial variation in soil chemical properties at the scale of individual trees and specific genotypes. While correlations among elements were observed both within and among sample types (soil, stem, root), above-belowground correlations were generally poor. We did not observe genotype-specific patterns in soil C in the top 10 cm, but we did observe genotype associations with soil acid-base chemistry (soil pH and base cations) and bulk density. Finally, a specific phenotype of interest (high vs low lignin) was unrelated to soil biogeochemistry. Our pilot study supports the usefulness of decade-old, genetically-variable, Populus bioenergy field test plots for understanding plant genotype effects on soil properties. Finally, this study contributes to the advancement of sampling methods and baseline data for Populus systems in the Pacific Northwest, USA. Further species- and region-specific efforts will enhance C predictability across scales in bioenergy systems and, ultimately, accelerate the identification of genotypes that optimize yield and carbon storage.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Data for Influence of Particle Size on NIR Spectroscopic Characterization of Sorghum Biomass for the Biofuel Industry

NIR spectroscopy is a rapid and accurate green technology for high-throughput biomass characterization, including sorghum ( Sorghum bicolor ), a promising energy crop for the biofuel industry. This study assessed the influence of particle size on NIR spectroscopic analysis (wavelength range: 867–2535 nm) of sorghum biomass composition. Grown under field conditions, a total of 113 types of genetically diverse sorghum accessions were dried, ground, and sieved (<250, 250–600, 600–850, and > 850 µm particle size) for developing partial least square regression (PLSR) prediction models for moisture, ash, extractive, glucan, xylan, acid-soluble lignin (ASL), acid-insoluble lignin (AIL), and total lignin (ASL + AIL). Overall, smaller particle sizes provided better model performance, while no single particle size provided the best performance for all the selected components. With only 9 selected bands and 4 latent variables (LVs), the best PLSR model was obtained for moisture with particle size of 600–850 µm with the square root of the coefficient of determination (R) of 0.85, the ratio of prediction to deviation (RPD) of 2.2, and the root mean square error (RMSE) of 0.46 % in external validation. Similar model performances were also obtained for ash, extractive, glucan, and xylan. This study showed that size reduction could effectively improve NIR spectroscopic analysis for lipid-producing sorghum biomass for the biofuel industry.

Biomass Analytics↗

DOE OSTI2024

Transcriptomic Analysis of the CAM Species Kalanchoë fedtschenkoi Under Low- and High-Temperature Regimes

Temperature stress is one of the major limiting environmental factors that negatively impact global crop yields. Kalanchoë fedtschenkoi is an obligate crassulacean acid metabolism (CAM) plant species, exhibiting much higher water-use efficiency and tolerance to drought and heat stresses than C 3 or C 4 plant species. Previous studies on gene expression responses to low- or high-temperature stress have been focused on C 3 and C 4 plants. There is a lack of information about the regulation of gene expression by low and high temperatures in CAM plants. To address this knowledge gap, we performed transcriptome sequencing (RNA-Seq) of leaf and root tissues of K. fedtschenkoi under cold (8 °C), normal (25 °C), and heat (37 °C) conditions at dawn (i.e., 2 h before the light period) and dusk (i.e., 2 h before the dark period). Our analysis revealed differentially expressed genes (DEGs) under cold or heat treatment in comparison to normal conditions in leaf or root tissue at each of the two time points. In particular, DEGs exhibiting either the same or opposite direction of expression change (either up-regulated or down-regulated) under cold and heat treatments were identified. In addition, we analyzed gene co-expression modules regulated by cold or heat treatment, and we performed in-depth analyses of expression regulation by temperature stresses for selected gene categories, including CAM-related genes, genes encoding heat shock factors and heat shock proteins, circadian rhythm genes, and stomatal movement genes. Our study highlights both the common and distinct molecular strategies employed by CAM and C 3 /C 4 plants in adapting to extreme temperatures, providing new insights into the molecular mechanisms underlying temperature stress responses in CAM species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

The Switchgrass Microbiome: A Review of Structure, Function, and Taxonomic Distribution

Switchgrass (Panicum virgatum L.) has been championed as a promising bioenergy crop due to its high productivity across a wide environmental range. The switchgrass microbiome—including bacteria, archaea, fungi, and other microbiota inhabiting soil and plant tissues—can influence plant function substantially. We conducted a review of the literature investigating switchgrass microbiome structure, key functional roles, and taxa isolated from field-grown plants. Although site conditions and plant compartment (i.e., location within shoots, roots, or root-influenced soil) appear to be the strongest drivers of switchgrass microbiome structure, the microbiome is also shaped by climate, season, and host genotype. Studies comparing across plant species show that the switchgrass microbiome is more similar to the microbiomes of other perennial plants than to the microbiomes of annual plants. Members of the switchgrass microbiome confer several benefits to their host. Most notably, mycorrhizal fungi can increase plant biomass many-fold, associative nitrogen-fixing bacteria can provide a substantial portion of the plant’s nitrogen demand, and fungal endophytes can improve plant tolerance to drought. Although the fungi and bacteria cultured from switchgrass represent only a portion of the microbiome, these serve as a valuable resource for researchers interested in investigating functional outcomes of the switchgrass microbiome. We highlight areas where additional research is necessary for a more comprehensive understanding of switchgrass microbiome structure, function, and potential to enhance sustainable bioenergy production. Key gaps include the role of understudied organisms (e.g., viruses, microeukaryotes, and nonmycorrhizal fungi), multitrophic relationships, mechanisms underpinning switchgrass–microbiome interactions, and field-scale validation of experimental findings.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Genetics of Flooding Tolerance in an F 2 Miscanthus sacchariflorus ssp. lutarioriparius × M. sinensis Population

Miscanthus is a warm-season, perennial grass cultivated as a feedstock for bioenergy and bioproducts. M. sacchariflorus ssp. lutarioriparius has high yield potential and is well-adapted to seasonal flooding, but little is known about the genetics of this adaptation. We conducted a quantitative trait locus (QTL) analysis on a population of 332 diploid Miscanthus ×giganteus (Mxg) F2s derived from an initial cross between diploid M. sacchariflorus ssp. lutarioriparius ‘PF30022’ and diploid M. sinensis ‘PMS-014’, followed by intermating 50 F 1 s. Using tanks in a greenhouse to assess the effects of partial submergence on actively growing plants, we compared an aerobic soil control to a 6-week flood treatment. The study's primary objectives were to (1) identify QTL for flooding tolerance in Miscanthus , (2) identify candidate genes and (3) compare ethylene response factors in Miscanthus with those in rice and Arabidopsis , sorghum and maize for binding site sequence homology and synteny, especially those associated with flooding tolerance. In total, 10 QTL and 66 candidate genes for partial submergence tolerance were identified (including many for ethylene signalling), a first report for Miscanthus . Notably, none of the Miscanthus candidates were orthologs of rice Sub1A, SK1 or SK2 , yet the ‘PF30022’ parent exhibited a snorkeling phenotype, indicating convergent evolution. This study will facilitate breeding of climate-resiliant Mxg.

abiotic stress tolerance↗

DOE OSTI2024

Impacts of Legacy and Contemporary Nitrogen Inputs on N 2 O and CO 2 Emissions in Miscanthus and Maize Cultivated Soils

ABSTRACT Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteus (M×g) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N 2 O) and carbon dioxide (CO 2 ) emissions, as well as key N cycling genes in soils where M×g and maize were grown. A 150‐day soil incubation experiment was conducted using soils from a long‐term M×g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha −1 year −1 ) and a contemporary amendment (60 mg N kg −1 ) with negative control (0 mg N kg −1 ). We observed significant increases in cumulative N 2 O emissions in Mxg soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amo A gene abundance, which plays a significant role in nitrification in nutrient‐rich soils, also increased with higher legacy fertilization rates in M×g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N 2 O emissions, but cumulative CO 2 emissions and amo A gene abundance significantly increased. The abundances of nor B genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N 2 O emissions, particularly for perennial bioenergy crops.

09 BIOMASS FUELS↗

DOE OSTI2026

Data for Impacts of Legacy and Contemporary Nitrogen Inputs on N2O and CO2 Emissions in Miscanthus and Maize Cultivated Soils

Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteu s ( M × g ) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N2O) and carbon dioxide (CO2) emissions, as well as key N cycling genes in soils where M × g and maize were grown. A 150-day soil incubation experiment was conducted using soils from a long-term M × g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha−1 year−1) and a contemporary amendment (60 mg N kg−1) with negative control (0 mg N kg−1). We observed significant increases in cumulative N2O emissions in M × g soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amoA gene abundance, which plays a significant role in nitrification in nutrient-rich soils, also increased with higher legacy fertilization rates in M × g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N2O emissions, but cumulative CO2 emissions and amoA gene abundance significantly increased. The abundances of norB genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N2O emissions, particularly for perennial bioenergy crops.

Carbon↗