Bacteriophages: sustainable and effective solution for climate-resilient agriculture

Abstract

Climate change entails significant challenges to global food security and agricultural sustainability, prompting the need for innovative solutions to enhance climate resilience in farming practices. Bacteriophages (phages), viruses that specifically target and infect bacteria, provide promising applications in numerous agricultural practices to address these challenges. With traits such as specificity towards bacterial pathogens along with self-replication, self-dosing, and adaptability properties phages offer potential as effective biocontrol agents while exerting minimal harm on non-target organisms or their surrounding environment. In this review, various applications of phages have been explored, including increasing crop resilience, improving soil health, preserving food, managing water resources, and adapting to emerging pests and diseases. Additionally, the benefits of these applications are also explored, such as improving sustainable practices, enhancing plant growth and yield, and supporting pollinator health. Although they offer great promise, there are still several obstacles such as limited host range, environmental stability, and regulatory challenges, so further research and policies are required for their integration into agricultural systems. Furthermore, education and public awareness are essential for farmers to adopt phage-based biocontrol. By harnessing the potential of phages, agriculture can mitigate the adverse effects of climate change, promote sustainability, and ensure food security in a changing climate.

Sustainability Statement.

The utilization of phages in agricultural practices presents a promising avenue to enhance climate resilience and promote sustainability in food production. By leveraging the specificity and adaptability of phages, we aim to mitigate the adverse effects of climate change on agriculture, contributing to the achievement of UN Sustainable Development Goal 2: Zero Hunger, and Goal 13: Climate Action. Through continued research and implementation, we aspire to foster environmentally friendly farming practices while ensuring food security for future generations.

Abbreviations

CAAI

Coastal Aquaculture Authority of India

EPA

United States Environmental Protection Agency

GRAS

Generally Recognized As Safe (US FDA)

HC

Health Canada

iLONO

Interim Letter of No Objection (HC)

MH

Ministry of Health

OMRI

Organic Materials Review Institute

US

United States

USDA

United States Department of Agriculture

Introduction

Climate change significantly threatens global food security, affecting agricultural systems and food production in various ways (Schmidhuber and Tubiello 2007). The complex interplay of rising temperatures, altered precipitation patterns, extreme weather events, and changing pest and disease dynamics poses challenges to the sustainability and resilience of agriculture (Skendžić et al. 2021, Grigorieva et al. 2023), a phenomenon known as ecosystem health. Climate change further contributes to ecosystem shifts, potentially causing biodiversity loss crucial for pest control and ecosystem services (natural benefits like pollination, soil fertility, pest control, and water purification) in agriculture (Civantos et al. 2012, Weiskopf et al. 2020, Muluneh 2021).

Elevated temperatures induce plant heat stress, adversely affecting the growth and development of various crops, with wheat, rice, and maize exhibiting heightened sensitivity to temperature extremes, leading to diminished yields (Liu et al. 2020, Waqas et al. 2021, Parthasarathi et al. 2022, Shrestha et al. 2022, Mishra et al. 2023, Ren et al. 2023). Concurrently, heatwaves can harm livestock, impacting their health and productivity by causing problems with the immune system, metabolic disruption, changes in fertility, and susceptibility to diseases (Lacetera 2018, Godde et al. 2021, Thornton et al. 2022, Cartwright et al. 2023). Ocean acidification and warming threaten marine ecosystems, impacting fisheries and aquaculture by threatening their growth and survival (Baag and Mandal 2022).

Alterations in precipitation patterns, characterized by intensified and more frequent droughts or floods, significantly influence water availability for agriculture, posing a substantial challenge to irrigation-dependent farming and reducing crop yields (Ali et al. 2017, Bhaga et al. 2020, Atanga and Tankpa 2021, Skendžić et al. 2021). Extreme weather events, encompassing hurricanes, cyclones, floods, and storms, have multifaceted consequences, such as physical damage to crops, disruption of supply chains, and soil erosion that compromises agricultural land fertility (Furtak and Wolińska 2023). These events also disrupt planting and harvesting cycles, directly affecting overall productivity (Arnell and Freeman 2021, Kumar et al. 2022). Altered climate conditions induce shifts in the distribution, behavior, and life cycles of pests and pathogens, creating conducive environments for certain pests and resulting in crop damage (Skendžić et al. 2021, Singh et al. 2023). Moreover, extreme weather events, deforestation, and altered precipitation patterns contribute to soil degradation, diminishing soil fertility and hindering crop growth (Lal 2012, Brevik 2013). All these climate-related disruptions subsequently influence agricultural planning, logistics, and transportation infrastructure, which can impede the timely movement of farm products, leading to global food shortages and price volatility (Jacob et al. 2018, Godde et al. 2021).

Climate change introduces heightened uncertainty and risk for farmers, impacting their ability to predict weather patterns and effectively plan agricultural activities (Thorlakson and Neufeldt 2012), leading to decreased agricultural productivity. This heightened risk may result in reduced farming investments and reluctance to adopt new technologies, especially among smallholder farmers (Mulwa et al. 2017, Wakweya 2023), necessitating a low-cost and simplified solution that these farmers can understand and implement. Climate-resilient agriculture becomes crucial amidst ongoing and projected climate change impacts on agricultural systems. Resilient agriculture ensures a stable and consistent food supply, enhancing crop adaptability and farming practices to contribute to reliable food production.

As climate conditions evolve, adaptation becomes essential, and climate-resilient agriculture involves developing practices that adapt to altered temperatures, precipitation patterns, and other climate-related variables. Farmers facing direct impacts of climate change benefit from climate-resilient practices that mitigate risks associated with extreme weather events, pests, and diseases, ensuring the sustainability of their livelihoods. Climate-resilient agriculture adapts to climate change, ensuring food security while minimizing environmental impact (Çakmakçı et al. 2023). For instance, in the study by Heeb et al. (2019), climate-smart pest management (CSPM) reduced crop losses, enhanced ecosystem services, and decreased greenhouse gas emissions. It strengthened the resilience of agricultural systems for global food security (Heeb et al. 2019). Climate-resilient agriculture contributes to agricultural ecosystems’ long-term health and productivity by emphasizing sustainable practices like efficient water use, soil conservation, and biodiversity conservation. Involving practices such as sustainable farming, precision agriculture, and agroforestry, climate-resilient agriculture contributes to mitigating climate change by reducing greenhouse gas emissions (Balasundram et al. 2023, Konfo et al. 2024). Amidst changing precipitation patterns and water scarcity, climate-resilient agriculture prioritizes technologies optimizing water use, thereby reducing environmental impacts (Iglesias and Garrote 2015). Promoting diverse crop varieties and resilient genetics, climate-resilient agriculture aids adaptation to changing environmental conditions through breeding programs (Gaba et al. 2021, Cooper and Messina 2022). Aligned with broader sustainable development goals, climate-resilient agriculture contributes to poverty reduction, environmental conservation, and food justice (Caron et al. 2018, Anser et al. 2023).

The capacity of agriculture to consistently furnish food for a burgeoning global populace holds paramount importance. Sustainable agriculture endeavors to adopt methodologies that will foster healthy disease-resistant flora and fauna, ensure the provision of safe sustenance for an expanding global community, and mitigate the environmental repercussions of agricultural activities (Ramankutty et al. 2018). The occurrence of bacterial ailments in plants and animals has persistently curtailed production ever since the inception of crop cultivation and animal husbandry techniques. Extensive employment of antibiotics has been instrumental in alleviating these losses. Nonetheless, the emergence of antimicrobial-resistant (AMR) bacteria, coupled with the consumer demand for antibiotic-free products, poses challenges that jeopardize sustainable agriculture. Bacteriophages (phages) are posited as alternatives for controlling bacterial populations instead of antibiotics (Svircev et al. 2018).

One promising solution for climate-resilient agriculture is the utilization of phages. Phages are the most abundant biological entity on Earth, with around 10³¹ in existence (Mushegian 2020) and surpassing all other organisms on Earth (Lafee and Buschman 2017). Phages play a significant role in fulfilling the sustainability goals outlined in “food system law,” including environmental, economic, and social objectives, while also substantially supporting the One Health paradigm (Holtappels et al. 2021). The food system law represents a legislative framework driving systemic change across all facets of food production and consumption, facilitating the rapid transition to sustainable food systems (Buttimer et al. 2017, Moye et al. 2018, Kasman and Porter 2022). Phages are viruses and the natural predators of bacteria. Representing a targeted and environmentally friendly biocontrol tool, phages offer an alternative to traditional chemical pesticides, aligning with sustainability principles (Moye et al. 2018, Holtappels et al. 2021). These viruses are obligately intracellular, requiring adsorption, infection, and replication within their host bacterial cell. Phage have high specificity for particular bacterial strains while sparing other organisms, including non-target prokaryotes and all archaea and eukaryotes (e.g. plants, animals, and humans) (Kasman and Porter 2022). Phages have emerged as a cutting-edge and sustainable solution for managing bacterial diseases in crops (Buttimer et al. 2017, Villalpando-Aguilar et al. 2022). As agriculture grapples with the challenges imposed by climate change, integrating phage-based biocontrol methods into farming practices presents a promising avenue toward resilient, environmentally friendly, and economically viable agricultural systems. The continuous exploration and adoption of phages highlight their potential to revolutionize disease management, contributing to a more sustainable future for global agriculture.

The aim of this review is to explore, summarize published literature, and advocate for the implementation of phages as a sustainable and effective solution in climate-resilient agriculture. It underscores the challenges climate change poses to global food security and agriculture while emphasizing the potential of bacteriophage use as a targeted and eco-friendly approach to managing bacterial diseases in crops and biodiversity. The study seeks to bridge the gap between climate change challenges in agriculture and the solutions offered by phages, aiming to inform policymakers, researchers, and the agricultural community about the benefits and possibilities of incorporating phages into sustainable and climate-resilient farming practices.

Bacteriophages (phages)

Phages are viruses with high host specificity that target and infect specific bacterial strains through interactions between phage proteins and bacterial host surface receptors. It is, however, important to note that some phages exhibit high host specificity, others can have a narrow host range (Stone et al. 2019, Taslem Mourosi et al. 2022). They exist naturally in every ecosystem, including, e.g. air, soil, water, and the human body, and are considered the most abundant and diverse entities in the biosphere (Clokie et al. 2011). Phage exhibit simple to complex structures consisting of genetic material (circular or linear ssDNA, dsDNA (Clokie et al. 2011), ssRNA, or dsRNA) surrounded by multiple copies of coat protein that constitute the quasi-spherical or icosahedral phage capsid, and, protruding from the capsid, a variety of tail types, or no tail, depending on the phage type, and some phage have a lipid-protein envelope that surrounds the nucleocapsid. The three fundamental structural phage types are an icosahedral (20-sided) capsid with a tail, an icosahedral capsid without a tail, and a filamentous form (Naureen et al. 2020) prototype phages include T4, T7, Lambda, P22, Qbeta, and Filamentous phage Ff (includes phages f1, fd, and M13) as shown in Fig. 1. Many phages are equipped with depolymerases that enable penetration of bacterial biofilm, a common defense barrier that protects from traditional chemical antibiotics. The variability of phage anatomy is reflective of significant genetic diversity in their genomes and the types of genes they carry (Parent et al. 2014, Rao et al. 2023). Phages can undergo either a lytic (virulent), lysogenic (temperate), or, in the case of filamentous phages, a chronic lifestyle. During the lytic life cycle, replication occurs rapidly within bacterial hosts, amplifying exponentially and, in the process of liberating progeny phages, destroying the bacterial host cell, a process that repeats until no host cells remain infected. Lytic phages can eliminate bacterial populations wherever they reside, including those that cause crop diseases and are resistant to traditional antibiotics and/or pesticides (Opperman et al. 2022, Ranveer et al. 2024). Temperate phages are equipped with genetic elements to integrate into the bacterial host chromosome and undergo vertical transfer as part of host cell replication. In a process known as lysogenic conversion, the temperate phage genome excises from the host chromosome, replicates, and pursues lysis to free phages into the environment. In the chronic life cycle, phages are slowly shed from the host cell over an extended period without eliciting an antibacterial effect to the host cell.

Figure 1.

Prototype phages [T4, T7, Lambda, Filamentous phage Ff (M13)] (created with BioRender.com).

Development of phage-resistant bacteria

Evolution of phage-resistant bacteria is an irrepressible heritage between phages and their bacteria hosts. The host bacteria invent diverse ways of outrunning infection by the phage, and on the other side, the phages develop several tactics for conquering the bacterial defenses. This cyclic interaction heralds the neutral action and reaction between these two organisms as they adjust constantly (Hibstu et al. 2022).

Phages are resistant on bacteria through alteration or obliteration of the surface receptors, which the phages use to gain entry into bacterial cells through adsorption processes. One of them is the process in bacteria where cells integrate segments of phage DNA into their own genome that enable the bacteria to be capable of recognizing and chopping the DNA from the phage at future invasions (Oechslin 2018). Moreover, bacteria also have restriction modification systems in which they synthesize enzymes that can clip foreign DNA, including the phages DNA but spare the bacterial DNA through methylation (McGee et al. 2023). Bacteria can activate aberrant infection schemes, a suicidal mechanism to counter phage proliferation, which leads to destruction of infected cells to save bacterial generation. Another strategy used by bacteria is the superinfection exclusion systems that keep out several phages for a cell that has already been infected by one phage by use of proteins that hinder the other phage from entering (Rahimi-Midani et al. 2021).

Since the problem of phage resistance is considered an emergent issue, researchers suggest different approaches to tackle this menace. The concept of using more phages for bacteria (phage cocktail) that develop different receptors or affect different cellular processes is known to minimize the chances of bacteria to evolve resistance to all the used phages. This approach of disassembling the bacterial particle makes it difficult for bacteria to evolve resistance for multiple phages (Duc et al. 2023). One strategy is using phage cocktails and switching between different phages or cocktails over time to avoid the formation of stable phage-resistant bacteria. The bacterial defense and anti-phage mechanisms such as CRISPR can also be used to improve phage action (Wang and Leptihn 2024). For instance, it is possible to alter the phage in a manner that they cannot be destroyed by the bacteria or to target undeviating bacterial processes, which would make resistance improbable (Wandro et al. 2022).

The use of phage therapy can also complement antibiotic use, especially in the promotion of bacterial eradication. Phages can degrade bacterial biofilms and decrease bacterial resistance to antibiotics, and at the same time antibiotics decrease beneficial bacteria and lower possibility of the formation of resistant mutants. Moreover, the genes encoding enzymes that break down bacterial biofilms, or interfering with the bacterial ability to communicate or form biofilms, can also be incorporated into the phages to diminish prospects of resistance emergence (Liu et al. 2023).

When the aspect concerned is the elimination of bacterial-related crop diseases, then phage therapy can easily fit into the current practice. The use of cocktails may be useful in eradicating a plurality of bacterial pathogens affecting crops in a versatile manner, that is, with a low resistance developing rate and broad spectrum action. The best approach to increase the efficacy of the entire process is to use phage therapy with other biological control agents, chemical treatments, and other practices that facilitate its application in agriculture (Villalpando-Aguilar et al. 2022). For example, phage administration along with beneficial bacteria that inhabit the biological niche of the pathogens can offer a synergistic approach to combating diseases. Supervision of the bacterial population for the growth of resistance strains and their subsequent modification in regard to phage compositions can maintain the efficiency of the phage solutions (Bozidis et al. 2024). This approach in the adaptive management can help in avoiding the occurrences of the resistance to affect the control of the diseases. Some of the methods that can be taken during the application of phages in the course of farming include timing, dosage, and phage delivery systems, and conducting field trials can increase the effectiveness of phage therapy in the farming sector (Abd-El Wahab et al. 2023)

When phage therapy is implemented as a supplementary to the existing means of combating bacterial-caused crop diseases, overall disease control is likely to be improved, chemical pesticides will be utilized sparingly, and environmentally friendly farming practices can be encouraged. This is mainly on the basis that a single strategy has its own weaknesses that can be compensated for by the other strategy to ensure there is satisfactory disease management. Taking into consideration the normalized techniques with microbes, the crop rotation, as well as sanitation measures can also improve the impact of phage factors. Moreover, raising the level of concern and knowledge among the population and the farming community in particular as to the usefulness of phage therapy and its correct application would help increase the overall rate of people and organizations embracing it as a regular practice in animal feeding.

Current approaches to phage use in agriculture

In agriculture, phages can be used as biocontrol agents to combat disease-causing bacteria in the soil microbiome (Harper 2021, Gildea et al. 2022, Nawaz et al. 2023). The high degree of specificity provided by the use of phages can be utilized to target and remove harmful bacteria responsible for or promoting diseases without adversely affecting commensal counterparts, offering an alternative to chemical pesticides and therapies and contributing to environmentally friendly and sustainable agricultural practices (Álvarez and Biosca 2017, Garvey 2022, Kuek et al. 2022). Their role extends to addressing AMR bacteria, showcasing their efficacy against strains that have developed resistance to traditional antibiotics, particularly in agriculture (Lin et al. 2017, Jo et al. 2023). Phages have been successfully applied in specific cases, such as treating bacterial spotting in soybeans, citrus, and grapes caused by antibiotic-resistant Pseudomonas savastanoi pv. glycinea (Psg) (Stefani et al. 2021). This study demonstrated that the application of phage P421 to the leaf of the soybean plant significantly reduced disease progression, and pre-inoculation of soybean seeds resulted in a significant reduction in the frequency of infected seedlings and the development rate of disease (Tarakanov et al. 2022). The use of phage-based products to mitigate disease loads on crops is permitted in the United States (US) with Environmental Protection Agency (EPA) registration, e.g. XylPhi-PD and AgriPhage^TM products. XylPhi-PD is a bactericide that has been registered by EPA to eliminate the bacterium, Xylella fastidiosa, which leads to Pierce’s disease in grapevines. Approved for organic use, it can be applied through an injection into the xylem of new growth of vines (Wilbur-Ellis 2024). AgriPhage^TM is also a certified biopesticide by the EPA, which is used to inhibit and eradicate bacteria on fruits and vegetables such as tomatoes, peppers, apples, pears, and citrus. This target pathogens such as Erwinia amylovora, the bacterium responsible for Fire Blight disease affecting apples and pears (Omnilytics 2022). Both products are commercially available (Omnilytics 2022, Wilbur-Ellis 2024).

The targeted and specific action of phages means that their use can preserve the natural microbiota balance in the environment that has been treated. Their role within the gut microbial community contributes to maintaining a healthy microbiota that can protect against harmful pathogens, such as Salmonella, preventing colonization in the digestive systems of poultry and livestock produced for human consumption and reducing the incidence of foodborne spread (Hu et al. 2018, El Haddad et al. 2022). Two recent studies demonstrated that prophylactic administration of phages significantly reduced Salmonella colonization in the guts of piglets and broiler chickens (Thanki et al. 2022, Thanki et al. 2023). Although there is a growing body of evidence to support the use of phages for such an application, there are limited commercial products available due to regulatory challenges. Access to the market remains highly regulated in most countries through stringent regulatory frameworks on antimicrobials, which poses great restraint on the introduction of new products such as phages into the agro-food chain. Presently, there is no clear path to market available for marketing phage in a broader perspective, although some individual countries may allow their use under some existing national regulations (Fernández et al. 2018).

The use of phage in agriculture presents sustainable advantages over conventional practices. It provides superior and dynamic precision over static conventional antibiotics and antibacterial chemicals through selective targeting and infection of bacteria (Jo et al. 2023). In addition, the use of phages reduces sector reliance on chemical pesticides, offering an environmentally friendly approach to pest control (Abedon and LeJeune 2005). This has prompted the integration of the EU’s Farm to Fork strategy (an initiative aimed at promoting sustainable food systems by addressing various aspects of food production, consumption, and distribution) as a sustainable farming practice which aims to decrease chemical pesticide use by 50% by 2030, endorsing the adoption of alternative methods like phage-based biocontrol (Björkbom 2023)).

The impact of phage use on crops and human gut microbiota

Wang et al. (2024) conducted the experiment of understanding whether the application frequency of the phage biocontrol against Ralstonia solanacearum phytopathogenic bacterium can be enhanced and whether the phage biocontrol gets influenced by the presence of GPSB (pathogen-suppressing bacteria) existing in the rhizosphere. It was demonstrated that the elevated usage of phages enhances R. solanacearum density control and thereby lowers bacterial wilt disease in both greenhouse and field trials using tomato. The high application frequency of the phage also helped in diversifying those resident rhizosphere microbiota and enhance several bacterial taxa that are related to the inhibition of pathogen densities. Attached to these taxa was a diverse phylum, mostly members of Actinobacteria that are associated with antibiotics production and suppression of soil-borne diseases. Thus, it was hypothesized that they might have had secondary inhibitory effects on R. solanacearum biocontrol; therefore, the isolation of Actinobacteria from Nocardia and Streptomyces genera was carried out in both in vitro and in planta assays. It was elicited from the evidence that these taxa could effectively restrict R. solanacearum multiplication and limit bacterial wilt disease, particularly when accompanied by phage cocktail (Wang et al. 2024). Considering this concept of using bacteria-destroying phage application that was proposed by Svircev et al. (2018) indicated that it can reduce the environmental impact of the antibiotic use in agriculture while presumably increasing profitability of the crop yields or preventing animal death in initial breeding phases (Svircev et al. 2018).

One of the major limitations of phages has been their host specificity, which has prevented them from being used as broad-spectrum clinical antimicrobials; specificity could, however, be an advantage when used in the form of microbiota-directing probiotics that people ingest with their food. While antibiotics often induce or aggravate microbiota imbalance or dysbiosis (Ranveer et al. 2024), phage can rather open another potential to modulate the gut microbiota in a nuanced and targeted manner. Some bacteriophages are regarded as safe for consumption by human beings, and have been approved by the US FDA. By assessing the breakdown products of a phage in the gut microbiota, it has been found that oral administration of a bacterial virus in the context of a dietary supplement in a healthy adult population was safe and generally well tolerated (Lin et al. 2022).

Febvre et al. (2019) carried out a double-blinded placebo-controlled crossover trial where they asked the participants to consume a commercial cocktail of Escherichia coli phages targeting the gut microbiota and measure its influence on mucosal and systemic inflammation among healthy adults for 28 days. It was found that there was a decrease in fecal E. coli loads, unlike the other measures of gut microbiota that appeared unchanged (alpha and beta diversities). Clostridium and Bacteroides were reduced, Eubacterium and several other unknown species were increased, and butyrate-producing specific microbial populations were changed. Short-chain fatty acid levels and most inflammatory markers and lipid metabolism were not different from the baseline, other than Il-4, which was numerically significantly lower with fecal microbiota transplantation). This implied that phages could selectively limit the subjective bacteria while not affecting the general gut microbiota (Febvre et al. 2019).

Among Bacteroides, Firmicutes (such as Clostridium, Lactobacillus, and Ruminococcus), Actinobacteria (including Bifidobacterium), Proteobacteria (though generally in smaller numbers), and Verrucomicrobia (such as Akkermansia) are usually found in the human gut. They are involved in varied processes in the human body, including food digestion, vitamin production, and acting as guards against invasion by pathogenic organisms (Hou et al. 2022). While phages can influence the bacterial concentration inside the human gut and can also kill bacterial cells, their presence can have an immense impact on the human gut microbiota in terms of avoiding overgrowth of any specific type of bacteria while maintaining the right balance. This regulation often assists in the prevention of dysbiosis, which is the imbalance in the gut microbiota related to problems like inflammatory bowel disease, obesity, and metabolic syndrome (Emencheta et al. 2023). Phages contribute to horizontal gene mobile transfer between bacteria that allows the exchange of useful genes or metabolic pathways such as phage resistance and metabolism within the context of the gastrointestinal tract. A positive effect of this process is the ability to increase the relative stability of the microbial structure and, therefore, improve the ability of the microbial community to adapt when exposed to unfavorable conditions or stress factors (Borodovich et al. 2022).

Applications of phages for climate-resilient agriculture

The application of phages in agriculture further presents an avenue for improving climate resilience in the pursuit of sustainable farming practices. By utilizing the natural predatory relationship between phages and bacteria, solutions can be developed to curb the challenges posed by climate change and promote eco-friendly farming methods in agricultural systems. Table 1 shows the diverse applications of bacteriophage in agriculture, and highlights the important role they play in improving plant health and yields and pioneering sustainable pest management solutions that are in harmony with the environment. The application of phages will be discussed in more detail in this section.

Table 1.

Applications of phages in climate-resilient agriculture.

Application Area	Description	Examples
Enhancing Crop Climate Resilience	Phages control plant-microbe interactions, enhancing tolerance to environmental stress.	Combatting R. solanacearum in various crops [125]
Sustainable Agricultural Practices	Serve as the alternative to chemical pesticides and antibiotics, aligning with sustainable farming practices.	Reducing the need for harmful substances in agriculture [57]
Improving Soil Health	Affects soil bacterial communities, promoting diversity, and stability.	Increasing microbial diversity and nutrient cycling [82]
Food Security	Rapidly destroy harmful bacteria, serving as natural food preservatives, reducing waste, and risk of foodborne illness.	Managing bacterial infections in dairy, meat, fruits, and vegetables [86]
Boosting Plant Growth and Yield	Promote soil bacteria, aiding stress resistance and nutrient uptake, and improve plant immunity against pathogens. They enhance soil health and plant vitality, boosting crop resilience to climate change.	Promoting plant growth, enhancing soil microbiomes, and engineering stress-resistant traits [89].
Managing Water Resources	Manage water quality by eliminating pathogens and indicating contamination, ensuring safety and sustainability in various water systems.	Treating water, reducing pollution, and detecting contamination in aquaculture, drinking water, and recreational water [93].
Supporting Pollinator Health	Protects pollinators from bacterial infections, preserving their vital role in plant reproduction and ecosystem resilience.	Phages target bacterial infections in pollinators, ensuring their survival and reproductive success [99].
Adapting to New Pests and Diseases	Offers targeted control against bacterial infections, overcoming antibiotic resistance, and evolving to counter new agricultural threats.	Phages combat antibiotic resistance, manage bacterial infections, and develop solutions for new agricultural challenges [100].

Enhancing crop climate resilience

Bacterial populations that exist in the environment help plants to solubilize nutrients, produce hormones, induce systemic resistance, and modulate plant gene expression by contributing to increased plant growth and productivity (Rogovskii et al. 2021). Phages can improve crop climate resilience by regulating interactions between plants and microbes. Preventing infectious disease and dysregulation of the microbial communities that exist synergistically with plants enhances tolerance to environmental stresses like heat, salinity, drought, and pests. Phages can affect the plant microbiome through various mechanisms. They can be used to combat pathogenic bacteria through targeted killing, decreasing the infection rate, and protecting crops from diseases. Climate change is increasing the incidence of wilt within populations of these economically relevant crops and phages provide a reliable, sustainable, and effective solution to this. By reducing damage from bacterial pathogens like R. solanacearum, which causes bacterial wilt in a variety of crops, they can also improve crop resilience (Abedon and LeJeune 2005). In addition, phages modify the interactions and aggressive relationships among bacterial groups in the plant microbiome. In this manner, they assist in forming the range and balance of the microbiome, which subsequently affects the fitness and overall performance of the plant life they inhabit (Baliyan et al. 2022, Hayat et al. 2023). A study by Yang et al. (2023) used metagenomics and direct experiments to causally test if differences in rhizosphere phage communities could explain variation in soil suppressiveness and bacterial wilt plant disease outcomes by plant-pathogenic R. solanacearum bacterium. Specifically, they tested two hypotheses. First, healthy plants are associated with stronger top-down pathogen control by R. solanacearum-specific phages (i.e. “primary phages”), and second “secondary phages” that target pathogen-inhibiting bacteria play a stronger role in diseased plant rhizosphere microbiomes by indirectly “helping” the pathogen. The study showed that rhizosphere phage communities can drive soil suppressiveness to bacterial wilt disease caused by R. solanacearum, a plant-pathogenic bacterium. They found that healthy plants were associated with higher abundances of R. solanacearum-specific phages that exerted strong top-down control of the pathogen density. They also found that secondary phages that targeted pathogen-inhibiting bacteria were more abundant in the diseased plant microbiomes, indirectly helping the pathogen. They validated these findings in greenhouse experiments and demonstrated that phages can reduce soil suppressiveness both directly and indirectly. Together, Yang et al. (2023) findings demonstrate that soil suppressiveness, which is most often attributed to bacteria, could be driven by rhizosphere phage communities that regulate R. solanacearum densities and strength of interference competition with pathogen-suppressing bacteria. Rhizosphere phage communities are hence likely to be important in determining bacterial wilt disease outcomes and soil suppressiveness in agricultural fields. Another study by De Carato (2020) reviewed the potential of soil microbiota manipulation to suppress soil-borne diseases and enhance crop productivity. The study highlighted the role of biocontrol agents, such as bacteria, fungi, and phages, in modulating the soil microbiome and antagonizing plant pathogens.

Sustainable agricultural practices

The current reliance on pesticides and antibiotics in agriculture is considered unsustainable since it has led to the ineffectiveness of biocontrol agents due to the development of resistance in bacterial species. Moreover, it has been demonstrated that the use of these chemicals is not environmentally beneficial as they have the potential to pollute the soil, water bodies, grasslands, and various plant life (Malagón-Rojas et al. 2020). Phages are, therefore, now being employed as a sustainable remedy to reduce the need for these harmful substances in agricultural practices (Nawaz et al. 2023). The use of phages in agriculture aligns with sustainable farming practices by offering an effective, environmentally friendly alternative to chemical pesticides and antibiotics. In the face of climate change, phages will adapt to their hosts (Nawaz et al. 2023), enabling both prevention and treatment of bacterial diseases at all levels, including water, soil, plant, and animal, as well as during the processing of crops and animals, respectively. Phage targeting unfavorable bacteria promotes healthy microbiomes, and as the profile of the healthy microbiome changes, phages will co-evolve to remain predatory (Rogovski et al. 2021) to their target bacterial host and continue to promote the productivity and resilience of crops.

Phages have the potential to, promote plant and animal growth, and prevent and treat bacterial diseases (Rogovski et al. 2021) and desired properties to be enhanced through selection or engineering, e.g. to broaden host range and withstand temperature, salinity, pH, and other environmental changes (Svircev et al. 2018). By serving as an alternative, phages have the potential to eliminate the adverse effects on the environment and biodiversity associated with the use of chemical pesticides and antibiotics in agriculture (Nawaz et al. 2023).

Chemical pesticides and antibiotics can remain active as a contaminant of water and soil, disrupting the balance of microbial populations, and jeopardizing the health of wildlife and people by causing microbial dysbiosis. Unlike chemical pesticides and antibiotics, phage-based biocontrol agents do not affect non-target organisms, do not leave hazardous metabolites behind, are effective against antibiotic-resistant bacterial hosts, and co-evolve against targeted bacteria that have become phage-resistant to maintain effectiveness. Without endangering beneficial microorganisms or the environment, phages can be employed to target particular bacterial illnesses in cattle and crops. Conversely, phages are self-amplifying, self-limiting, specialized, and biodegradable (Svircev et al. 2018, El-Sayed and Kamel 2020). They only replicate while their bacterial hosts are present. By stopping the spread of bacterial illnesses, phages can also contribute to the preservation of the genetic variety of plants and animals (Zia and Alkheraije 2023). Phages can help manage bacterial infections in dairy products like cheese, yogurt, and milk, as well as in cattle, like mastitis, diarrhea, and respiratory diseases. In this example, phages are viable tools for the implementation of a sustainable dairy chain.

Improving soil health

The output of crops and food security are anticipated to be significantly impacted by climate change because of variations in temperature, precipitation, CO₂ concentration, and extreme weather. Additionally, soil health and the relationships between soil microbes and plants can be impacted by climate change (Raza et al. 2019). For instance, the makeup and activity of soil bacteria can change due to climate change, which can have an impact on the decomposition of organic matter, the cycling of nutrients, and the prevention of illness. By changing plant physiology, immunology, and phenology, climate change can potentially impact a plant’s vulnerability to bacterial infections (Nakayinga et al. 2021). As previously mentioned, unlike chemical pesticides and antibiotics, the application of phages targets unfavorable bacteria while leaving beneficial bacteria unharmed. In this way, the phages help to preserve the diversity and balance of the bacteria in the soil and surrounding environment. The interplay of biological, chemical, and physical elements, including soil microbes, determines the health of the soil (Raza et al. 2019, Nakayinga et al. 2021).

The decomposition of organic matter, the stimulation of plant development, the inhibition of disease, and the cycling of nutrients are all facilitated by soil bacteria. Predation, competition, drought, salinity, and temperature are just a few of the biotic and abiotic stressors that affect the soil microbiome. By adjusting soil bacterial diversity, abundance, and activity, targeted phages can affect soil resilience and health. The diversity and stability of soil bacterial communities can be modulated by phages, which can decrease the number of pathogenic or unfavorable dominant bacteria (Musheer et al. 2020, Waturangi et al. 2021). Enhancement of soil health contributes to resilience towards climate-prompted stressors, which include drought, salinity, and temperature fluctuations, helping sustainable crop production in the long run.

The use of phages in agriculture highlights a promising road for boosting weather resilience in crops. Phages provide targeted control of climate-induced bacterial infections and promote soil and crop health as well as their productiveness amidst climate-induced stressors. They additionally make contributions to soil health by improving microbial range and nutrient cycling while stimulating plant growth through diverse mechanisms. However, interactions among phages, bacteria, the organisms that harbor them, such as plants, animals, and insects, and the environment are complex, requiring a greater understanding of the interactions as well as the persistence and spread of the applied phages to mitigate unforeseen consequences. Integrated tactics are therefore needed to maximize the benefits of utilizing phage to promote sustainable crop resilience in the face of climate change (Musheer et al. 2020).

Food (and feed) production

Climate change can increase food safety risks by creating situations conducive to the increase and spread of pathogenic bacteria (Duchenne-Moutien and Neetoo 2018). Numerous tactics, including the use of different chemical antibacterials, have been employed to lessen the contamination of food with harmful bacteria; however, these are static and have unintended side effects, such as consumer allergic reactions and the emergence of bacteria that are resistant to the antibacterial agent. The vulnerability of the food supply chain is better served with a dynamic and sustainable solution to eliminate bacterial contaminants. Phages provide a rapid and selective approach to controlling the bacteria, promoting food safety in the face of climate-associated changes in environmental conditions (Waturangi et al. 2021). The abundance of phage in our environment, our constant exposure to phage, ability of phages to rapidly destroy the targeted harmful bacteria, and self-dose make them suitable for use as a natural antibacterial for foods before, during, and after production and/or processing. Only obligately lytic phages incapable of genetic transduction that target specific (unfavorable) bacteria are candidates for application in the food industry as an antibacterial (Martínez et al. 2019). Qualified phages can be mixed to expand the bacterial host range and can also be selected under pressure to enrich for desired enhanced properties, which directly contributes to climate-resilient and sustainable use of phages.

Mixtures of phages are employed as a natural, dynamic, and efficient means of managing bacterial contamination and spoilage in food items, including certain raw and/or ready-to-eat dairy, pork, poultry, eggs, red meat, beef, fresh and saltwater seafood (fish and shellfish) as well as fresh and processed fruits and vegetables (Waturangi et al. 2021). Currently, existing methods for extending the shelf life of items include biopreservation using antibacterial chemicals derived from plants or protective bacterial cultures and their antimicrobial products (Waturangi et al. 2021). As an alternative to chemical antibiotics, phage-based strategies to Lysins, the phage component that elicits bacterial cell death, are an emerging type of biological antibacterial for foods. These enzymes function as antibacterial agents by rupturing bacterial membranes without external exposure to the cell; however, lysins are not self-dosing and unable to adapt to bacteria resistant to their bactericidal effect (Ramos-Vivas et al. 2021).

Boosting plant growth and yield

Climate-related conditions, which include drought, salinity, heat, and nutrient shortages, can negatively affect plant growth and productivity. Phages can assist in mitigating those effects by promoting the proliferation of plant growth-promoting bacteria (PGPB) in the soil microbiome, which is the microbial population that resides in and around the roots and leaves of plants (Fiodor et al. 2021). Plant growth, well-being, and ability to endure stress can all be influenced by the microbiome of the plant. Through the secretion of different metabolites and hormones, nitrogen fixation, and mineral solubilization, PGPB can increase plant development and promote soil bioremediation.

In this context, phages can be utilized to promote plant growth by targeting and eradicating unfavorable bacteria that oppose or compete with PGPB. Phages can shape plant microbiomes through immune system modulation. Plant defense mechanisms against pathogens, including the release of ethylene, salicylic acid, jasmonic acid, and reactive oxygen species, can be triggered by phages (Poria et al. 2022). The activation of genes that improve plant development and resilience to biotic and abiotic stressors can be activated by these signaling molecules. Additionally, plant defense mechanisms against beneficial bacteria, such as the inhibition of nitric oxide and callose deposition, can be suppressed by phages. These processes may make it easier for PGPB to colonize and form symbiotic relationships with plants (Jones et al. 2012, Poria et al. 2022).

Climate-related challenges relevant to agriculture such as drought, salinity, heat, and nutrient shortages make the use of phages to increase plant growth and yield particularly pertinent. Plant development and production can be adversely affected by specific environmental stresses, and they can also make plants more vulnerable to disease. Phages enable selective editing of unfavorable bacteria from the soil and/or plant microbiome to promote plant health furthermore, phage can be engineered to deliver genes to commensal bacteria in the plant microbiome that encode for stress-related proteins such as thermal shock proteins, oxygen-preserving substances, and antioxidants, to improve plant stress resistance and improve crop resilience to conditions brought about by climate change, thereby addressing the impact of climate change on agriculture (Jones et al. 2012, Poria et al. 2022, Fasusi et al. 2023).

Managing water resources

Phages have the potential to be utilized as water management tools for monitoring and ensuring the safety of available water to address water scarcity (Jassim et al. 2016). They offer a variety of possible uses in the management of water resources, particularly when it comes to reducing water pollution and recycling water (Batinovic et al. 2019). Pathogenic bacteria present in wastewater, such as Salmonella, Vibrio, Legionella, and E. coli, can be reduced or eliminated by phages. Aquaculture, wastewater, drinking water, and recreational water are just a few of the environments where phages have been effectively used to address bacterial contamination (Ji et al. 2021).

When detected in water samples, phages signal potential contamination with fecal matter, which may contain harmful pathogens such as bacteria and viruses. As they can help determine the presence of human or animal waste, phages can also be employed as markers of viral or fecal pollution in water. Phages can reside longer in water than bacteria and offer a more accurate indicator of water quality because they are more resilient to environmental stresses.

Supporting pollinator health

Pollinators consisting of bees, butterflies, moths, flies, and beetles are critical for the reproduction of many flowering plants and crops (Khalifa et al. 2021). However, they face numerous challenges, including infections, invasive species, habitat loss, chemical exposure, and parasites (Khalifa et al. 2021, Proesmans et al. 2021). Climate change can further contribute to these challenging situations by changing habitat suitability, increasing the prevalence of pathogenic bacteria, and disrupting pollinator-plant interactions. Climate change can also affect pollinators by changing plant phenology, transferring the distribution of floral resources, and increasing the frequency and depth of extreme weather events. These adjustments can exacerbate present stressors on pollinator populations, making them more vulnerable to diseases (Proesmans et al. 2021).

Phages could be utilized to protect pollinators from bacterial infection. Many flowering plants and crops depend on pollinators for their reproduction. Bacterial infections can seriously impair pollinators’ ability to survive, reproduce, and carry out their necessary pollination activity. For instance, the bacteria Paenibacillus larvae cause the highly contagious and fatal disease known as American foulbrood in honey bees. Spiroplasma bacteria can also infect butterflies and bumblebees, shortening their lives and decreasing their fertility.

Without affecting the environment or the favorable bacteria in pollinators’ microbiomes, phages can be utilized to target and eradicate particular bacteria and prevent or treat diseases. Phages can be included in pollen or nectar of blooming plants, or they can be delivered to pollinators indirectly, such as by spraying them on bee colonies or adding them to sugar water (Sieiro et al. 2020). Phages provide a focused and environmentally friendly method to defend pollinators from bacterial infections, thereby improving their potential to deal with climate-associated challenges and contributing to the resilience of pollinator-established ecosystems.

Adapting to new pests and diseases

Climate change is expected to lead to shifts in the distribution and abundance of pests and pathogens, creating new challenges for agricultural production. As an alternative to antibiotics, phages have been suggested for improving the safety and quality of soil, water, and food as well as managing bacterial infections in plants and animals. Specificity, adaptability, self-dosing ability, tolerability, and efficacy against bacteria, including AMR forms, and ease of genetic modification are some of its advantages over antibiotics (Fernández et al. 2018). The fast adaptation of bacteria to phage infection, which can lead to the emergence of phage-resistant strains, is one of the primary obstacles to using phages in agriculture. Phages, on the other hand, evolve to circumvent the bacteria’s resistance mechanisms. The common strategy to overcome the emergence of phage resistance is to employ a mixture of phages with varying but complementary properties (e.g. targeting different host receptors).

As a tool, phages are adaptable to changing pest and disease situations. The application of phages can take various forms, including spraying, dipping, irrigation, injection, and oral administration, contingent upon the organism to be targeted and the surrounding conditions. To increase their durability and effectiveness, phages can also be mixed with other biocontrol agents such as fungi, insects, or beneficial bacteria. Furthermore, it is possible to modify phages to express desired characteristics such as increased host range, lytic activity, stability, or delivery (Rogovskii et al. 2021).

Commercial applications of phages in agriculture

For the commercial application of phages in agriculture, certain lifestyle characteristics are essential. The phages must have an obligately lytic lifestyle, ensuring that they consistently lyse and kill the host bacteria upon infection, which is crucial for managing bacterial populations that threaten crop health (Buttimer et al. 2017). Their genome should be free of attachment sites, integrase genes, bacterial virulence factors, and antibacterial drug resistance genes, which means they cannot integrate into the host’s genome or contribute to the spread of virulence and resistance (Villalpando-Aguilar et al. 2022). Phages should also be incapable of both specialized and generalized transduction, preventing them from transferring bacterial DNA thereby avoiding the spread of unwanted genetic material among bacterial populations. When applicable, the phage must possess the ability to penetrate biofilms, which is a common defense mechanism among bacteria, particularly in phytopathogens that affect crops (Abedon et al. 2021). The ability of phage to eradicate biofilms and infect the target bacterial cells within is a distinct advantage over chemical antibiotics that cannot breach the protective biofilm barrier (the bacteria within biofilm are resistant to traditional chemical antibiotics).

Functionally, these phages are required to eliminate target bacteria that are pathogenic or otherwise undesirable, which can help in creating favorable population dynamics. They can also be engineered to deliver genes that confer advantages to non-pathogenic bacteria, such as osmoprotectants that help bacteria—and, by extension, crops—tolerate stressful conditions like drought (Jaglan et al. 2022). The use of a combination of different phages, known as a cocktail, can extend the range of target bacteria or introduce multiple beneficial genes, thus increasing the effectiveness and adaptability of phages in agricultural applications. This biotechnological approach holds promise for enhancing crop protection and productivity in a sustainable manner (Jo et al. 2023).

In the agricultural sector, the use of both naturally isolated and engineered phages is gaining traction for their potential to protect crops and promote sustainable farming practices (Svircev et al. 2018). Monophage products, which consist of a single phage type, and multi-phage cocktails that combine various natural and engineered phages, are being explored for their efficacy in this field. Naturally occurring phages can replicate within specific bacterial hosts found in agricultural settings, while genetically engineered phages can be tailored to a particular bacteria strain/species or act as delivery vehicles for beneficial genes. These genes could be carried in the phage genome or within plasmids, and they can be designed to target either harmful bacteria that affect crop health or beneficial commensal bacteria that can enhance plant growth and resilience, such as by delivering genes that improve drought resistance (Villalpando-Aguilar et al. 2023). The action of these phages can vary; some may inhibit bacterial growth (bacteriostatic), while others may kill bacteria (bactericidal). Certain phages are also capable of penetrating biofilms, which is particularly important for reaching bacteria that form protective layers around themselves, a common mechanism of antibiotic resistance in plant pathogens (Svircev et al. 2018).

Companies like Omniltyics and A&P Inphatec have developed registered phage products for this purpose. Omniltyics offers a range of AgriPhage™ products, each designed to combat specific bacterial pathogens affecting crops such as tomatoes, peppers, apples, and pears. These products are recognized as Phage Bactericide by the US EPA and are certified organic by USDA OMRI. A&P Inphatec’s XylPhi-PD™ is formulated to prevent and treat Pierce’s Disease in grapevines, caused by the bacterium X. fastidiosa, and holds similar certifications. XylPhi-PD, manufactured by A&P Inphatec, is a bacteriophage-based bactericide for treatment and prevention use in grapevines that infects and kills X. fastidiosa, the cause of Pierce’s Disease (Fortuna et al. 2023, El-Shibiny and El-Sahhar 2017, Vandamme and Mortelmans 2019). XylPhi-PD may be used in certified organic production or food processing and handling according to the United States Department of Agriculture (USDA) Organic Program regulations (listed by the Organic Materials Review Institute [OMRI]) (Rogovskii et al. 2021). OmniLytics, Inc. has five agriculture phage-based bactericides registered for use on tomatoes, peppers, apples, pears, citrus, peaches, cherries, almond, walnut, and hazelnut (AgriPhageTM-Spot and Speck, AgriPhageTM-Tomato Canker, AgriPhageTM-Fire Blight, AgriPhageTM-Citrus Canker, AgriPhageTM-Nut and Stone Fruit). The use of such phage products represents a significant advancement in sustainable agriculture, providing farmers with effective tools to protect their crops while minimizing environmental impact.

Table 2 provides an overview of various agricultural phage products, their target bacteria, and relevant certifications.

Table 2.

Commercial phage products and their target bacteria.

Company	Phage product(s)	Target bacteria and organism treated	Registration and certification
Omnilytics	AgriPhageTM-Fire Blight AgriPhageTM-Citrus Canker AgriPhageTM-Spot and Speck AgriPhageTM-Tomato Canker AgriPhageTM-Nut and Stone Fruit	Targets include Xanthomonas campestris pv. vesicatoria, Pseudomonas syringae pv. tomato, Clavibacter michiganensis subsp. Michiganensis, Xanthomonas citri subsp. citri, Erwinia amylovora, Xanthomonas arboricola pv. pruni, Xanthomonas arboricola pv. juglandis, Xanthomonas arboricola pv. corylina. Treat crops, including tomatoes, peppers, apples, pears, citrus, peaches, cherries, almonds, walnuts, and hazelnuts.	Phage Bactericide, US EPA Organic, USDA OMRI HC iLONO
A&P Inphatec	XylPhi-PDTM	Prevent/treat grapevine Pierce’s Disease caused by Xylella fastidiosa.	US EPA OMRI
Intralytix	ListShieldTM SalmoFreshTM EcoShieldTM ShigaShieldTM	Listeria monocytogenes Salmonella spp. (Typhimurium, Enteritidis, Heidelberg, Newport, Hadar, Kentucky, Thompson, Georgia, Agona, Grampian, Senftenberg, Alachua, Infantis, Reading, Schwarzengrund) Shigella spp. E. coli O157:H7.	US FDA GRAS HC iLONO Israel MH Star K-certified kosher, IFANCA-certified halal OMRI
Proteon Pharmaceutical	Bafacol® Bafasal + G® Bafasal Bafador®	Feed additive to prevent Avian pathogenic E. coli Feed additive to prevent Salmonella in poultry Feed additive to prevent Salmonella in poultry Feed additive to prevent Pseudomonas and Aeromonas in pond-based aquaculture.	EFSA (Bafasol) CAAI (Bafador)

For agricultural applications, it is crucial to thoroughly characterize all phages, whether natural or engineered. The development of engineered phages may require more resources to create, optimize, and characterize compared to natural phages. There are also regulatory considerations, such as whether engineered phages can be certified as organic or receive a Generally Recognized As Safe (GRAS) designation, which is particularly relevant for crops intended for organic markets. GRAS (Generally Recognized As Safe) bacteriophage products are innovative solutions in the food safety industry, harnessing the specificity of phages to target and neutralize harmful bacteria. These products contain carefully selected phages or phage cocktails that can effectively combat bacterial strains like Salmonella, ensuring the safety of various food items (Batinovic et al. 2019). Companies such as Micreos and GPIBiotech have developed such products, which have undergone rigorous GRAS evaluations. For instance, Micreos’s Salmonelex utilizes F018 and S16 phages against Salmonella enterica, applied to pork, poultry, and seafood to maintain food safety (Williams 2018). These phage-based interventions are pivotal in enhancing food quality and consumer protection, marking a significant shift towards natural and precise antimicrobial strategies.

Market acceptance of phage products, whether natural or engineered, is an important factor to consider, especially if the products claim antibacterial properties. In such cases, bacterial surveillance and monitoring of the activity of the phages may be necessary to ensure ongoing effectiveness, which might involve updating the phage strains used in the products.

Establishing the presence of a true obligate lytic phage implicates several challenges because of the layers of complexities involved in phage-host interactions, as well as the constraints of the techniques available to detect phages (Jia et al. 2023). Spiralling across the bacteria cell wall and membrane, entering it and using the bacterial DNA as the substrate for new phage particles and destroying the bacterial cell in the process, this characteristic sets the obligate lytic phages apart from temperate phages, which undergo the lysogenic cycle in addition to the lytic one (Venturini et al. 2022). This characteristic is important, especially in the application of phage therapy, where the aim is to totally clear bacterial pathogens without danger of conversion to lysogens.

Most of the time, samples collected from environmental sources consist of a number of phages, which are both lytic and temperate, and thus it is challenging to obtain samples comprised of obligate lytic phages only (Hyman 2019). Genomic data are often sparse or have imperfections in terms of annotation, this hinders the identification of genes that influence. Also, while infected with some phages, the bacteria may undergo the lysogenic cycle, and during this stage, temperate phages integrate their DNA with the bacteria and do not lyse the host. Biochemical tests that rely on cell lysis would not detect these dormant phages. Even obligate lytic phages might be influenced by environmental conditions, and the presence of stressors could potentially trigger a dormant temperate phage within a lysogenic bacteria to switch to the lytic cycle (Doss et al. 2017). Hence, biochemical tests alone may be insufficient to confirm whether a phage is strictly obligate lytic.

Genome sequences can be compared between phages using bioinformatics, and one can determine whether or not the genes involved in lysogeny are present, as integrase/repressor gene sequences will be present in lysogeny. The integrase gene encodes an enzyme that allows the phage genome to integrate into the host bacteria’s chromosome, while the repressor gene produces a protein that represses the genes responsible for the lytic cycle (Fogg et al. 2011). Together, they ensure the phage stays integrated with the bacteria and replicates along with it without immediately destroying the host. Phage Search Tool Enhanced Release (PHASTER) can identify phages that infect and lysogenize bacteria, and what regions in the bacterial genomes can be liable to phage lysogeny. When analyzing genomes of the phages, they should be compared with the obligate lytic and temperate phages to find out more obligate lytic-phage specific genes (Arndt et al. 2019). Based on the genomic characteristics, the phage can be categorically categorized as lytic or temperate using training sets of phylogenetic data (Boeckman et al. 2022). However, additional techniques might be needed for definitive obligate lytic phage identification due to limited specificity in phage identification (lack of identifiable lysogenic features) and imperfect phylogenetic training caused by immense phage diversity (Zrelovs et al. 2021). Some CRISPR spacers originate from phage genomes that may have infected bacteria in the past, which suggests that analysis of CRISPR spacer sequences can give indications of previous phage infections (Dion et al. 2021). When spacers coincide with phage sequences, it implies an encounter and may even shed light on the lifestyle of the referenced phage.

An easy and efficient method of detecting lytic phages is by performing serial dilution on bacterial lawns and conducting plaque assays in order to observe the formation of clear plaques as a sign of cell lysis (Glonti and Pirnay 2022). However, this is not decisive for obligate lytic behavior anyway but only representative for the facultative lytic growth behavior at least. Another method of testing for the inability to form lysogens is to check on the result of the bacterial culture once it has been lysed to establish whether or not it is able to resume growth again (Al-Anany et al. 2021). Hosts for true obligate lytic phages can be reproduced only if the bacteria do not survive. Another approach includes exposing bacterial cultures infected with candidate phages to agents that induce lysogenic cycle in temperate phages (e.g. mitomycin C) (Vu et al. 2024). An obligately lytic phage represents a phage that could not respond to induction or was not able to be induced at all (Zhang et al. 2022). By directly illustrating the lytic cycle of phage infection and replication without any sign of a lysogenic phase through the use of electron microscopy, the cycles within bacterial cells can be presented. PCR can be used to detect the presence of lysogeny that is associated with certain genotypes such as integrase. After transferring the bacterial culture to a new tube, diluting it, and centrifuging it, quantitative PCR can be used to determine the replication rate of the phage making it easier to differentiate between lytic and temperate cycles (Refardt 2012).

To increase the overall efficiency in deciphering true obligate lytic phages, it is effective to integrate informatics and wet lab approaches. For example, the list of candidates for further consideration can be shortened by using bioinformatics screening for the exclusion of lysogeny-associated genes, whereas columnar assays consisting of plaque assay and induction tests will determine their obligate lytic genotype and phenotype in a laboratory setting. Thus, with the help of task-oriented interdisciplinary methods and approaches, it is possible to increase the efficiency of the identification and confirmation of obligate lytic phages for purposes of phage therapy or other future biotechnological pursuits.

Challenges and future directions

In exploring the potential of phages, we must acknowledge the challenges that accompany their integration into agricultural practices. The fragility of the protein capsid and tail and nucleic acid core of phages makes them susceptible to physical stressors in agricultural environments, potentially limiting their stability and effectiveness. A whole virus particle typically comprises an inner nucleic acid core (either DNA or RNA), an exterior protein shell known as a capsid, and a capsid-protruding protein tail that confers specificity and enables infectivity (Burrell et al. 2017). Agricultural settings expose phages to various stressors, such as UV radiation, temperature fluctuations, desiccation, moisture availability, acidic conditions, and other environmental conditions, potentially affecting their viability and performance (Gomez et al. 2022, Gayder et al. 2023, Jo et al. 2023). For instance, inadequate nutrition, poor environments, and transitions to stationary growth phases reduce phage infection productivity (Fister et al. 2016). Depending on their properties, such as morphology, phages can tolerate different amounts of acidity; nonetheless, most become vulnerable when the pH falls below 4 (Jurczak-Kurek et al. 2016). Phages often exhibit high host specificity, which is generally considered to be a benefit of their use; however, in some cases, this can limit their effectiveness to specific bacterial strains and necessitate the identification and isolation of multiple phages for different strains within a species (Zhan et al. 2015, Jeon et al. 2016).

Engineering approaches, such as modifying phages to expand their host range, are being investigated to overcome the limitations of their narrow specificity in phage therapy (Hibstu et al. 2022). Just as with antibiotics, there is a risk of bacteria developing resistance to specific phages over time through spontaneous mutations and acquisition of a restriction-modification system, necessitating continuous monitoring and adaptation of phage treatments (Ling et al. 2022). Phages may need to be formulated to improve their availability and practicality in agricultural applications. For instance, phage preparations typically require refrigerated storage (2–8°C), emphasizing proper temperature control to maintain their efficacy (Moye et al. 2018).

Obtaining regulatory approval for the use of phages in agriculture can be challenging. In many regions, clear guidelines and standards are needed to navigate regulatory processes and adequately understand the risks and benefits. Adherence to Good Manufacturing Practices (GMP) is required for phages to ensure that products are manufactured in a consistent and controlled manner (controlled according to predefined quality standards) (Liu et al. 2023, Yang et al. 2023). Integrating phages into existing agricultural practices and systems may require adjustments and education for farmers to adopt these biocontrol agents effectively. Educational programs must be implemented to familiarize farmers with the benefits and application of phages in biocontrol (Vázquez et al. 2022) as opposed to traditional chemical antibacterials, based on robust data on phages in controlling bacterial diseases in crops (Kuek et al. 2022). Agricultural extension services must be engaged to disseminate knowledge and support farmers in adopting bacteriophage-based biocontrol (Kuek et al. 2022). Ultimately, integration of phages as biocontrol agents needs to be as simple as possible, e.g. occur without overhauling existing production pipelines, minimizing disruptions for farmers, and economical (Huss and Raman 2020).

Current research explores the diversity of phages to find those with high specificity against harmful bacteria and optimize delivery systems to ensure phages reach their target sites on plants and effectively combat bacterial infections (Lin et al. 2017, Jia et al. 2023, Ranveer et al. 2024). Researchers are studying factors influencing phage stability and survival under varying conditions (Jończyk et al. 2011, Ly-Chatain 2014, Selcuk et al. 2024). The potential development of new phage strains for climate-related challenges in agriculture involves creating tailored solutions, including heat-resistant and drought-tolerant phages (Svircev et al. 2018), targeting emerging pests and pathogens influenced by climate change (Pandit et al. 2022), enhancing plant stress tolerance (Villalpando-Aguilar et al. 2022), adapting to altered growing seasons (Singh et al. 2023), formulating versatile phage products for diverse environments (Villalobos-López et al. 2022), and considering ecological impacts (Meaden and Koskella 2013), all contributing to climate-resilient and sustainable agricultural practices. At the end of the supply chain, incorporating phages into food items as preservatives can prolong their freshness. The market already offers a variety of these preservatives. Research by NexaBiome has shown that using a mix of phages targeting a spoilage strain of P. fluorescens can enhance the shelf life of salads by 50% (equivalent to one additional day), especially when the phages are attached to the packaging itself. It is anticipated that refining this mix of phages could lead to even greater extensions in shelf life (NexaBiome 2022).

Table 3 outlines such challenges, from their narrow host range to the regulatory and public acceptance hurdles that must be addressed. It emphasizes the significance of the research, regulatory framework improvement, and public engagement to harness the benefits of bacteriophage for climate-resilient agriculture.

Table 3.

Challenges and future directions in bacteriophage use.

Challenge	Description	Future directions
Limited host range	Phages are highly specific, which may limit their application across diverse pathogens.	Research into broadening host range through multi-phage mixtures and genetic engineering
Environmental stability	Stability and efficacy can be affected by pH, temperature, UV light, and soil type.	Developing formulations to enhance stability under environmental conditions
Regulatory hurdles	The lack of clear regulatory frameworks can impede the use of phages in agriculture.	Establishing clear guidelines and standards for phage use in agriculture
Public acceptance	Concerns over safety and unfamiliarity with phages may hinder adoption.	Education and awareness programs for farmers and consumers
Continuous evolution of resistance	Bacteria can develop resistance to phages, necessitating ongoing adaptation.	Leveraging bacteriophage adaptability and exploring synergies with other biocontrol agents

Conclusion and recommendation

Phages offer diverse solutions to climate change-related challenges in agriculture. They have the potential to be utilized as suitable biocontrol agents capable of enhancing crop resilience, reducing the use of chemical pesticides and thus promoting sustainable agricultural practices, improving soil health, preserving food, boosting plant growth and yield, managing water resources, supporting pollinator health, and mitigating emerging pests and bacterial diseases. However, challenges such as limited host range, environmental stability, and regulatory hurdles are crucial to be addressed to fully utilize their full potential in agriculture. To facilitate their integration into agricultural systems and maximize their benefits, it is recommended that research and development efforts be prioritized to understand phage diversity and stability mechanisms in the agriculture environments; clear regulatory frameworks should be established for their use; farmer education programs should be implemented to promote adoption; foster collaboration among stakeholders; and invest in innovation and technology transfer to scale up production and distribution. By implementing these recommendations, agriculture can effectively harness the capabilities of phages to mitigate the adverse effects of climate change, promote sustainability, and ensure food security in a changing climate.

Author contributions

Kehinde Favour Siyanbola (Conceptualization [Equal], Writing – original draft [Equal], Writing – review & editing [Equal]), Ovinuchi Ejiohuo (Writing – original draft [Equal], Writing – review & editing [Equal]), Olusegun A. Ade-adekunle (Writing – original draft [Equal], Writing – review & editing [Equal]), Feranmi O. Adekunle (Writing – original draft [Equal], Writing – review & editing [Equal]), Helen Onyeaka (Conceptualization [Equal], Supervision [Equal], Validation [Equal], Writing – original draft [Equal], Writing – review & editing [Equal]), Carrie-Lynn Langlais Furr (Validation [Equal], Writing – review & editing [Equal]), Francesca E. Hodges (Writing – review & editing [Equal]), Pedro Carvalho (Writing – review & editing [Equal]), and Elijah Kolawole Oladipo (Writing – review & editing [Equal])

Conflict of interest

The authors declare no conflict of interest.

Funding

No funding received.

Data availability

This is not applicable as no new data were generated