Glossary

Abiotic stress is the negative impact (damage) non-living factors can have on living organisms in a specific environment. Abiotic stressors can include drought, salinity, low or high temperatures, and other environmental extremes.

Albedo is the ability or measure of a surface to reflect solar radiation. In environmental contexts, areas covered by ice and snow have high albedo, reflecting sunlight and helping to keep the earth cool; as climate change causes increased global warming, snow- and ice-covered regions, especially in the Arctic are melting, decreasing albedo and contributing to further warming.

Biobased (and bio-derived) processes and materials are those that function or occur through biological activity or are made of or derived from biological components, often through fermentation. Note: the United States Department of Agriculture’s BioPreferred Program has a further definition of “biobased” that we find helpful, available at https://www.biopreferred.gov/BioPreferred/faces/pages/BiobasedProducts.xhtml

Biocement and bioconcrete are formed through the biological accumulation or precipitation of calcium carbonate/calcite, silica, or other minerals, to create limestone and other hard material products; biocement is a component of bioconcrete. While this process can occur naturally, engineering biology has been used to accelerate material formation and provide dynamic (i.e., self-repairing) activity.

Biocrusts, or biological soil crusts, are communities of living microbes that form a layer at the soil surface, most often in water-limited environments; biocrusts are typically comprised of mosses, lichens, and cyanobacteria (and sometimes also algae and fungi) that flourish in arid and semi-arid environments.¹Bowker, M. A., Reed, S. C., Maestre, F. T., & Eldridge, D. J. (2018). Biocrusts: The living skin of the earth. Plant and Soil, 429(1), 1–7. View Publication.

Biofabricated materials are materials, such as textiles, produced by living cells and microbes, such as bacteria, yeast, and mycelium. For further information, please see Understanding ‘Bio’ Material Innovation: a primer for the fashion industry.²Biofabricate. (2021). Understanding “Bio” Material Innovations Report. Biofabricate and Fashion for Good 2021.pdf | Powered by Box. View Publication.

Biofuel is any fuel derived from biomass, including plants (typically switchgrass or miscanthus, corn, soybean, or sugarcane) or algae.

Biomass is the amount of biological material that can be used for a process; when used directly for energy production, the term “biofuel” is often used interchangeably.

Biomaterial is any biological substance that has been engineered to interact with biological systems or derived from biological systems for non-biological use.

Biomining is the process of using microbes to extract economically-valuable materials from rock ores, mining waste, or other solid materials (including electronic waste).

Biomolecules are one of several major classes of biological molecules or complexes, such as proteins (including enzymes), nucleic acids, lipids, and glycans. For more about engineering biomolecules, please see EBRC’s Engineering Biology: A Research Roadmap for the Next-Generation Bioeconomy.³Engineering Biology Research Consortium (EBRC). (2019). Engineering Biology: A Research Roadmap for the Next-Generation Bioeconomy. Retrieved from http://roadmap.ebrc.org. doi: 10.25498/E4159B.

Biosensor is a device or technology which uses living organism(s) or biological molecules or systems (including cell-free systems) to detect the presence of molecules, including chemicals or other cells.

Biosequestration is the process of storing or preventing escape of a specific substance (typically a pollutant) within a biological organism or biomaterial.

Biosorption is the process of binding or accumulating ions or other target molecules onto a surface, typically another biological surface such as cell membranes or biofilms.

Biosphere (or ecosphere) is the portion of Earth’s surface, oceans and other bodies of water (hydrosphere), and atmosphere that contains life.

Biotic stress is the negative impact (damage) to an organism by other living organisms. Biotic stressors can include viruses, bacteria, fungi, and parasites, as well as insects, plants, and animals, particularly invasive species.

Carbon capture is the process of capturing carbon dioxide (CO₂) at its emission source, preventing it from entering the atmosphere.

Carbon carrying capacity is the amount of carbon that a system (organism or ecosystem) can absorb and store. “Carbon” in this sense is typically considered to be CO₂.

Carbon-Concentrating Mechanism (CCM) is a biological adaptation that enables a number of photosynthetic organisms to maximize their photosynthetic efficiency under low-CO₂ conditions (aqueous environments).

Carbon fixation is the process by which biological organisms convert inorganic carbon into organic compounds, which are then used for energy storage or biomolecule production.

Carbon flux is the rate of exchange of carbon between systems (a.k.a. carbon pools), such as carbon exchange between the oceans and the atmosphere. Carbon flux is typically measured in gigatons per year (GtC/yr).

Carbon negative is a process that achieves net carbon dioxide removal, effectively removing CO₂ from the atmosphere and locking it up in products.

Carbon oxides are molecules consisting only of carbon and oxygen including carbon monoxide (CO) and carbon dioxide (CO₂).

Carbon removal is the process of capturing and eliminating carbon, primarily CO₂ from the atmosphere, keeping the gas sequestered for long periods of time. Carbon removal, also referred to as carbon dioxide removal or CDR, can be a naturally-occurring process, or can be accelerated through technology.

Carbon storage is the long-term containment of captured or removed (sequestered) carbon (including CO and CO₂) in oceans, soils, vegetation, and geologic formations. Carbon storage typically occurs on the timeframe of centuries to millennia.

Carbon utilization is used to describe the many different ways that captured CO and CO₂ can be used or recycled to produce economically-valuable products (e.g., materials, chemicals, fuels).

Catabolism is the sequence of enzyme-catalyzed reactions by which relatively large molecules in living cells are broken down or degraded to release energy.

Cell-free systems are synthetic biological systems that consist of components to activate biological reactions without the environment of a living cell. Typically produced by isolating subcellular fractions, a cell-free system is an engineering biology tool for more controlled study of cellular reactions; simplified production of desired chemicals, biomolecules, or materials; or production or measurement in extreme or non-natural environments or with non-natural precursors or components.

Chassis, in engineering biology, is a cell/organism that serves as a foundation to physically house and support the genetic material and other biomolecules and materials necessary for biological function.

Distributed metabolism enables a biological system, such as a microbiome, to utilize many or all components of the system to cooperatively produce or degrade chemicals, materials, or compounds. For more, please see EBRC’s Microbiome Engineering: A Research Roadmap for the Next-Generation Bioeconomy.⁴Engineering Biology Research Consortium (EBRC). (2020). Microbiome Engineering: A Reseach Roadmap for the Next-Generation Bioeconomy. Retrieved from http://roadmap.ebrc.org. doi: 10.25498/E4QP4T.

Effector-triggered immunity, first identified in plants, refers to a second stage of plant defense against microbial pathogens, triggered when pathogen-associated effector proteins are recognized by cognate plant Resistance proteins. This is similar in microbes, where an internalized toxin triggers a direct transcriptional immune response.⁵Rajamuthiah, R., & Mylonakis, E. (2014). Effector triggered immunity. Virulence, 5(7), 697–702. View Publication.

Electroactive microbes are species that naturally, or through engineered mechanisms, transfer electrons across cell membranes; they are commonly used for microbial fuel cells and electrosynthesis.⁶Sydow, A., Krieg, T., Mayer, F., Schrader, J., & Holtmann, D. (2014). Electroactive bacteria—Molecular mechanisms and genetic tools. Applied Microbiology and Biotechnology, 98(20), 8481–8495. View Publication.

Emission intensity (or carbon intensity) refers to the amount of pollution emitted relative to the product (such as crop production, energy, or gross domestic product).

Engineering Biology is the design and construction of new biological entities such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. Engineering biology builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes engineering biology from traditional molecular and cellular biology is the focus on the design and construction of core components (e.g., parts of enzymes, genetic circuits, metabolic pathways) that can be modeled, understood, and tuned to meet specific performance criteria, and the assembly of these smaller parts and devices into larger integrated systems to solve specific problems. Unlike many other areas of engineering, biology is incredibly dynamic, non-linear, and less predictable, and there is less knowledge of specific parts and how they interact. Hence, the overwhelming physical details of natural biology (e.g., gene sequences, protein properties, interactive biological components) must be organized and recast via a set of design rules that hide information and manage complexity, thereby enabling the engineering of many-component integrated biological systems. It is only when this is accomplished that designs of significant scale will be possible. The term “engineering biology” is often used synonymously with “synthetic biology;” EBRC considers engineering biology to encompass the field of synthetic biology.

Exometabolites are metabolic products, typically small molecules, that are lysed or diffused from the microbe or produced by processes that occur outside of the cell. Exometabolomics can be a powerful tool to measure activity of microbiomes and environmental impacts.

Feedstocks are the raw or unprocessed (biological) materials that are used or consumed. Feedstocks can be abiotic, including gases and metals, or biotic.

Foundational species are the organisms that play a major role in creating or maintaining a habitat in order to support other species in an ecosystem. Foundational species are often the most dominant or abundant organisms, and primary producers, within an ecosystem.

Genetic rescue is a strategy/tool to introduce or restore genetic diversity within a population, typically for species at (high) risk of extinction. Genetic rescue can include “genetically informed translocations of a species from one geographical region to another, other breeding strategies, and more extreme interventions such as gene editing.”⁷Paez, S., Kraus, R. H. S., Shapiro, B., Gilbert, M. T. P., Jarvis, E. D., & VERTEBRATE GENOMES PROJECT CONSERVATION GROUP. (2022). Reference genomes for conservation. Science, 377(6604), 364–366. View Publication.

Greenhouse gases (GHG) are gases that absorb and emit radiant energy within the thermal infrared range, causing the greenhouse effect. The primary greenhouse gases in Earth’s atmosphere are carbon dioxide (CO₂), methane (CH₄), nitrous oxide (N₂O), and ozone (O₃).

Heat stress is defined as an increased temperature level sufficient to cause (sometimes irreversible) damage to an organism’s growth and development or performance. For more, see Buckley & Huey, 2016.⁸Buckley, L. B., & Huey, R. B. (2016). How Extreme Temperatures Impact Organisms and the Evolution of their Thermal Tolerance. Integrative and Comparative Biology, 56(1), 98–109. View Publication.

Host is an organism that serves as a chassis or contained system for biological activity; typically a microbe, such as bacteria, plant or animal cell. For more about host engineering, please see EBRC’s Engineering Biology: A Research Roadmap for the Next-Generation Bioeconomy.⁹Engineering Biology Research Consortium (EBRC). (2019). Engineering Biology: A Research Roadmap for the Next-Generation Bioeconomy. Retrieved from http://roadmap.ebrc.org. doi: 10.25498/E4159B.

Hygroscopic means to attract and hold water molecules from the surrounding environment, whether by absorption or adsorption.

Indoor farming (see Vertical farming).

Keystone species are species that have an extremely high impact on a particular ecosystem relative to its population. Keystone species fill a critical niche in an ecosystem and have low functional redundancy – if they are lost, the ecosystem is likely to collapse.

Microalgae are photosynthetic algae/phytoplankton that are found in both marine and freshwater environments.

Microbial electrosynthesis is the process of providing electrons/electricity to microbes (from a cathode), which are taken up and used by the microbes to convert CO₂ into compounds and products through reduction; this is opposite of the activity of a microbial fuel cell. See also Electroactive microbes and Microbial fuel cell.

Microbial fuel cell is a system in which oxidation reactions within a microbe produce electrons for transfer (outside the cell/to an anode), generating electricity. See also Electroactive microbes.

Microbiomes are communities of diverse microbes that are found in a given environment. For more, please see EBRC’s Microbiome Engineering: A Research Roadmap for the Next-Generation Bioeconomy.¹⁰Engineering Biology Research Consortium (EBRC). (2020). Microbiome Engineering: A Reseach Roadmap for the Next-Generation Bioeconomy. Retrieved from http://roadmap.ebrc.org. doi: 10.25498/E4QP4T.

Non-photochemical quenching (NPQ) refers to a process by which photosynthetic organisms dissipate excess light that cannot be used for photosynthesis as heat.

Nutrient cycling (or ecological recycling) is the flux/pathway (movement and exchange) of nutrients and matter (biotic and abiotic) between an organism or system and the environment.

Photosynthetic capacity is a measure of the amount or maximum rate at which an organism is able to fix carbon (CO₂) during photosynthesis.

Rhizosphere is the area of soil around a plant root that is influenced by biochemicals associated with the plant and the surrounding microbes, the root microbiome.

Precision agriculture is a farming approach that leverages technology innovations, such as sensing technologies, to enable growers to increase crop yield through data. Precision agriculture aims to increase yield and quality of crops and reduce variability, while improving management of fertilizer and other resource use.

Protoplasts are plant cells where the cell wall has been removed, thus removing the challenge of penetrating the cell wall during transformation.

Regeneration (plants) is the process by which an individual engineered plant cell or protoplast can be grown into an entire plant.

Synthetic biology (See Engineering biology).

Transformation (plants) is the process by which DNA is delivered into a cell and causes a genetic change in the plant cell DNA.

Vertical farming/vertical agriculture or indoor farming is the practice of growing crops, most often indoors and in or close to urban centers, in vertical layers in a controlled environment (controlling for temperature, light, CO₂, and water levels) to optimize crop yield while reducing resource use. Vertical farming aims to reduce the negative environmental impacts of agriculture, particularly by growing food closer to where consumers live.

Footnotes

1. Bowker, M. A., Reed, S. C., Maestre, F. T., & Eldridge, D. J. (2018). Biocrusts: The living skin of the earth. Plant and Soil, 429(1), 1–7. https://doi.org/10.1007/s11104-018-3735-1
2. Biofabricate. (2021). Understanding “Bio” Material Innovations Report. Biofabricate and Fashion for Good 2021.pdf | Powered by Box. https://app.box.com/s/amjq9anszv8hvwdexoxg6wubes4aaxqa
3. Engineering Biology Research Consortium (EBRC). (2019). Engineering Biology: A Research Roadmap for the Next-Generation Bioeconomy. Retrieved from http://roadmap.ebrc.org. doi: 10.25498/E4159B.
4. Engineering Biology Research Consortium (EBRC). (2020). Microbiome Engineering: A Reseach Roadmap for the Next-Generation Bioeconomy. Retrieved from http://roadmap.ebrc.org. doi: 10.25498/E4QP4T.
5. Rajamuthiah, R., & Mylonakis, E. (2014). Effector triggered immunity. Virulence, 5(7), 697–702. https://doi.org/10.4161/viru.29091
6. Sydow, A., Krieg, T., Mayer, F., Schrader, J., & Holtmann, D. (2014). Electroactive bacteria—Molecular mechanisms and genetic tools. Applied Microbiology and Biotechnology, 98(20), 8481–8495. https://doi.org/10.1007/s00253-014-6005-z
7. Paez, S., Kraus, R. H. S., Shapiro, B., Gilbert, M. T. P., Jarvis, E. D., & VERTEBRATE GENOMES PROJECT CONSERVATION GROUP. (2022). Reference genomes for conservation. Science, 377(6604), 364–366. https://doi.org/10.1126/science.abm8127
8. Buckley, L. B., & Huey, R. B. (2016). How Extreme Temperatures Impact Organisms and the Evolution of their Thermal Tolerance. Integrative and Comparative Biology, 56(1), 98–109. https://doi.org/10.1093/icb/icw004
9. Engineering Biology Research Consortium (EBRC). (2019). Engineering Biology: A Research Roadmap for the Next-Generation Bioeconomy. Retrieved from http://roadmap.ebrc.org. doi: 10.25498/E4159B.
10. Engineering Biology Research Consortium (EBRC). (2020). Microbiome Engineering: A Reseach Roadmap for the Next-Generation Bioeconomy. Retrieved from http://roadmap.ebrc.org. doi: 10.25498/E4QP4T.