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A practical guide to the discovery of biomolecules with biostimulant activity
A practical guide to the discovery of biomolecules with biostimulant activity
A practical guide to the discovery of biomolecules with biostimulant activity
3797–3817, 2024
https://doi.org/10.1093/jxb/erae156 Advance Access Publication 17 April 2024
REVIEW PAPER
Received 13 November 2023; Editorial decision 4 April 2024; Accepted 16 April 2024
Abstract
The growing demand for sustainable solutions in agriculture, which are critical for crop productivity and food quality
in the face of climate change and the need to reduce agrochemical usage, has brought biostimulants into the spot-
light as valuable tools for regenerative agriculture. With their diverse biological activities, biostimulants can con-
tribute to crop growth, nutrient use efficiency, and abiotic stress resilience, as well as to the restoration of soil health.
Biomolecules include humic substances, protein lysates, phenolics, and carbohydrates have undergone thorough
investigation because of their demonstrated biostimulant activities. Here, we review the process of the discovery
and development of extract-based biostimulants, and propose a practical step-by-step pipeline that starts with ini-
tial identification of biomolecules, followed by extraction and isolation, determination of bioactivity, identification of
active compound(s), elucidation of mechanisms, formulation, and assessment of effectiveness. The different steps
generate a roadmap that aims to expedite the transfer of interdisciplinary knowledge from laboratory-scale studies to
pilot-scale production in practical scenarios that are aligned with the prevailing regulatory frameworks.
Keywords: Bioactivity, bioassay, biomolecule, biostimulant discovery and development, effectiveness, efficacy, extraction,
formulation.
Introduction
The extensive and prolonged use of synthetic agrochemicals alternatives for crop production and management (European
carries enduring long-term health risks, despite strict regula- Council, 2022). One such alternative lies in the adoption
tory measures governing maximum residual levels (Marchand, of plant biostimulants, which are either microbial or non-
2019). In addition, there is a pressing need to curtail the usage microbial products that, applied in modest quantities, enhance
of mined and synthetic fertilizers (Horton et al., 2021). In crop yield and quality (Zhang and Schmidt, 1999; du Jardin,
Europe, the ‘Farm to Fork Strategy’ advocates for a 20% re- 2015; Rouphael and Colla, 2020). Biostimulants are defined
duction in chemical fertilizer application by 2030, instigating by their agronomic functionalities. When applied to either the
an agricultural transformation that demands a diverse array of plant or the rhizosphere, they stimulate the plant development
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3798 | Li et al.
process, leading to improvements in nutrient use efficiency, re- property protection and commercialization (a process typi-
silience to abiotic stress, and crop quality. These functions are cally spanning 2–5 years), and a relatively low percentage of
independent of the biostimulants’ nutrient composition (du patentable end-products (are characterized by high turnover
Jardin et al., 2020). Extract-based biostimulants, derived from a rates (<10%; EBIC, 2023a). A particularly noteworthy chal-
diverse variety of plant, microbial, or animal biomass (Harvey lenge lies in the absence of clearly defined standards that guar-
et al., 2015), commonly consist of a wide spectrum of pri- antee the effectiveness of biostimulant products, a factor that
mary and/or secondary metabolites, such as monomers, oligo- contributes to public scepticism surrounding their use (EBIC,
mers, polymers, and various small molecules that participate 2021). The European Committee for Standardization (CEN)
in a diverse array of metabolic processes. These biomolecules has proposed an obligation to provide both evidence about the
influence gene regulation and protein activity to inducing claimed effects and relevant instructions for use and this will
wide diversity of biomolecule sources, encompassing plants, an- Step 1: mining of biomolecules in natural extracts
imal by-products, microbial cell-free supernatants, and culture
filtrates. In addition, we examine recent technological advances Living organisms synthesize a vast array of metabolites, result-
in other botanical drug industries that expedite pre-market de- ing in a wide spectrum of chemicals that potentially offer
velopment of agri-health biological materials. The develop- promising avenues for bioactivity screening (Rinschen et al.,
ment of extract-based biostimulants encompasses the extraction 2019). The fundamental building blocks of large biomolecules
of biomolecules from target organisms, the detection of bioac- (ranging from 10−5 to 10−3 mm in length) are oxygen, carbon,
tivity, the determination of efficacy, formulation, and the assess- nitrogen, hydrogen, phosphorus, and sulfur (Marth, 2008) (Fig.
ment of effectiveness either in controlled greenhouse settings 2A). Within living organisms, these macromolecules serve pur-
or field conditions (Fig. 1). These steps form a decision-making poses such as structural support, energy storage (carbohydrates,
tree comprising six pivotal considerations. lipids), metabolic catalysis, signaling (proteins), and conveyance
3800 | Li et al.
of genetic information (nucleic acids) (Dhara and Nayak, 2022). is one that allows the utilization of organic waste (e.g. crop
Plant-derived small molecules (< 1000 Da) constitute ~67.3% residues) or by-products collected along the agri-food supply
of the compounds cataloged in the ‘Dictionary of Natural chain. To reduce variation of metabolic content, raw resources
Products’, followed by animal-derived (12.6%), and microbes should be selected with minimal geographical, temporal, and
(18.8%) (Ntie-Kang and Svozil, 2020). and the diverse distri- organ-specific divergence, in other words plant material from
bution of biomolecular metabolites by class produced in these genetically related families and cultivated in specific geological
three groups is illustrated in Fig. 2B. Notably, plants represent regions under similar climates (Kessler and Kalske, 2018). This
one of the most adaptable life forms and account for up to can be facilitated by using the KNApSAcK metabolite–plant
82.5% of the Earth’s total biomass, equivalent to 450 Gt of species database, which has systematically integrated geograph-
carbon (Bar-On et al., 2018). Remarkably, an estimated 15% ical zone–species relationships with searchable metabolite in-
of land plants remain to be discovered (Brummitt et al., 2021). formation (Afendi et al., 2012).
Secondary metabolites typically have a specialized function in Having identified a suitable potential resource, the next step
plant development and play a role in the responses to biotic involves the anticipation of it providing biological function-
and abiotic stresses (Kessler and Kalske, 2018). The selection of ality in facilitating plant growth predicated upon the estab-
individual plants with important agronomic traits has included lished composition of biomolecules. Examples of biomolecules
those with an altered secondary metabolite profile, and has that have previously been identified as harboring biostimu-
contributed to crop domestication (Alseekh et al., 2021). The lant activity together with their modes of action are listed in
secondary metabolites play diverse signaling and regulatory Table 1. Recent advances in omics methodologies have led
roles and represent valuable sources of biostimulants (ben Mrid to a proliferation of annotated biomolecule repositories, cat-
et al., 2021; Maeda and Fernie, 2021). Their production is egorized by species (Sorokina and Steinbeck, 2020). Notably,
frequently induced by environmental cues or at specific de- the Plant Metabolic Network database (https://plantcyc.org)
velopmental stages (Kliebenstein and Lunn, 2023). Molecules encompasses metabolic profiles from a diverse array of sources,
produced by microorganisms have become the second-largest including algae, model organisms, crops, and medicinal plants
source of crop protection agents (Sparks et al., 2023). Natural (Hawkins et al., 2021) Biomolecular networks are progres-
resources from higher plants, animal by-products, algae (e.g. sively being elucidated through the integration of multi-omics
seaweed, microalgae), and cell-free supernatants or filtrates modeling with augmented metagenomic data (Dorado et al.,
from microorganisms are employed to generate novel biostim- 2021). In one particular breakthrough, Skinnider et al. (2020)
ulants (Matthews et al., 2022) (Fig. 3A). predicted the previously unelucidated structure of secondary
For the large-scale production of biostimulants from biomass metabolites from microbial genome sequences and biosynthetic
sources, several key principles should be considered. These in- pathways. This approach offers a novel pathway for exploring
clude effective management of quality control and consist- previously untested natural products and identifying organisms
ency of supply, minimizing costs for collection and storage, that produce similar biomolecules. Compounds exhibiting
and striving to use homogeneous resources (Xu and Geelen, structural similarities tend to also share similar physiochem-
2018). An economical and bio-accessible raw material resource ical attributes and biological functionalities (Lo et al., 2018).
Guide to the discovery of biomolecules with biostimulant activity | 3801
The potential biological roles of biomolecules can be surmised while preserving their bioactivity. Biomass is notable for its
based on their chemical configurations and data derived from complexity and heterogeneity, stemming from the significant
publicly accessible bioactivity databases, such as ChEMBL spatial and temporal variations present within living organ-
(Mendez et al., 2019) and PubChem (Kim et al., 2023), al- isms (Resch and Ladisch, 2020). In many instances, a crude
though there is a lack of specialized sections for plant bioas- extraction is conducted for screening of bioactivity, particularly
says. The prevalence and/or specialization of specific classes of when there are no specific classes of biomolecules that have
biomolecules can thus be identified through the aggregation been identified that would necessitate a specialized extraction
of data about the chemical constitution and bioactivities of a process (Fig. 1). Alternatively, where individual biomolecules of
given biomass source, and this information can influence sub- interest are known to be present, targeted extractions can be car-
sequent extraction methodologies and the design of appro- ried out using established or custom-made protocols. The rate-
priate bioassays. limiting factors in biomolecule extraction are diffusivity and
solubility, both of which are interconnected with the size and
Step 2: extraction and characterization of biomolecules physiochemical properties of the biomolecules in question
and the choice of extraction solvent (Zhang et al., 2018). The
The next challenge involves extracting the identified biomole- extraction of metabolites from plant material requires ef-
cules from the natural source in a way that achieves a high yield fective cell lysis through mechanical or chemical disruption
Table 1. Biomolecule classes harboring biostimulant activity and their modes of action
ucts, and lignans (flavonoids, phenolic acids, through interaction with phytohormone signaling dants that stabilize cellular redox status by biotic nitrogen fixation (Okazaki et al.,
coumarins, lignin) (Laoué et al., 2022). scavenging reactive oxygen species (e.g. 2013)
• Quercetin derivatives (flavonoids) antagonize ABA through their hydroxyl groups on B-ring) (Agati • Flavonoids stimulate fungal growth in
and induce stomatal closure to regulate water loss et al., 2012). arbuscular mycorrhizal symbiosis and
and gas exchange (Watkins et al., 2017) • Lignin biosynthesis and deposition enhance phosphorus acquisition (Tian et al.,
• Ortho-dihydroxy B-ring-substituted flavonoids plant tolerance to environmental stresses in- 2019)
modulate auxin signaling and transport by regulat- cluding heavy metals (Liu et al., 2018) • Metal chelating with flavonoids
ing PINOID (PID) proteins (Brunetti et al., 2018). increases the bioavailability of micro-
• Phenolic acids serve as structural units in lignin bi- nutrients and soil quality (Cesco et al.,
osynthesis and cell wall formation (Antonova et al., 2010)
2012). • Coumarins are involved in the
• Salicylic acid (phenolic acid) is a growth regu- microbiome-to-root-to-shoot communica-
lator involved in root development, plant growth, tions that shape microbiome composition
and crop yield (Hassoon and Abduljabbar, 2019; and iron mobilization (Stassen et al., 2021)
Bagautdinova et al., 2022) • Humic and fulvic acids interact with
• cis-Cinnamic acid (phenolic acid) is a natural plant plant growth-promoting bacteria leading
growth-promoting compound that stimulates cell to root biomass increase, nutrient ab-
division and expansion (Steenackers et al., 2019) sorption, and stress damage control (da
Silva et al., 2021)
Terpenoids (diterpenes, triterpenes, tetrater- • Gibberellins (diterpenes), abscisic acid (tetraterpe- • Sterols (triterpenes) are cell membrane • Strigolactones (sesquiterpene) signal
penoids, sesquiterpenes, isoprenoids) noids, derived from carotenoids), strigolactones components that regulate cell wall develop- the interaction with beneficial arbuscular
(sesquiterpenes, derived from carotenoids), and ment and hormone signaling (Rogowska and mycorrhiza and nodulation (López-Ráez
brassinosteroids (triterpenes) are phytohormones Szakiel, 2020) et al., 2017)
with primary roles in plant growth (De Bruyne et al.,
2014)
• Carotenoids (isoprenoids) are photosynthetic
complex-bound and function in light-harvesting and
photoprotection (Sun et al., 2022)
• The apocarotenoid signal derived from cis-carotene
activates chloroplast development and promotes
leaf virescence (Cazzonelli et al., 2020).
Carbohydrates (chitosan, oligosaccharides, • Chitosan and related oligosaccharides promote • Soluble sugars scavenge reactive oxygen • The root system serves as a carbon sink
fructan, pectin) plant growth by regulating photosynthesis, C/N species and are osmoprotectants that stabi- in response to sugar transport in plant–
metabolism, and plant stress (Mukhtar Ahmed et lize membranes (Keunen et al., 2013) rhizobacteria interactions (Hennion et
al., 2020) al., 2019)
• Fructan regulates plant growth via phytohormone
signaling (Márquez-López et al., 2022)
• Pectin affects plant signaling by regulating stem
cells, cell morphogenesis, and cell–cell communi-
cations (Shin et al., 2021)
Amino acids and their specialized sustainable (Rahman et al., 2022); Table 2 shows comparisons
of various eco-friendly, cost-effective, and scalable pretreat-
ment techniques for biostimulant production. Briefly, non-
thermal techniques, such as steam/CO2 explosion and pulsed
electric field, are more effective and sustainable. The extraction
sphere and/or soil)
None
None
High
Low
Low
Moderate
Low
Low
Low
Low
Moderate
Moderate
Moderate
High
High
Low
Low
Low
Moderate
Moderate
Short
Long
Long
Moderate
Moderate
Moderate
Moderate
High
High
Low
Low
Moderate
High
High
High
High
High
Low
Low
Thermal
Fig. 4. The agricultural functions of biostimulants and corresponding plant traits, bioactivities, and underlying mechanisms. Biostimulants are
characterized by three distinct categories of agricultural functions that highlight their impact on plant traits, their bioactivities, and the underlying
mechanisms that are driven by the active biomolecules. Illustrative examples of each of these categories are listed. Created with BIorender.com.
3806 | Li et al.
Agricultural function Biostimulant activity/plant trait1 Example evaluation indices References for example descriptions of bioas-
says
Crop yield and quality Agronomical trait Yield, height, stem diameter, leaf number, leaf area, fresh Gallegos-Cedillo et al. (2021); Li et al. (2021)
weight, root system quality parameters
Marketable trait Nutritional properties Proteins, lipids, trace elements, vitamins, amino acids Capstaff and Miller 2018); Yu and Tian (2018)
Organoleptic properties Appearance, related metabolites (e.g. sugars, organic acids, Pott et al. (2019); Bashir et al. (2023)
phenolics, terpenoids, volatiles)
Techno-functional properties2 Related metabolites for food, feed, energy, cosmetics, phar- Kai et al. (2018); Rashwan et al. (2024)
macology, building materials (e.g. proteins, polysaccharides,
lignin, pectins)
Abiotic stress tolerance Thermal Visual damage, biomembrane functions, chlorophyll fluores- Ramel et al., (2012); Potocka and Szymanowska-Pulka
Light cence, water potential, heat-shock proteins, phytohormones, (2018); Ding et al. (2019); Sun et al. (2020); Van Zelm et
Mechanical anthocyanin, reactive oxygen species, antioxidants al. (2020); Geange et al. (2021); Shi et al. (2022)
Water
Chemical
Xenobiotic
Nutrient use efficiency Nutrient availability Chemical soil analysis of nutrient status based on extractable Marschner and Rengel (2012)
quantity, mobility, spatial availability (i.e. rhizosphere)
Uptake efficiency Root ion uptake kinetics Griffiths and York (2020)
Utilization efficiency Plant biomass or organic compounds produced per unit of Santa-María et al.( 2015)
nutrient over a given period
1
Examples are adapted from CEN (2022).
2
Physio-chemical attribute that impacts the transformation process or end use.
biomolecules, the biological interactions, including synergistic, 2020). The combination of bioactive molecules within the ex-
additive, potentiation, and antagonism effects, and their corre- tract gives it a ‘metabolic fingerprint’, and together with rapid
lation with the biological EC50 values within the context of bioassay tests it can serve as quality assessment tools for batch
composition–structure–activity relationships should be deter- evaluation, whether for the industrial-scale production of pure
mined (Yadav et al., 2015). compounds or for mixed forms of prospective biomolecules
In the pursuit of consistent extracts in mixed forms such (Li et al., 2019). Well-documented and quality-validated pro-
as biostimulants, the practice of traditional Chinese medicine cedures are imperative to ensure the integrity of the entire
(TCM) serves as a pertinent paradigm for popular botanical product supply chain during the extraction of biostimulants.
products that incorporate complex mixtures; however, despite For industrial-scale production, the metabolic fingerprint of
increasing demand for public health applications, quality con- bioactive components in mixtures can function as an indi-
cerns related to TCM have emerged as a significant barrier cator of quality, leading to a more reproducible and predictable
to global market entry (Song et al., 2013). Regional regula- product. This approach can help mitigate against variations
tory authorities have employed ‘Pharmacopoeia’ guidelines to arising from batch effects in plant materials, extracts, and
apply standardized and comprehensive instructions for various fractions.
aspects of TCM production, including plant collection, ex- At the molecular level, biostimulant activity is determined
traction, storage, quality assays, and processing (Leong et al., by analysing the biochemical changes in transcript, protein,
Table 4. Biosensors used to monitor signaling pathways for in vivo plant bioassays
Signaling molecule Functional group Biosensors for in vivo detection in plant bioassay
3808 | Li et al.
and metabolite levels (Xu et al., 2020). Biostimulants are well- made on a case-by-case basis, taking into account specific plant
recognized for their ability to modulate plant signaling path- developmental stages, to ensure optimal efficacy.
ways, including hormones and secondary messengers (Yakhin Drawing from over 30 years of experience of biophar-
et al., 2017). These signaling pathways can be observed using maceutical development, the technique of high-throughput
biosensors (Akter et al., 2021), allowing investigation in vivo formulation (HTF) has been adapted, coupled with high-
(Table 4). In vivo biomarker imaging, incorporating multi- throughput analysis, in the orthogonal design of experiments
parameter fluorescent indicators in plants, facilitates detailed to rapidly screen for optimal formulation stability and activity
monitoring of molecular dynamics and simultaneous bio- (Arvinte et al., 2018). Capelle et al. (2007) have described the
logical processes (Waadt et al., 2021). Identifying the active practical considerations of applying HTF for stabilizing ther-
molecule(s) and comprehending the molecular mechanism of apeutic proteins, and the associated physical and chemical
Region Country Recognition of biostimulants? Latest regulation (year issued) Legislation status1 Reference
Europe European Union countries Recognizes biostimulants as a distinct Regulation (EU) 2019/1009 (2019) Adopted European Union (2019)
category
North America United States Provides a federal definition of biostimu- Plant Biostimulant Act (2023) Proposal US Congress (2023)
lants and excludes them from the Federal
Insecticide, Fungicide, and Rodenticide Act
(FIFRA)
Canada No definition of biostimulants and they are Fertilizers Regulations (2020) Adopted Government of Canada
regulated as supplements (2020)
South America Brazil Regulates biostimulants separately as Decree No. 10.375 (2020) Adopted Diário Oficial da União (2023)
biofertilizers
Argentina No definition of biostimulants Resolution number 1004/2023 (2003) Adopted Gottems (2023)
Asia China No definition of biostimulants and they are Measures for the Administration of Ferti- Adopted Lagre (Beijing) Agriculture
regulated as other fertilizer products lizer Registration (Measures) (2022) Technology (2022)
India Defines biostimulants that do not include Fertilizer (Inorganic, Organic or Mixed) Adopted Government of India (2021)
pesticides or plant growth regulators (Control) Amendment Order (2021)
Oceania Australia No definition of biostimulants and they are The Agricultural and Veterinary Chemi- Adopted Australian Pesticides and Vet-
regulated as biological agricultural products cals Code Act (Agvet Code) (1994), The erinary Medicines Authority
Biosecurity Act (2015), and The Gene (2022)
Technology Act (2020)
Africa South Africa Regulated as a Group 3 fertilizer. A product Fertilizers, Farm Feeds, Seeds and Rem- Adopted South African Government
can be both a biostimulant and a biopes- edies Act 36 of 1947 (2019) (2019)
ticide
1
The legislation status is simplified to proposal and adopted, based on European Parliament (1999).
Author contributions discovery: advances and opportunities. Nature Reviews Drug Discovery 20,
200–216.
JL: investigation, visualization, writing—original draft; RL, SM, and DG: Australian Pesticides and Veterinary Medicines Authority. 2022.
writing—review and editing, supervision; JL and DG: conceptualization. Guideline for the regulation of biological agricultural products. https://
www.apvma.gov.au/registrations-and-permits/data-requirements/agricul-
tural-data-guidelines/biological. Accessed January 2024.
Bagade SB, Patil M. 2019. Recent advances in microwave assisted ex-
Conflict of interest traction of bioactive compounds from complex herbal samples: a review.
Critical Reviews in Analytical Chemistry 51, 138–149.
The authors declare that they have no conflicts of interest in relation to
Bagautdinova ZZ, Omelyanchuk N, Tyapkin AV, Kovrizhnykh VV,
this work.
Lavrekha VV, Zemlyanskaya EV. 2022. Salicylic acid in root growth and
development. International Journal of Molecular Sciences 23, 2228.