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At least 289 records · Page 16

Contrasting effects of bioenergy crops on biodiversity

Agriculture is driving biodiversity loss, and future bioenergy cropping systems have the potential to ameliorate or exacerbate these effects. Using a long-term experimental array of 10 bioenergy cropping systems, we quantified diversity of plants, invertebrates, vertebrates, and microbes in each crop. For many taxonomic groups, alternative annual cropping systems provided no biodiversity benefits when compared to corn (the business-as-usual bioenergy crop in the United States), and simple perennial grass–based systems provided only modest gains. In contrast, for most animal groups, richness in plant-diverse perennial systems was much higher than in annual crops or simple perennial systems. Microbial richness patterns were more eclectic, although some groups responded positively to plant diversity. Future agricultural landscapes incorporating plant-diverse perennial bioenergy cropping systems could be of high conservation value. However, increased use of annual crops will continue to have negative effects, and simple perennial grass systems may provide little improvement over annual crops.

09 BIOMASS FUELS↗

A rapid thioacidolysis method for biomass lignin composition and tricin analysis

Abstract Background Biomass composition varies from plant to plant and greatly affects biomass utilization. Lignin is a heterogeneous phenolic polymer derived mainly from p -coumaryl, coniferyl, and sinapyl alcohols and makes up to 10–25% of lignocellulosic biomass. Recently, tricin, an O -methylated flavone, was identified as a lignin monomer in many grass species. Tricin may function as a nucleation site for lignification and is advocated as a novel target for lignin engineering to reduce lignin content and improve biomass digestibility in grasses. Thioacidolysis is an analytical method that can be adapted to analyze both lignin monomeric composition and tricin content in the lignin polymer. However, the original thioacidolysis procedure is complex, laborious, and time consuming, making it difficult to be adopted for large-scale screening in biomass research. In this study, a modified, rapid higher throughput thioacidolysis method was developed. Results In combination with gas chromatography–mass spectrometry (GC–MS) and liquid chromatography–mass spectrometry (LC–MS), the modified thioacidolysis method can be used to simultaneously characterize the lignin composition and tricin content using 2–5 mg of dry samples. The modified method eliminates the solvent extraction and drastically improves the throughput; 80 samples can be processed in one day per person. Our results indicate that there is no significant difference in the determination of lignin S/G ratio and tricin content between the original and modified methods. Conclusions A modified thioacidolysis protocol was established. The results demonstrate that the modified method can be used for rapid, high-throughput, and reliable lignin composition and tricin content analyses for screening transgenic plants for cell wall modifications or in large-scale genome-wide association studies (GWAS).

09 BIOMASS FUELS↗

Targeting hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase for lignin modification in Brachypodium distachyon

Abstract Background Hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT) is a central enzyme of the so-called “esters” pathway to monolignols. As originally envisioned, HCT functions twice in this pathway, to form coumaroyl shikimate and then, in the “reverse” direction, to convert caffeoyl shikimate to caffeoyl CoA. The discovery of a caffeoyl shikimate esterase (CSE) that forms caffeic acid directly from caffeoyl shikimate calls into question the need for the reverse HCT reaction in lignin biosynthesis. Loss of function of HCT gives severe growth phenotypes in several dicot plants, but less so in some monocots, questioning whether this enzyme, and therefore the shikimate shunt, plays the same role in both monocots and dicots. The model grass Brachypodium distachyon has two HCT genes, but lacks a classical CSE gene. This study was therefore conducted to evaluate the utility of HCT as a target for lignin modification in a species with an “incomplete” shikimate shunt. Results The kinetic properties of recombinant B. distachyon HCTs were compared with those from Arabidopsis thaliana , Medicago truncatula , and Panicum virgatum (switchgrass) for both the forward and reverse reactions. Along with two M. truncatula HCTs, B. distachyon HCT2 had the least kinetically unfavorable reverse HCT reaction, and this enzyme is induced when HCT1 is down-regulated. Down regulation of B. distachyon HCT1, or co-down-regulation of HCT1 and HCT2, by RNA interference led to reduced lignin levels, with only modest changes in lignin composition and molecular weight. Conclusions Down-regulation of HCT1, or co-down-regulation of both HCT genes, in B. distachyon results in less extensive changes in lignin content/composition and cell wall structure than observed following HCT down-regulation in dicots, with little negative impact on biomass yield. Nevertheless, HCT down-regulation leads to significant improvements in biomass saccharification efficiency, making this gene a preferred target for biotechnological improvement of grasses for bioprocessing.

09 BIOMASS FUELS↗

Chapter 24: The Compound Middle Lamella as a Target for Improved Deconstruction of Woody Biomass

The compound middle lamella (CML) of woody angiosperm species, such as poplar (Populus spp.), birch (Betula spp.), and alder (Alnus spp.), and gymnosperm species, such as pine (Pinus spp.), Douglas fir (Pseudotsuga menziesii), and spruce (Picea spp.), is an amalgam of lignin, hemicellulosic xylans, and pectic polysaccharides that is the major site of cell-cell adhesion of fibre cells and tracheary elements. In grass species, such as sorghum (Sorghum bicolor), switchgrass (Panicum virgatum), and sugarcane (Saccharum officinarum), a phenylpropanoid network deposited in xylan-rich primary walls extends into the lignified CML. This review traces the early history of discovery of the molecular components of the CML and presents the current state of knowledge on the development of the CML in bioenergy-relevant woody species and grasses. This chapter emphasises the role of the CML in the recalcitrance of biomass to deconstruction by mechanical and enzymatic means for conversion to biofuels and valuable bioproducts. The use of genetic engineering to alter CML composition and structure to facilitate biomass deconstruction and to redesign wood to generate materials with novel properties is discussed.

BIOMASS FUELS↗

Plant-Nitrifier Interactions in Topsoil and Subsoil

Plants can influence soil microbes through resource acquisition and interference competition, with consequences for ecosystem function such as nitrification. However, how plants alter soil conditions to influence nitrifiers and nitrification rates remains poorly understood, especially in the subsoil. Here, coupling the 15N isotopic pool dilution technique, high throughput sequencing and in situ soil O2 monitoring, we investigated how a deep-rooted perennial grass, miscanthus, versus an adjacent shallow-rooted turfgrass reference shapes nitrifier assembly and function along 1 m soil profiles. In topsoil, the suppression of ammonia (NH3) oxidizing archaea (AOA) and gross nitrification rates in miscanthus relative to the reference likely resulted from nitrifiers being outcompeted by plant roots and heterotrophic bacteria for ammonium (NH4+). The stronger tripartite competition under miscanthus may have been caused in part by the lower soil organic matter (SOM) content, which supported lower gross nitrogen (N) mineralization, the major soil process that produces NH4+. In contrast, below 10 cm soil depth, significantly greater gross nitrification rates were observed in miscanthus compared to the reference. This was likely driven by the significantly lower oxygen (O2) in miscanthus than reference subsoil, which selected against aerobic heterotrophic bacteria but in favor of AOA. Overall, we found that plants can regulate AOA community structure and function through different mechanisms in topsoil and subsoil, with suppression of nitrification in topsoil and enhancement of nitrification in subsoil.

Field Data↗

Data for Microbial-Explicit Processes and Refined Perennial Plant Traits Improve Modeled Ecosystem Carbon Dynamics

Globally, soils hold approximately half of ecosystem carbon and can serve as a source or sink depending on climate, vegetation, management, and disturbance regimes. Understanding how soil carbon dynamics are influenced by these factors is essential to evaluate proposed natural climate solutions and policy regarding net ecosystem carbon balance. Soil microbes play a key role in both carbon fluxes and stabilization. However, biogeochemical models often do not specifically address microbial-explicit processes. Here, we incorporated microbial-explicit processes into the DayCent biogeochemical model to better represent large perennial grasses and mechanisms of soil carbon formation and stabilization. We also take advantage of recent model improvements to better represent perennial grass structural complexity and life-history traits. Specifically, this study focuses on: 1) a plant sub-model that represents perennial phenology and more refined plant chemistry with downstream implications for soil organic matter (SOM) cycling though litter inputs, 2) live and dead soil microbe pools that influence routing of carbon to physically protected and unprotected pools, 3) Michaelis-Menten kinetics rather than first-order kinetics in the soil decomposition calculations, and 4) feedbacks between decomposition and live microbial pools. We evaluated the performance of the plant sub-model and two SOM cycling sub-models, Michaelis-Menten (MM) and first-order (FO), using observations of net ecosystem production, ecosystem respiration, soil respiration, microbial biomass, and soil carbon from long-term bioenergy research plots in the mid-western United States. The MM sub-model represented seasonal dynamics of soil carbon fluxes better than the FO sub-model which consistently overestimated winter soil respiration. While both SOM sub-models were similarly calibrated to total, physically protected, and physically unprotected soil carbon measurements, the models differed in future soil carbon response to disturbance and climate, most notably in the protected pools. Adding microbial-explicit mechanisms of soil processes to ecosystem models will improve model predictions of ecosystem carbon balances but more data and research are necessary to validate disturbance and climate change responses and soil pool allocation.

Field Data↗

Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon

Long terminal repeat retrotransposons (LTR-RTs) are powerful mutagens regarded as a major source of genetic novelty and important drivers of evolution. Yet, the uncontrolled and potentially selfish proliferation of LTR-RTs can lead to deleterious mutations and genome instability, with large fitness costs for their host. While population genomics data suggest that an ongoing LTR-RT mobility is common in many species, the understanding of their dual role in evolution is limited. Here, we harness the genetic diversity of 320 sequenced natural accessions of the Mediterranean grass Brachypodium distachyon to characterize how genetic and environmental factors influence plant LTR-RT dynamics in the wild. When combining a coverage-based approach to estimate global LTR-RT copy number variations with mobilome-sequencing of nine accessions exposed to eight different stresses, we find little evidence for a major role of environmental factors in LTR-RT accumulations in B. distachyon natural accessions. Instead, we show that loss of RNA polymerase IV (Pol IV), which mediates RNA-directed DNA methylation in plants, results in high transcriptional and transpositional activities of RLC_BdisC024 (HOPPLA) LTR-RT family elements, and that these effects are not stress-specific. This work supports findings indicating an ongoing mobility in B. distachyon and reveals that host RNA-directed DNA methylation rather than environmental factors controls their mobility in this wild grass model.

59 BASIC BIOLOGICAL SCIENCES↗

Deciphering the microbial and molecular responses of geographically diverse Setaria accessions grown in a nutrient-poor soil

The microbial and molecular characterization of the ectorhizosphere is an important step towards developing a more complete understanding of how the cultivation of biofuel crops can be undertaken in nutrient poor environments. The ectorhizosphere of Setaria is of particular interest because the plant component of this plant-microbe system is an important agricultural grain crop and a model for biofuel grasses. Importantly, Setaria lends itself to high throughput molecular studies. As such, we have identified important intra- and interspecific microbial and molecular differences in the ectorhizospheres of three geographically distant Setaria italica accessions and their wild ancestor S . viridis . All were grown in a nutrient-poor soil with and without nutrient addition. To assess the contrasting impact of nutrient deficiency observed for two S . italica accessions, we quantitatively evaluated differences in soil organic matter, microbial community, and metabolite profiles. Together, these measurements suggest that rhizosphere priming differs with Setaria accession, which comes from alterations in microbial community abundances, specifically Actinobacteria and Proteobacteria populations. When globally comparing the metabolomic response of Setaria to nutrient addition, plants produced distinctly different metabolic profiles in the leaves and roots. With nutrient addition, increases of nitrogen containing metabolites were significantly higher in plant leaves and roots along with significant increases in tyrosine derived alkaloids, serotonin, and synephrine. Glycerol was also found to be significantly increased in the leaves as well as the ectorhizosphere. These differences provide insight into how C 4 grasses adapt to changing nutrient availability in soils or with contrasting fertilization schemas. Gained knowledge could then be utilized in plant enhancement and bioengineering efforts to produce plants with superior traits when grown in nutrient poor soils.

59 BASIC BIOLOGICAL SCIENCES↗

Integrating Characteristic Arctic Vegetation in a Land Surface Model Improves Representation of Carbon Dynamics Across a Tundra Landscape: Modeling Archive

This modeling archive is in support of the Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) publication "Integrating Characteristic Arctic Vegetation in a Land Surface Model Improves Representation of Carbon Dynamics Across a Tundra Landscape", by Murphy et al. (2025). This archive contains model input files and outputs from landscape-scale simulations conducted using ELM, the land model component of the Department of Energy’s Energy Exascale Earth System Model (E3SM), at the Council NGEE Arctic field site (Council Road mile marker 71) on Alaska’s Seward Peninsula. Input data and model output from two sets of ELM simulations are provided. The first set of simulations were conducted with the two default ELM Arctic plant functional types (PFTs; broadleaf deciduous boreal shrub and a C3 grass) and the second set of simulations were conducted with a set of nine Arctic-specific PFTs including nonvascular mosses and lichens, graminoids, forbs, evergreen dwarf shrubs, three height classes of deciduous shrubs (dwarf, low, and low to tall), and deciduous alder shrubs (Sulman et al., 2021). Parameter names and major parameter changes in the Arctic-specific PFT configuration are described in Sulman et al. (2021) and archived in the Sulman et al. (2021) dataset (see below). Simulations were spatially explicit, covering an approximately 6.4X3.3 km domain at the Council site with a spatial resolution of 100 m for a total of 2,112 simulated grid cells under each ELM PFT configuration. The modeling archive contains meteorological forcing (seven *.nc files and one *.txt file), a domain definition file (one *.nc files), land surface configuration files (two *.nc files), parameter files (two *.nc files), annual ELM output files spanning 1980-2014 (68 *.nc files), and a User’s Guide (*pdf file). Additional information on the provided files is in the “Modeling Archive Contents” section of the User’s Guide. Model outputs are aggregated to the column scale (i.e. PFT-specific outputs are not provided here).

Murphy, Bailey [ORNL] (ORCID:0000000203995221)↗

AmeriFlux US-Jo2 Jornada Experimental Range Mixed Shrubland

This is the AmeriFlux version of the carbon flux data for the site US-Jo2 Jornada Experimental Range Mixed Shrubland. Site Description - The study area is in a mixed shrub-dominated portion of the San Andres Mountain piedmont, along the southeastern boundary of the Jornada Experimental Range (JER) in southern New Mexico, USA. The JER was established in 1912 as a response of scientis and landowner to the shrub enchroachment and loss of grasses due to extended grazing during the late 1800s, fire and climate change. JER has been a NSF LTER site since 1981.The study site is a small watershed (4.67 ha) in an alluvial slope or bajada, with three major areas (north-, south- and west-facing hillslopes) with low to moderate slopes (∼0–6°) with a mean slope of 2.6°, while the channel banks and propagating channel heads have higher slopes (∼15–25°). The site is charactetized by a high bare soil coverage (∼66%), ∼28% of mixed shrubs coverage and a low coverage of grass (∼4%) and weeds (∼2%).

Vivoni, Enrique R.↗

AmeriFlux US-KM1 KBS Marshall Farms Corn

This is the AmeriFlux version of the carbon flux data for the site US-KM1 KBS Marshall Farms Corn. Site Description - The site was planted to smooth brome grass under the USDA’s Conservation Reserve Program (CRP) grassland since 1987 before conversion. The grass was cut every three years but left in place. The site was converted to no-till soybean in 2009 and to no-till continuous corn from 2010 onwards.

Robertson, G. Philip↗

AmeriFlux US-KM2 KBS Marshall Farms Prairie

This is the AmeriFlux version of the carbon flux data for the site US-KM2 KBS Marshall Farms Prairie. Site Description - The site was planted to smooth brome grass under the USDA’s Conservation Reserve Program (CRP) grassland since 1987 before conversion. The grass was cut every three years but left in place. The site was converted to no-till soybean in 2009 and to perennial native prairie from 2010 onwards. Starting from 2011, the prairie is harvested every autumn/fall.

Robertson, G. Philip↗

AmeriFlux US-KM3 KBS Marshall Farms Switchgrass

This is the AmeriFlux version of the carbon flux data for the site US-KM3 KBS Marshall Farms Switchgrass. Site Description - The site was planted to smooth brome grass under the USDA’s Conservation Reserve Program (CRP) grassland since 1987 before conversion. The grass was cut every three years but left in place. The site was converted to no-till soybean in 2009 and to perennial switchgrass from 2010 onwards. Starting from 2011, the switchgrass is harvested every autumn/fall.

Robertson, G. Philip↗

AmeriFlux US-Jo1 Jornada Experimental Range Bajada Site

This is the AmeriFlux version of the carbon flux data for the site US-Jo1 Jornada Experimental Range Bajada Site. Site Description - The Jornada Basin Experimental Range (JER) covers 783 km2 in the La Jornada del Muerto Plain of the northern Chihuahuan Desert and is located 20km of Las Cruces, NM. Extensive livestock grazing at the JER and througout the US Southwest was coincident with large-scale grassland deterioration and transition to shrubland begining in the 1800s. The JER was established n 1912 to investigate these rangeland changes and has since become a central location for understanding dryland ecology. This flux tower monitors CO2 and H2O dynamics in a representative shrubland on the piedmont slope (bajada) of the San Andreas mountains. The dominant shrubs are evergreen Larrea tridentata (Creosote) and winter-deciduous Prosopis glandulosa (Honey Mesquite). Other cover types include Flourensia cernua (tarbush) and patchy occurences of the grasses Muhlenbergia porteri (Bush Muhly) and Dasyochloa pulchella (Fluff Grass). The site is occasionally visited by stray domestic cattle, free-ranging introduced Oryx, and other native herbivores (Jack Rabbits, Desert Pronghorn). Soils at the site are Ustic Calciargids and parent material consists of limestone, other sedimentary rock, and some igneous rock. Virtual Site Visit: https://youtu.be/v1uJCKuicqs​

Tweedie, Craig↗

AmeriFlux FLUXNET-1F US-Jo2 Jornada Experimental Range Mixed Shrubland

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-Jo2 Jornada Experimental Range Mixed Shrubland. This is the FLUXNET version of the carbon flux data for the site US-Jo2 Jornada Experimental Range Mixed Shrubland produced by applying the standard ONEFlux (1F) software. Site Description - The study area is in a mixed shrub-dominated portion of the San Andres Mountain piedmont, along the southeastern boundary of the Jornada Experimental Range (JER) in southern New Mexico, USA. The JER was established in 1912 as a response of scientis and landowner to the shrub enchroachment and loss of grasses due to extended grazing during the late 1800s, fire and climate change. JER has been a NSF LTER site since 1981.The study site is a small watershed (4.67 ha) in an alluvial slope or bajada, with three major areas (north-, south- and west-facing hillslopes) with low to moderate slopes (∼0–6°) with a mean slope of 2.6°, while the channel banks and propagating channel heads have higher slopes (∼15–25°). The site is charactetized by a high bare soil coverage (∼66%), ∼28% of mixed shrubs coverage and a low coverage of grass (∼4%) and weeds (∼2%).

Vivoni, Enrique R.↗

AmeriFlux FLUXNET-1F US-Jo1 Jornada Experimental Range Bajada Site

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-Jo1 Jornada Experimental Range Bajada Site. This is the FLUXNET version of the carbon flux data for the site US-Jo1 Jornada Experimental Range Bajada Site produced by applying the standard ONEFlux (1F) software. Site Description - The Jornada Basin Experimental Range (JER) covers 783 km2 in the La Jornada del Muerto Plain of the northern Chihuahuan Desert and is located 20km of Las Cruces, NM. Extensive livestock grazing at the JER and througout the US Southwest was coincident with large-scale grassland deterioration and transition to shrubland begining in the 1800s. The JER was established n 1912 to investigate these rangeland changes and has since become a central location for understanding dryland ecology. This flux tower monitors CO2 and H2O dynamics in a representative shrubland on the piedmont slope (bajada) of the San Andreas mountains. The dominant shrubs are evergreen Larrea tridentata (Creosote) and winter-deciduous Prosopis glandulosa (Honey Mesquite). Other cover types include Flourensia cernua (tarbush) and patchy occurences of the grasses Muhlenbergia porteri (Bush Muhly) and Dasyochloa pulchella (Fluff Grass). The site is occasionally visited by stray domestic cattle, free-ranging introduced Oryx, and other native herbivores (Jack Rabbits, Desert Pronghorn). Soils at the site are Ustic Calciargids and parent material consists of limestone, other sedimentary rock, and some igneous rock. Virtual Site Visit: https://youtu.be/v1uJCKuicqs​

Tweedie, Craig↗

AmeriFlux FLUXNET-1F US-Var Vaira Ranch- Ione

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-Var Vaira Ranch- Ione. This is the FLUXNET version of the carbon flux data for the site US-Var Vaira Ranch- Ione produced by applying the standard ONEFlux (1F) software. Site Description - Located in the lower foothills of the Sierra Nevada Mountains on privately owned land, the Vaira Ranch site is classified as a grassland dominated by C3 annual grasses. Managed by local rancher, Fran Vaira, brush has been periodically removed for cattle grazing. Species include a variety of grasses and herbs, including purple false brome, smooth cat's ear, and rose clover. Growing season is confined to the wet season only, typically from October to early May.

Ma, Siyan↗

AmeriFlux FLUXNET-1F US-Ton Tonzi Ranch

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-Ton Tonzi Ranch. This is the FLUXNET version of the carbon flux data for the site US-Ton Tonzi Ranch produced by applying the standard ONEFlux (1F) software. Site Description - The Tonzi Ranch is located on the lower foothills of the Sierra Nevada Mountains. The site is classified as an oak savanna woodland (Davis et al, 2016) and is situated on privately owned land. This site is representative of the oak savanna ecosystem that rings the Great Central Valley of California and inhabits the lower reaches of the Sierra Nevada foothills. This ecosystem is a natural laboratory for studying how ecosystem scale carbon and water fluxes respond to environmental change. The temperatures range between 0 and 40 C, the autumn, winter and spring are wet and cool, while the summer growing season is hot, dry and rainless. The overstory is dominated by blue oak trees (40% of total vegetation) with intermittent grey pine trees (3 trees/ha). Understory species include a variety of grasses and herbs, including purple false brome, smooth cat's ear, and rose clover. These two distinctive layers operate in and out of phase from one another. Growing season of the understory is confined to the wet season only, typically from October to early May. In contrast, the deciduous blue oak trees are dormant and leafless during the rainy winter months. The trees tend to leaf out in March and reach maximum LAI in April. During the rainless summers, the grasses in the understory die and the leaves experience soil moisture deficit stress References Davis, F., et al. (2016). "Oak woodlands." Ecosystems of California: 509–529.

Ma, Siyan↗