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Crude oil, a transformed biogenic substance
Natural gum, a secretion from Hevea brasiliensis

A biogenic substance is a product made by or of life forms. While the term originally was specific to metabolite compounds that had toxic effects on other organisms,[1] it has developed to encompass any constituents, secretions, and metabolites of plants or animals.[2] In context of molecular biology, biogenic substances are referred to as biomolecules. They are generally isolated and measured through the use of chromatography and mass spectrometry techniques.[3][4] Additionally, the transformation and exchange of biogenic substances can by modelled in the environment, particularly their transport in waterways.[5]

The observation and measurement of biogenic substances is notably important in the fields of geology and biochemistry. A large proportion of isoprenoids and fatty acids in geological sediments are derived from plants and chlorophyll, and can be found in samples extending back to the Precambrian.[4] These biogenic substances are capable of withstanding the diagenesis process in sediment, but may also be transformed into other materials.[4] This makes them useful as biomarkers for geologists to verify the age, origin and degradation processes of different rocks.[4]

Biogenic substances have been studied as part of marine biochemistry since the 1960s,[6] which has involved investigating their production, transport, and transformation in the water,[5] and how they may be used in industrial applications.[6] A large fraction of biogenic compounds in the marine environment are produced by micro and macro algae, including cyanobacteria.[6] Due to their antimicrobial properties they are currently the subject of research in both industrial projects, such as for anti-fouling paints,[1] or in medicine.[6]

History of discovery and classification

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Biogenic sediment: limestone containing fossils

During a meeting of the New York Academy of Sciences' Section of Geology and Mineralogy in 1903, geologist Amadeus William Grabau proposed a new rock classification system in his paper 'Discussion of and Suggestions Regarding a New Classification of Rocks'.[7] Within the primary subdivision of "Endogenetic rocks" – rocks formed through chemical processes – was a category termed "Biogenic rocks", which was used synonymously with "Organic rocks". Other secondary categories were "Igneous" and "Hydrogenic" rocks.[7]

In the 1930s German chemist Alfred E. Treibs first detected biogenic substances in petroleum as part of his studies of porphyrins.[4] Based on this research, there was a later increase in the 1970s in the investigation of biogenic substances in sedimentary rocks as part of the study of geology.[4] This was facilitated by the development of more advanced analytical methods, and led to greater collaboration between geologists and organic chemists in order to research the biogenic compounds in sediments.[4]

Researchers additionally began to investigate the production of compounds by microorganisms in the marine environment during the early 1960s.[6] By 1975, different research areas had developed in the study of marine biochemistry. These were "marine toxins, marine bioproducts and marine chemical ecology".[6] Following this in 1994, Teuscher and Lindequist defined biogenic substances as "chemical compounds which are synthesised by living organisms and which, if they exceed certain concentrations, cause temporary or permanent damage or even death of other organisms by chemical or physicochemical effects" in their book, Biogene Gifte.[1][8] This emphasis in research and classification on the toxicity of biogenic substances was partly due to the cytotoxicity-directed screening assays that were used to detect the biologically active compounds.[6] The diversity of biogenic products has since been expanded from cytotoxic substances through the use of alternative pharmaceutical and industrial assays.[6]

In the environment

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Hydroecology

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Model of movement of marine compounds

Through studying the transport of biogenic substances in the Tatar Strait in the Sea of Japan, a Russian team noted that biogenic substances can enter the marine environment due to input from either external sources, transport inside the water masses, or development by metabolic processes within the water.[5] They can likewise be expended due to biotransformation processes, or biomass formation by microorganisms. In this study the biogenic substance concentrations, transformation frequency, and turnover were all highest in the upper layer of the water. Additionally, in different regions of the strait the biogenic substances with the highest annual transfer were constant. These were O2, DOC, and DISi, which are normally found in large concentrations in natural water.[5] The biogenic substances that tend to have lower input through the external boundaries of the strait and therefore least transfer were mineral and detrital components of N and P. These same substances take active part in biotransformation processes in the marine environment and have lower annual output as well.[5]

Geological sites

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Oncolitic limestone: the spheroidal oncolites are formed via deposition of calcium carbonate by cyanobacteria[9][10]

Organic geochemists also have an interest in studying the diagenesis of biogenic substances in petroleum and how they are transformed in sediment and fossils.[4] While 90% of this organic material is insoluble in common organic solvents – called kerogen – 10% is in a form that is soluble and can be extracted, from where biogenic compounds can then be isolated.[4] Saturated linear fatty acids and pigments have the most stable chemical structures and are therefore suited to withstanding degradation from the diagenesis process and being detected in their original forms.[4] However, macromolecules have also been found in protected geological regions.[4] Typical sedimentation conditions involve enzymatic, microbial and physicochemical processes as well as increased temperature and pressure, which lead to transformations of biogenic substances.[4] For example, pigments that arise from dehydrogenation of chlorophyll or hemin can be found in many sediments as nickel or vanadyl complexes.[4] A large proportion of the isoprenoids in sediments are also derived from chlorophyll. Similarly, linear saturated fatty acids discovered in the Messel oil shale of the Messel Pit in Germany arise from organic material of vascular plants.[4]

Additionally, alkanes and isoprenoids are found in soluble extracts of Precambrian rock, indicating the probable existence of biological material more than three billion years ago.[4] However, there is the potential that these organic compounds are abiogenic in nature, especially in Precambrian sediments. While Studier et al.'s (1968) simulations of the synthesis of isoprenoids in abiogenic conditions did not produce the long-chain isoprenoids used as biomarkers in fossils and sediments, traces of C9-C14 isoprenoids were detected.[11] It is also possible for polyisoprenoid chains to be stereoselectively synthesised using catalysts such as Al(C2H5)3 – VCl3.[12] However, the probability of these compounds being available in the natural environment is unlikely.[4]

Measurement

[edit]
Chromatographic separation of chlorophyll

The different biomolecules that make up a plant's biogenic substances – particularly those in seed exudates - can be identified by using different varieties of chromatography in a lab environment.[3] For metabolite profiling, gas chromatography-mass spectrometry is used to find flavonoids such as quercetin.[3] Compounds can then be further differentiated using reversed-phase high-performance liquid chromatography-mass spectrometry.[3]

When it comes to measuring biogenic substances in a natural environment such as a body of water, a hydroecological[13] CNPSi model can be used to calculate the spatial transport of biogenic substances, in both the horizontal and vertical dimensions.[5] This model takes into account the water exchange and flow rate, and yields the values of biogenic substance rates for any area or layer of the water for any month. There are two main evaluation methods involved: measuring per unit water volume (mg/m3 year) and measuring substances per entire water volume of layer (t of element/year).[5] The former is mostly used to observe biogenic substance dynamics and individual pathways for flux and transformations, and is useful when comparing individual regions of the strait or waterway. The second method is used for monthly substance fluxes and must take into account that there are monthly variations in the water volume in the layers.[5]

In the study of geochemistry, biogenic substances can be isolated from fossils and sediments through a process of scraping and crushing the target rock sample, then washing with 40% hydrofluoric acid, water, and benzene/methanol in the ratio 3:1.[4] Following this, the rock pieces are ground and centrifuged to produce a residue. Chemical compounds are then derived through various chromatography and mass spectrometry separations.[4] However, extraction should be accompanied by rigorous precautions to ensure there is no amino acid contaminants from fingerprints,[14] or silicone contaminants from other analytical treatment methods.[4]

Applications

[edit]
Cyanobacteria extracts inhibiting the growth of Micrococcus luteus

Anti-fouling paints

[edit]

Metabolites produced by marine algae have been found to have many antimicrobial properties.[1] This is because they are produced by the marine organisms as chemical deterrents and as such contain bioactive compounds. The principal classes of marine algae that produce these types of secondary metabolites are Cyanophyceae, Chlorophyceae and Rhodophyceae.[1] Observed biogenic products include polyketides, amides, alkaloids, fatty acids, indoles and lipopeptides.[1] For example, over 10% of compounds isolated from Lyngbya majuscula, which is one of the most abundant cyanobacteria, have antifungal and antimicrobial properties.[1][6] Additionally, a study by Ren et al. (2002) tested halogenated furanones produced by Delisea pulchra from the Rhodophyceae class against the growth of Bacillus subtilis.[15][1] When applied at a 40 μg/mL concentration, the furanone inhibited the formation of a biofilm by the bacteria and reduced the biofilm's thickness by 25% and the number of live cells by 63%.[15]

These characteristics then have the potential to be utilised in man-made materials, such as making anti-fouling paints without the environment-damaging chemicals.[1] Environmentally safe alternatives are needed to TBT (tin-based antifouling agent) which releases toxic compounds into water and the environment and has been banned in several countries.[1] A class of biogenic compounds that has had a sizeable effect against the bacteria and microalgae that cause fouling are acetylene sesquiterpenoid esters produced by Caulerpa prolifera (from the Chlorophyceae class), which Smyrniotopoulos et al. (2003) observed inhibiting bacterial growth with up to 83% of the efficacy of TBT oxide.[16]

Photobioreactor used to produce microalgae metabolites

Current research also aims to produce these biogenic substances on a commercial level using metabolic engineering techniques.[1] By pairing these techniques with biochemical engineering design, algae and their biogenic substances can be produced on a large scale using photobioreactors.[1] Different system types can be used to yield different biogenic products.[1]

Examples of photobioreactor use for biogenic compound production
Photobioreactor type Algae species cultured Product Reference
Seaweed type polyurethane Scytonema sp.TISTR 8208 Cyclic dodecapeptide antibiotic effective against Gram-positive bacteria, filamentous fungi and pathogenic yeasts Chetsumon et al. (1998)[17]
Stirred tank Agardhiella subulata Biomass Huang and Rorrer (2003)[18]
Airlift Gyrodinium impundicum Sulphated exopolysaccharides for antiviral action against encephalomyocarditis virus Yim et al. (2003)[19]
Large scale outdoor Haematococcus pluvialis Astaxanthin compound Miguel (2000)[20]

Paleochemotaxonomy

[edit]

In the field of paleochemotaxonomy the presence of biogenic substances in geological sediments is useful for comparing old and modern biological samples and species.[4] These biological markers can be used to verify the biological origin of fossils and serve as paleo-ecological markers. For example, the presence of pristane indicates that the petroleum or sediment is of marine origin, while biogenic material of non-marine origin tends to be in the form of polycyclic compounds or phytane.[21] The biological markers also provide valuable information about the degradation reactions of biological material in geological environments.[4] Comparing the organic material between geologically old and recent rocks shows the conservation of different biochemical processes.[4]

Metallic nanoparticle production

[edit]
Scanning electron microscope image of silver nanoparticles

Another application of biogenic substances is in the synthesis of metallic nanoparticles.[3] The current chemical and physical production methods for nanoparticles used are costly and produce toxic waste and pollutants in the environment.[22] Additionally, the nanoparticles that are produced can be unstable and unfit for use in the body.[23] Using plant-derived biogenic substances aims to create an environmentally-friendly and cost-effective production method.[3] The biogenic phytochemicals used for these reduction reactions can be derived from plants in numerous ways, including a boiled leaf broth,[24] biomass powder,[25] whole plant immersion in solution,[23] or fruit and vegetable juice extracts.[26] C. annuum juices have been shown to produce Ag nanoparticles at room temperature when treated with silver ions and additionally deliver essential vitamins and amino acids when consumed, making them a potential nanomaterials agent.[3] Another procedure is through the use of a different biogenic substance: the exudate of germinating seeds. When seeds are soaked, they passively release phytochemicals into the surrounding water, which after reaching equilibrium can be mixed with metal ions to synthesise metallic nanoparticles.[27][3] M. sativa exudate in particular has had success in effectively producing Ag metallic particles, while L. culinaris is an effective reactant for manufacturing Au nanoparticles.[3] This process can also be further adjusted by manipulating factors such as pH, temperature, exudate dilution and plant origin to produce different shapes of nanoparticles, including triangles, spheres, rods, and spirals.[3] These biogenic metallic nanoparticles then have applications as catalysts, glass window coatings to insulate heat, in biomedicine, and in biosensor devices.[3]

Examples

[edit]
Chemical structure of lupeol, a triterpenoid derived from plants[28]

Table of isolated biogenic compounds

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Chemical class Compound Source Reference
Lipopeptide[1]
  • Lyngbyaloside
  • Radiosumin
  • Klein, Braekman, Daloze, Hoffmann & Demoulin (1997)[29]
  • Mooberry, Stratman & Moore (1995)[30]
Fatty acid[1]
  • Gustafson et al. (1989)[31]
  • Ohta et al. (1994)[32]
Terpene[6]
  • Prochlorothrix hollandica, Messel oil shale
  • Simonin, Jürgens & Rohmer (1996),[33] Albrecht & Ourisson (1971)[4]
Alkaloid[1]
  • Saker & Eaglesham (1999)[34]
  • Zhang & Smith (1996)[35]
Ketone[4]
  • Arborinone
  • Messel oil shale
  • Albrecht & Ourisson (1971)[4]

Abiogenic (opposite)

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An abiogenic substance or process does not result from the present or past activity of living organisms. Abiogenic products may, e.g., be minerals, other inorganic compounds, as well as simple organic compounds (e.g. extraterrestrial methane, see also abiogenesis).

See also

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References

[edit]
Revisions and contributorsEdit on WikipediaRead on Wikipedia

Biogenic substance

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A biogenic substance is a or material produced by living organisms or derived from biological processes, encompassing everything from organic metabolites to inorganic structures formed through vital activities. These substances are integral to life processes, serving as building blocks, signaling molecules, and energy sources within ecosystems, while also contributing to geological formations over time. Biogenic substances can be classified into several categories based on their chemical nature and origin, including biogenic amines, biogenic volatile organic compounds (BVOCs), and biogenic minerals. Biogenic amines, such as and , are low-molecular-weight organic nitrogenous bases formed via the of by microbial or endogenous enzymes, playing roles in physiological regulation but also posing risks in . BVOCs, emitted primarily by plants, include and monoterpenes that influence , plant defense, and interactions with pollinators and herbivores. Biogenic minerals, like silica from diatoms or from marine organisms, form structures such as shells and contribute to sedimentary rocks essential for understanding Earth's biological history. The importance of biogenic substances spans , , and industry, where they drive nutrient cycles—such as the carbon and nitrogen cycles—and support efforts by breaking down pollutants. In and , they enable green synthesis of nanoparticles for and , offering eco-friendly alternatives to synthetic chemicals due to their and low . Additionally, monitoring biogenic substances like amines in food helps prevent health issues such as hypertensive crises, underscoring their dual role as vital and potential hazards.

Fundamentals

Definition and Scope

Biogenic substances are chemical compounds or materials produced directly by living organisms through biological processes, encompassing metabolites, structural components, and emissions that originate from metabolic activities or physiological functions. These substances include both organic and inorganic products, such as volatile organic compounds emitted by and carbonates formed in shells by marine organisms. Unlike the broader concept of , which refers to the total derived from living or recently deceased organisms used primarily as a source, biogenic substances emphasize specific molecular or structural outputs rather than bulk material. The term "biogenic" derives from the Greek roots "bio-" meaning and "-genic" meaning producing or originating from, first appearing in in the late to describe processes or products arising from living organisms. Initially applied in contexts like early pharmacological studies of biologically derived compounds, its usage has since expanded to denote any life-generated materials across natural systems. The scope of biogenic substances extends across multiple scientific disciplines, including where they underpin metabolic pathways and ecological interactions, where they influence element cycling in sediments and rocks, where they affect atmospheric and aquatic chemistry, and where they inspire biomimetic designs for sustainable technologies. In contrast to abiogenic substances formed through non-biological geological or chemical processes, biogenic substances are distinctly tied to biological origins, highlighting their role in life's integration with Earth's systems.

Types and Biological Origins

Biogenic substances are broadly categorized into organic and inorganic types, each produced through distinct biological processes in living organisms. Organic biogenic substances primarily consist of carbon-based compounds essential to , including carbohydrates, , proteins, and nucleic acids, which form the structural and functional building blocks of cells. A prominent subclass is biogenic volatile organic compounds (BVOCs), such as and monoterpenes, emitted mainly by terrestrial as part of stress responses or metabolic byproducts; global emissions of BVOCs are estimated at approximately 760 Tg C per year, with accounting for about 70% and monoterpenes for 11%. Inorganic biogenic substances, in contrast, include minerals like silica and carbonates formed by organisms for structural purposes, such as biogenic silica () produced by diatoms and other silica-depositing , and synthesized by marine calcifiers including , coccolithophores, and corals. Annual global production of biogenic is estimated at 0.5–2.0 Pg C, while biogenic silica production is around 255 Tmol Si (equivalent to approximately 15 Pg bSiO₂), contributing significantly to sediment formation and the . The biological origins of these substances stem from metabolic pathways that vary by organism and environmental demands. Primary metabolism generates compounds vital for growth and reproduction, such as sugars produced via in and algae, where enzymes like ribulose-1,5-bisphosphate carboxylase/oxygenase () fix into glucose as the foundational energy source. Secondary metabolism yields non-essential but adaptive compounds, often for defense, including alkaloids in that deter herbivores through or bitterness; these pathways are activated under stress and derive from primary metabolites like . Microbial processes further diversify biogenic production, as seen in methanogenic (methanogens) that generate as a metabolic end product under anaerobic conditions, using enzymes like methyl-coenzyme M reductase to reduce CO₂ or . Synthesis of biogenic substances relies on enzymatic and genetic to ensure precise control over production rates and timing. Enzymes facilitate key reactions, such as silicate transporters in diatoms for biogenic silica deposition or in calcifying organisms for precipitation, often within specialized organelles like silica deposition vesicles. Genetic occurs through transcriptional control of biosynthetic clusters; in , transcription factors like MYC2 upregulate pathways for BVOC emission, while in microbes, and sigma factors modulate secondary metabolite genes in response to nutrient availability. Organism-specific production highlights these mechanisms: predominantly synthesize carbohydrates and volatiles via chloroplast-based pathways, animals produce proteins and through ribosomal and processes (though less emphasized for biogenic export), and microbes excel in inorganic gases like or antibiotics via cytoplasmic complexes.

Historical Development

Early Discoveries

Early observations of biogenic substances trace back to ancient natural history and philosophical inquiries. In the 4th century BCE, Aristotle noted the organic-like forms of fossils, attributing their resemblance to animals and plants to the Earth's "plastic force" that could shape mineral matter into organic appearances, rather than recognizing them as preserved biological remains. This perspective, echoed in alchemical traditions, represented an early, albeit misinterpreted, acknowledgment of materials with biological characteristics embedded in geological contexts. Pre-modern naturalists, building on such ideas, began distinguishing organic origins through empirical descriptions in texts like those of Pliny the Elder, though systematic identification remained elusive until the scientific revolution. In the 17th century, Nicolaus Steno's work in 1669 advanced this understanding by proposing that fossils were remains of once-living organisms, laying groundwork for paleontology. The marked a pivotal shift with the advent of , exemplified by Friedrich Wöhler's 1828 synthesis of from inorganic . This achievement directly challenged the doctrine of , which posited that organic compounds required a life force for synthesis, demonstrating that biological molecules could be produced abiotically while underscoring the specificity of biogenic pathways in nature. Wöhler's work laid the groundwork for recognizing biogenic substances as chemically replicable yet distinctly tied to living processes, influencing subsequent studies on compounds like and sugars derived from biological sources. In the , key advancements illuminated the persistence and transformation of biogenic substances in natural reservoirs. During the 1930s, Alfred Treibs identified porphyrin derivatives of and in samples, providing molecular evidence for the biological origins of fossil fuels through these stable biomarkers. Concurrently, early toxicological research in the 1910s advanced the understanding of biogenic amines; for instance, studies by Henry Dale and colleagues characterized , derived from in tissues, as a potent mediator of physiological responses and toxicity.

Classification Evolution

In the 19th century, the classification of biogenic substances was heavily influenced by the vitalist perspective, which posited that organic compounds—those derived from living organisms—could only be produced through a unique "vital force" inherent to life, distinguishing them from inorganic substances that lacked this force. This view, rooted in the works of chemists like , created a binary divide where biogenic substances were seen as fundamentally different from abiotic materials, limiting synthesis to biological processes alone. However, Friedrich Wöhler's synthesis of from inorganic precursors challenged , paving the way for mechanistic interpretations that emphasized chemical pathways over mystical forces, gradually shifting classifications toward structural and synthetic similarities between organic and inorganic realms. By the , classifications evolved to incorporate specialized groupings, particularly in and . In , the 1960s marked the introduction of biomarker systems, pioneered by Geoffrey Eglinton and , who classified lipid-derived compounds as "chemical fossils" based on their structural fidelity to biological precursors, enabling the identification of ancient biogenic origins in sediments through categories like alkanes and sterols. Concurrently, in during the 1930s and 1950s, biogenic amines—such as epinephrine (identified in 1901 but classified as s by the 1950s), norepinephrine, , and serotonin—were grouped by their roles in neural signaling, with key advancements including Ulf von Euler's confirmation of norepinephrine as a sympathetic transmitter in 1946 and the acceptance of these amines as a distinct class by the mid-1950s. Modern frameworks for classifying biogenic substances adopt hierarchical systems that integrate biological origin, , and functional roles, providing a more integrated approach across disciplines. Substances are often categorized as primary metabolites (essential for growth and reproduction, such as and carbohydrates) or secondary metabolites (non-essential for basic but involved in defense and , including terpenoids, phenolics, and alkaloids), with structural subgroups like terpenoids (hydrocarbon-based) and phenolics (aromatic compounds) further delineating complexity. Functional distinctions emphasize roles in signaling (e.g., hormones like auxins) versus structural support (e.g., lignins in cell walls), guided by IUPAC recommendations for organic nomenclature that standardize naming based on parent chains and functional groups to ensure consistency in biochemical contexts. In the 2000s, this evolution extended to biogenic nanomaterials, where nanoparticles synthesized via biological reducing agents (e.g., plant extracts or microbial enzymes) are classified by morphology—such as spherical, rod-like, or triangular shapes—and by the agents' influence on size and stability, reflecting applications in and .

Natural Occurrence

Aquatic Environments

In aquatic environments, biogenic substances originate primarily from biological processes involving , , and , contributing significantly to the pool. release dissolved organic matter (DOM), including and other exudates, which form a major component of the marine . Bacterial exudates further enrich DOM pools through metabolic byproducts, while feces, often in the form of fecal pellets, serve as particulate sources that facilitate vertical flux of organic material to deeper waters. These sources collectively drive the export of biogenic carbon from surface to deep ocean layers. Marine algae, particularly , produce approximately 50% of global oxygen through , with associated biogenic playing a key role in carbon export and structuring. These substances influence hydroecological roles such as nutrient cycling, where biogenic phosphorus from algal biomass and detritus promotes in nutrient-limited systems, leading to enhanced and potential hypoxic conditions. In carbon sequestration, particulate organic carbon (POC) derived from these biogenic sources sinks at rates varying by region, with global estimates indicating burial of approximately 0.2 Pg C per year in marine sediments, contributing to long-term CO₂ mitigation. Specific examples highlight the diversity of biogenic substances in aquatic settings. Biogenic carbonates, primarily and , form the structural basis of reefs through calcification by scleractinian corals and , supporting and coastal protection. Volatile sulfur compounds, such as (DMS), are produced by marine microbes like and , influencing and cloud formation over oceans. Ocean acidification, driven by rising CO₂, exacerbates dissolution of biogenic ; studies indicate significant reductions, such as 20-30% in shell density for some species like dogwhelks, under projected declines, threatening calcifying organisms and reef integrity.

Terrestrial and Geological Settings

In terrestrial ecosystems, biogenic substances originate primarily from the of , microbial activity, and animal wastes, contributing to and nutrient cycling. , such as fallen leaves and woody debris, undergoes microbial to form humic acids, complex organic polymers that enhance and water retention. For instance, basidiomycete fungi like Collybia dryophila break down humic acids derived from pine forest litter, facilitating the transformation of fresh plant material into stable soil . Soil microbes further produce biogenic iron oxides through oxidation processes, where precipitate ferrous iron into oxyhydroxides that influence nutrient availability and pollutant sorption in redox-variable environments. Animal wastes, including , supply organic carbon and essential nutrients like and , improving when incorporated into agricultural systems. These substances play critical roles in maintaining and serving as paleoclimate proxies. Biological by in roots and free-living soil diazotrophs replenishes , with rates typically ranging from 100 to 200 kg N per per year in legume-based systems, supporting productivity without synthetic fertilizers. wax from terrestrial , preserved in sediments, provide isotopic signatures—such as and carbon isotopes in n-alkanes—that reconstruct past patterns and shifts, offering insights into hydroclimatic variability over millennia. In contrast to dynamic aquatic systems, terrestrial biogenic substances accumulate in static profiles, enabling long-term benefits. Geological records preserve biogenic substances as markers of ancient life, with steranes—diagenetic products of eukaryotic sterols—evidencing the presence of complex eukaryotes as far back as approximately 1.6 billion years ago in sediments. These biomarkers, found in bituminous shales, indicate early eukaryotic diversification and oxygen-dependent . Iconic sites like the in preserve fossilized soft-bodied biogenic structures, including non-mineralized carapaces and traces from organisms, revealing exceptional biotas through rapid burial in anoxic mudslides. In the deep biosphere, crustal microbes generate biogenic methane through methanogenesis in organic-rich subsurface rocks, with estimates suggesting annual release of 5–25 Tg CH₄ from marine sediments.

Analytical Methods

Detection Techniques

Detection of biogenic substances relies on a suite of analytical techniques that leverage spectroscopic, chromatographic, and isotopic properties to identify and characterize compounds of biological origin. These methods are essential for distinguishing biogenic materials in complex environmental matrices, such as sediments, water, and air samples. Spectroscopic approaches, particularly , play a central role in identifying volatile biogenic substances. Gas chromatography- (GC-MS) is widely used for analyzing biogenic volatile organic compounds (BVOCs) and other small molecules, offering high sensitivity and the ability to resolve structural isomers at low ppm levels or lower. For instance, GC-MS has been applied to detect biogenic amines like in matrices through electron impact ionization and spectral library matching. (NMR) spectroscopy complements by providing detailed structural elucidation of biogenic compounds, such as metabolites and natural products, without requiring derivatization; it excels in resolving proton environments in polar and non-volatile species through 1H and 13C NMR experiments. Chromatographic techniques enable the separation and detection of a broad range of biogenic substances based on their polarity and . High-performance liquid chromatography (HPLC), often coupled with or mass detection, is particularly effective for polar biogenic compounds like amines and , allowing baseline separation in complex samples with detection limits around 1–10 ppm. For insoluble or high-molecular-weight biogenic organics, such as those in or , pyrolysis-gas chromatography (Py-GC) is employed; this method thermally decomposes samples into volatile fragments for subsequent GC analysis, facilitating identification of polymeric structures like lignins or proteins derived from biological sources. Isotopic analysis provides a robust means to confirm biogenic origins by examining stable isotope ratios, which reflect biological fractionation processes. Carbon stable isotope ratios, expressed as δ13C, typically range from -20‰ to -30‰ for biogenic carbon due to preferential incorporation of 12C by enzymes in metabolic pathways, contrasting with abiogenic carbon that often exceeds -10‰; this distinction is critical in for tracing in rocks and sediments. Emerging detection methods, including biosensors and , are expanding field capabilities for real-time monitoring of biogenic substances. Electrochemical biosensors, utilizing enzymes or aptamers immobilized on electrodes, offer rapid and selective detection of biogenic amines with sensitivities down to nanomolar levels, suitable for on-site and environmental analysis. Recent LC-MS/MS advancements (as of 2025) enable rapid quantification of biogenic amines in with limits of detection in the ng/g range. In , drone-based technologies have been developed in the 2020s to estimate BVOC emissions over forest areas by mapping and at high spatial resolutions (e.g., tree-level), aiding in emission inventorying.

Measurement Challenges

Measuring biogenic substances presents significant challenges due to their occurrence at trace levels, often in the parts-per-billion (ppb) or lower range for biomarkers in complex environmental matrices such as sediments. These low concentrations necessitate preconcentration techniques, such as or microwave-assisted extraction, to achieve detection limits suitable for gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-mass spectrometry (LC-MS) analysis. However, matrix effects from high organic content and interfering compounds in sediments can suppress or cause signal distortion, reducing method accuracy and requiring matrix-matched calibration standards. Temporal and spatial variability further complicates quantification, as emissions of biogenic volatile organic compounds (BVOCs) exhibit diurnal fluctuations peaking at midday due to and influences, with variations up to 10-fold over short periods. Seasonal changes and environmental stressors also contribute to inconsistent profiles, making it difficult to establish reliable baselines for monitoring. Additionally, rapid degradation during sampling and storage poses a major issue; for instance, highly reactive BVOCs like have atmospheric half-lives of minutes to hours owing to oxidation by hydroxyl radicals, while some biogenic amines can degrade within less than an hour under oxidative conditions, leading to underestimation if not handled promptly with stabilizers. The absence of universal standardization exacerbates these problems, with inter-laboratory variability in isotopic ratio measurements (e.g., δ¹³C for organic compounds) reaching up to a few per mil (e.g., 1.8–3.5‰) due to differences in , , and materials. Efforts to mitigate this include the development of , but inconsistencies persist across methods like (IRMS). Climate change introduces additional measurement difficulties by altering emission profiles; warming temperatures and shifting vegetation patterns can significantly increase BVOC emissions (e.g., up to several-fold in some studies), complicating the differentiation of biogenic signals from anthropogenic influences and requiring updated baseline models.

Applications

Industrial and Environmental Uses

Biogenic substances play a significant role in industrial applications, particularly in developing eco-friendly alternatives to synthetic materials. In the maritime industry, anti-fouling paints incorporating biogenic enzymes, such as oxidases or proteases derived from microorganisms, have been utilized to prevent on ship hulls. These enzymes catalyze the oxidation or of organic compounds in biofilms, effectively deterring the attachment of marine organisms without relying on toxic like or tin. This approach has demonstrated potential to reduce consumption by 5-10% through smoother hull surfaces and lower drag, as evidenced in field trials on commercial vessels. Environmental remediation efforts leverage biogenic surfactants produced by microorganisms to address pollution challenges, notably in oil spill cleanup. Rhamnolipids, glycolipid surfactants biosynthesized by bacteria like Pseudomonas aeruginosa, enhance the emulsification and biodegradation of hydrocarbons in contaminated soils and water. Studies have shown that rhamnolipids can achieve up to 80% degradation efficiency of petroleum hydrocarbons under optimized conditions, outperforming traditional chemical dispersants by promoting microbial activity while minimizing secondary pollution. This method has been applied in real-world scenarios, such as the cleanup of coastal oil spills, where it facilitates the natural attenuation of pollutants. Beyond remediation, biogenic polymers serve as sustainable materials in manufacturing, offering biodegradable options to supplant petroleum-derived . (PHAs), accumulated as intracellular storage compounds by various such as , exhibit properties comparable to conventional plastics, including high tensile strength and thermal stability, but degrade fully in natural environments within months. Industrial production of PHAs has scaled up through processes, enabling their use in , medical devices, and agricultural films, thereby reducing reliance on non-renewable feedstocks and mitigating plastic waste accumulation. In the bioenergy sector, contribute to carbon management strategies, particularly through the handling of biogenic CO2 emissions from processing. Under the European Union's post-2020 revised Directive (RED II), biogenic CO2—originating from renewable sources like wood or agricultural residues—is granted credits in frameworks, allowing it to be distinguished from fossil-based emissions for capture and utilization purposes. This policy incentivizes technologies such as bioenergy with (BECCS), where biogenic CO2 is sequestered to achieve negative emissions, supporting industrial facilities in meeting sustainability targets.

Scientific and Biomedical Applications

Biogenic substances play a pivotal role in paleochemotaxonomy, where fossilized biomarkers such as hopanes—derived from bacterial —are analyzed to reconstruct ancient microbial ecosystems and environmental conditions. Hopanes serve as taxon-specific indicators for ancient bacterial populations, enabling scientists to infer and ecological shifts over geological timescales. For instance, elevated hopane concentrations in Permian-Triassic boundary sediments have been linked to bacterial activity and anoxic conditions contributing to approximately 90–96% marine species loss during the end-Permian mass , approximately 252 million years ago. In advanced materials , biogenic substances facilitate the of metallic nanoparticles, offering eco-friendly alternatives to methods. Plant extracts rich in polyphenols, such as those from longa (), reduce ions to form nanoparticles with controlled sizes typically ranging from 10 to 50 nm, stabilized by curcumin's functional groups. These biogenic nanoparticles exhibit enhanced catalytic activity, for example, in reducing environmental pollutants like to , demonstrating superior efficiency compared to chemically synthesized counterparts due to their biocompatible surface coatings. Biomedically, biogenic amines like serotonin function as key neurotransmitters, modulating mood, sleep, and cognition through interactions with G-protein-coupled receptors in the . Pharmacological interventions targeting imbalances, such as selective serotonin reuptake inhibitors (SSRIs) like , increase synaptic serotonin levels to treat disorders including and anxiety, with clinical efficacy established in meta-analyses showing response rates of 50-60% in patients. Additionally, produced by bacteria, such as from , offer broad-spectrum activity against Gram-positive pathogens by disrupting cell membranes, with applications in and as adjuvants in antibiotic-resistant infections, reducing minimum inhibitory concentrations by up to 8-fold in combination therapies. Biogenic volatile organic compounds (BVOCs), emitted primarily by , contribute to modeling by influencing formation and dynamics. Oxidation of BVOCs like and monoterpenes produces secondary organic aerosols that act as (CCN), enhancing reflectivity and potentially offsetting 10-20% of anthropogenic radiative forcing through indirect cooling effects, as estimated in global models integrated into IPCC assessments. This biogenic feedback is critical for projecting future scenarios, where warming could amplify BVOC emissions by 20-50% under high-emission pathways, altering patterns and .

Examples

Prominent Biogenic Compounds

is a key biogenic pigment essential for in , , and , featuring a magnesium- ring structure that enables the absorption of light energy. This tetrapyrrole-based molecule coordinates a central magnesium within its porphyrin ring, facilitating electron excitation and transfer during the light-dependent reactions of . Its green coloration results from selective absorption of red and blue wavelengths, making it vital for converting into in ecosystems. Lignin represents a major biogenic structural in vascular , providing rigidity and resistance to cell walls, particularly in . Composed of phenylpropanoid units, it constitutes 20-30% of in trees, contributing to the mechanical strength that supports plant growth and transport. This complex, heterogeneous 's cross-linked aromatic structure renders plant tissues more resistant to microbial degradation and physical stress. Biogenic opal, formed as amorphous silica (SiO₂·nH₂O) by diatoms, creates intricate exoskeletons with -like nanopatterns that enhance light manipulation for . These hierarchical structures, featuring periodic pores and hexagonal lattices, act akin to photonic crystals, guiding and confining light through and in aquatic environments. The geometry optimizes photon capture in low-light conditions, supporting diatoms' role in global . Isoprene (C₅H₈), a volatile biogenic emitted by many , particularly from leaves under stress, aids in thermotolerance by stabilizing photosynthetic membranes at high temperatures. This non-polar molecule, produced via the methylerythritol phosphate pathway, volatilizes rapidly and reinforces membranes against heat-induced damage. Certain biogenic compounds confer ecological advantages, such as , an in and that acts as an and , deterring herbivores and overexploitation. Economically, derived from the latex of trees supports a global industry valued for its elasticity and durability in tires, gloves, and adhesives, with production dominated by Southeast Asian plantations.

Comparative Table of Examples

The following table provides a comparative overview of diverse biogenic substances, highlighting their chemical nature, origins across biological kingdoms, physical and chemical properties, and functional roles. Examples are selected to represent , protists, fungi, , and animals, including a recent microbial isolate.
Compound NameTypeBiological SourceKey PropertiesPrimary Role/Application
((NH₂)₂CO)OrganicMammals (e.g., liver in humans and other vertebrates, via from )Molecular weight 60.06 g/mol; 133 °C; highly soluble in (108 g/100 mL at 20 °C); stable under neutral conditions but hydrolyzes in strong acids/bases as principal product of ; used in fertilizers and products
Biomineralized (Fe₃O₄)Inorganic (e.g., like Magnetospirillum)Nanocrystals 35–120 nm in size; single-domain or superparamagnetic; ~5.2 g/cm³; high Magnetotaxis for navigation in ; potential in biomedical and
(CaCO₃)InorganicProtists and animals (e.g., coccolithophores, mollusks, and for shells)Rhombohedral ; Mohs 3; 2.71 g/cm³; soluble in acids but stable in neutral for skeletal support and protection; source of deposits and carbon
((C₈H₁₃O₅N)ₙ)OrganicFungi (cell walls) and animals (e.g., exoskeletons like and crustaceans)Linear of ; high molecular weight (>100 kDa); insoluble in , biodegradable, tensile strength ~200 MPaStructural reinforcement in exoskeletons and cell walls; applications in wound dressings and
((C₆H₁₀O₅)ₙ)Organic (primary cell walls, e.g., in and wood) and (e.g., )Linear β-1,4-glucan ; 300–15,000; insoluble in , high crystallinity (up to 70%), tensile strength 200–600 MPa structure providing rigidity and flexibility; industrial uses in , textiles, and biofuels
OrganicAnimals (e.g., connective tissues in mammals, birds, and )Triple-helical glycoprotein; molecular weight ~300 kDa per α-chain; high tensile strength (50–100 MPa); biodegradable and biocompatibleStructural support in skin, bones, tendons, and cartilage; biomedical applications in tissue engineering and cosmetics
Histamine (C₅H₉N₃)OrganicAnimals (e.g., mast cells and basophils in mammals)Molecular weight 111.15 g/mol; -soluble (1 g/1 mL); basic (pKa 9.8); hygroscopicLocal immune response mediator, vasodilation, and gastric secretion; role in allergies and neurotransmission
Biogenic Opal (SiO₂·nH₂O)InorganicProtists (e.g., diatoms and radiolaria for frustules)Amorphous hydrous silica; 1.9–2.3 g/cm³; porous microstructure (pore sizes 10–200 nm); dissolves in alkaline solutionsProtective exoskeletons aiding buoyancy and predation defense; silica in oceans and diatomaceous earth applications
(CaCO₃)InorganicAnimals (e.g., corals, mollusks, and brachiopods for shells)Orthorhombic ; Mohs 3.5–4; 2.93 g/cm³; metastable, converts to calcite over timeFormation of hard skeletons and pearls; contributes to reef building and calcium carbonate deposition in marine environments
LigninOrganic (e.g., vascular tissues in trees and grasses)Complex phenolic ; molecular weight 1,000–20,000 g/mol; insoluble in , hydrophobic, thermal stability up to 250 °C lignification for mechanical strength and water transport resistance; biofuel and adhesive production
Amphiphilic Exopolysaccharide (NAPS L.p)Organic (e.g., probiotic strain Lactobacillus plantarum)Polysaccharide with amphiphilic moieties; forms self-assembling nanoparticles (30–84 nm); biocompatibleVaccine adjuvant delivery platform enhancing immune responses; applications in immunotherapy and prophylaxis (characterized in 2024)

Abiogenic Counterparts

Key Differences

Abiogenic substances are chemical compounds or materials formed through non-biological processes, such as geological or inorganic reactions, without the involvement of living organisms. For instance, can be produced abiogenically at hydrothermal vents through serpentinization, where reacts with ultramafic rocks like to generate that reduces . Structural differences between biogenic and abiogenic substances often manifest in isotopic compositions and molecular . Biogenic substances typically exhibit isotopic , resulting in lighter carbon ratios, such as δ¹³C values for ranging from -50‰ to -110‰ due to enzymatic preferences during biological synthesis. In contrast, abiogenic shows heavier δ¹³C values, generally greater than -25‰, reflecting equilibrium processes without biological . Regarding , biogenic compounds produced by enzymes display , favoring one , while abiogenic formations yield racemic mixtures lacking such asymmetry. Compositional contrasts further distinguish the two: biogenic substances are predominantly organic molecules enriched in carbon, hydrogen, oxygen, and nitrogen, forming complex biomolecules essential for life processes. Abiogenic substances, however, frequently consist of inorganic minerals rich in silicates, metals, or simple volatiles, lacking the intricate organic architectures seen in biogenic materials. Detection criteria for differentiating biogenic from abiogenic origins often rely on enantiomeric excess, where biogenic samples show a high excess (>50%, frequently approaching 100%) of one due to biological selectivity, whereas abiogenic samples are characterized by racemic mixtures with near-zero enantiomeric excess.

Implications in Geochemistry

In the study of life's origins, distinguishing biogenic substances from abiogenic ones has profound implications for interpreting extraterrestrial materials, particularly in carbonaceous s like the Murchison chondrite, which fell in in 1969. Analyses of extracted from this meteorite revealed non-racemic distributions, with L-enantiomers present in excess—such as up to 9% for isovaline, a non-proteinogenic α-methyl —suggesting potential extraterrestrial biological processing or asymmetric synthesis mechanisms predating Earth's . These findings challenge purely abiotic formation models and support hypotheses of interstellar delivery of prebiotic organics, influencing models of by highlighting enantiomeric biases as possible biosignatures in primitive solar system bodies. In resource , geochemical differentiation of biogenic from abiogenic hydrocarbons is crucial for efficient and reducing exploration risks. Biomarkers such as pristane, an isoprenoid derived from degradation, serve as indicators of biological input in crude oils, enabling correlation between source rocks and reservoirs while distinguishing them from rare abiogenic seeps or serpentinization-derived gases. This approach enhances drilling accuracy by confirming biogenic origins through ratios like pristane to n-C17 , which reflect maturation and depositional environments, thereby minimizing outcomes in frontier basins. Planetary science benefits from such distinctions in assessing habitability on Mars, where rover missions grapple with ambiguous organic detections amid abiotic interferences. The Perseverance rover, operating in Jezero Crater since 2021, has identified diverse organic-mineral associations, including aromatic compounds preserved in sulfates, potentially biogenic but complicated by abiotic perchlorates that oxidize organics and produce chlorinated artifacts during analysis. These findings underscore the need for sample return missions to resolve biogenic signatures, as in-situ instruments like SHERLOC detect carbon-based molecules but cannot fully rule out abiotic synthesis from volcanic or hydrothermal processes. Recent advancements, powered by the (JWST), extend these implications to exoplanets by probing atmospheric biosignatures like (DMS), a gas produced by marine phytoplankton on and indicative of biogenic cycling. In 2023-2024 observations of the Hycean world K2-18 b, JWST detected tentative DMS signals alongside and , suggesting possible ocean worlds with , though abiotic alternatives like volcanic remain viable explanations requiring further spectral confirmation. However, subsequent analyses in 2025 have found insufficient evidence to confirm the DMS detection, emphasizing the need for additional observations. This detection highlights the geochemical challenge of isolating biogenic volatiles from abiotic in distant atmospheres, advancing search-for-life strategies across the cosmos.

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