Phage bioaugmentation reveals the potential of lysogeny for soil bioremediation

Abstract

Pollution of natural ecosystems is a global concern, with industrialisation contaminating millions of soil and water sites. These contaminants threaten human health, agricultural productivity, and ecological balance. Traditional bioaugmentation strategies, while cost-effective and sustainable, face challenges including slow degradation rates and environmental constraints on microbial efficacy. This mini review examines phage bioaugmentation, which uses bacteriophages to enhance microbial pollutant degradation and support a circular economy. We focus on lysogenic phages that integrate auxiliary metabolic genes into bacterial hosts to improve degradation capacity, synthesise current knowledge, identify challenges, and propose a conceptual workflow for implementation.

This mini review introduces phage bioaugmentation, a strategy to enhance soil bioremediation by using lysogenic bacteriophages to transfer pollutant-degrading genes to bacteria.

Introduction

Ecosystem pollution is a major global environmental concern¹ that affects health, causes agricultural losses, and puts stress on organisms^2–4. Pollutants such as arsenic, chromium, polychlorinated biphenyls, pesticides, petroleum hydrocarbons, and excess nutrients disrupt ecosystem function by impairing microbial communities essential for soil health and nutrient cycling⁵. These impacts degrade groundwater quality, threatening drinking water resources. Safeguarding soil microbiomes is critical for ecosystem resilience, the environment and public health⁶.

Pollutant impacts on microbial communities are established^7,8. Bacteria also breakdown and bioremediate pollutants⁹. This dichotomy shapes bioremediation research. Ex situ land farming and biopiling are effective but costly. In situ bioventing, biostimulation, and bioaugmentation are cost-effective and sustainable approaches, but are constrained by slow degradation and inhibition of microbial activity^5,10. Bioaugmentation often fails due to dilution, washout, competition, and microbial mortality¹¹.

Here we consider phage bioaugmentation, using lysogenic bacteriophages - viruses that infect bacteria and integrate into their host’s genomes without immediately killing them - containing pollutant-degrading genes, bolstering the bacteria’s genetic repertoire for bioremediation¹². We propose that leveraging phage–bacteria interactions enhances bioaugmentation over current bioaugmentation techniques. This mini review presents the conceptual framework, summarizes current evidence, and identifies key research priorities.

We first introduce phage bioaugmentation as a complementary bioremediation strategy by highlighting key lysogenic phage features and framing discussion of auxiliary metabolic genes (AMGs) and lysogeny. The review then explores the biological and chemical constraints of soil and known phage interactions, followed by comparing phage-based and conventional approaches, including limitations and applications. Lastly, we discuss the risks and future directions.

Results

Phage biology and lysogeny as a foundation for bioaugmentation

Phages are gene vectors that reshape microbial capabilities

Phages exist wherever bacteria do, with ~10³¹ particles globally, 10 times that of bacteria¹³. Infection begins with receptor binding and nucleic acid injection^14,15, leading to a lytic cycle—where progeny are released¹⁶, or a lysogenic cycle—with integration into the host genome as a prophage that replicates with the bacteria¹⁷. Phages depend on host survival, often adopting lysogeny to promote host fitness under stress.

Phages transfer AMGs that alter host metabolism, via integration or the horizontal gene transfer (HGT) transduction¹⁸. Lytic phages’ AMGs provide short-term benefit, lysogenic phages offer AMGs that improve ongoing host viability by enhancing fitness¹⁹. In oligotrophic soils, traits passed to progeny are genes aiding stress tolerance, nutrient acquisition, and metabolic flexibility¹⁸. For bioremediation, lysogenic phages can enhance host contaminant access and metabolism by encoding genes for pollutant transformation, resistance, or stress mitigation.

Soil phages carry 13 AMGs categories crucial to ecosystem function, including metabolism for nutrients, energy, amino acids, fatty acids, antibiotic production, biofilm formation, and sporulation²⁰. Quantifying AMG impacts in soil remains challenging; insights from marine ecosystems suggest they play crucial ecological roles^21–23. We propose that phage bioaugmentation, particularly with phages carrying pollutant-degrading AMGs, represents a promising strategy to enhance native microbial function and accelerate biodegradation in terrestrial ecosystems.

Phage AMGs support host stress tolerance and pollutant transformation in contaminated soils

Phage AMGs enhance microbial stress tolerance, metabolic flexibility, and persistence in contaminated soils. Most studies report indirect effects linked to resistance, detoxification, and ecosystem functioning, fewer show direct pollutant transformation. Virome screening for such genes is important for evaluating the feasibility of phage-assisted bioaugmentation, which has been explored mainly in metalloid and pesticide contaminated soil.

In chromium (Cr) and arsenic (As) contaminated soils, phage communities shift composition, function, and host interactions. Lysogenic phage are enriched in detoxification genes, e.g., arsC, GSTs, and RND pumps, and AMGs linked to CR(VI) reduction^24,25. Temperate-to-lytic ratios, and AMGs rise in heavily polluted soils. Phages form mutualistic associations with bacteria in contaminated soils, whereas predation dominates in contaminant-free soils²⁶.

Contaminated soil viromes have arsC, arsR, arsD AMGs for resistance and detoxification, arsM for methylation, and Pst, Pit for transport, for arsenic transformation^27,28. Microcosm studies show phage-mediated As(V) reduction and As(III) methylation with >100-fold increases in arsC and arsM²⁷. A prophage in Citrobacter portucalensis carrying arsRDABC and arsP/yraQ detoxification clusters were induced by arsenic and antimony, conferring resistance to methylated arsenicals²⁹.

Organochlorine pesticide–contaminated (OCP) soils show higher viral richness, AMG diversity, and phage–host activity^30,31. Viral genes such as aldehyde dehydrogenase, L-2-haloacid dehalogenase, and trzN indicate pollutant-specific catabolic potential^30,32. AMGs linked to metabolism and element cycling correlate with soil multifunctionality, while OCP stress reduces bacterial diversity but increases viral diversity, AMGs, and gene flow^31,33.

Microcosm studies using fertilizer phage confirmed phage-mediated pesticide degradation. Viromes contained detoxification AMGs (phnP, nfrA2, coaBC, cysH, moeB). In p-NCB soils, degradation reached 64% with phage- or bacteria-only transplants and 77% with combined treatments (38% control). Rates correlated strongest with AMG diversity (r = 0.90), then bacterial diversity (0.65), phage diversity/abundance (0.58, 0.56), and bacterial/AMG abundance (0.30, 0.26)³⁴.

These studies indicate phages influence microbial performance by enhancing host stress tolerance, resistance, and metabolic capacity. In some microcosms, phage-encoded functions directly transform pollutants. Overall, phages mostly aid soil remediation by modulating microbial community function.

Lysogenic AMG transcription indicates host adaptation

Lysogenic phages modify host function through AMG expression. Environmental evidence remains limited due to difficulties isolating phage nucleic acids and historical focus on bacterial genes³⁵. In λ phage–E. coli, repressors silence lytic genes while permitting lysogenic expression³⁶; AMGs are expressed when their levels exceed repressor control needed to maintain lysogeny³⁷.

Prophage genes, including putative AMGs, are actively transcribed³⁸ during lysogeny in model systems^37,39. Environmental studies show similar patterns, such as high expression of phage-associated pmoC in methane-rich lakes and moisture-driven phage transcription in soils, though lysogenic versus lytic origins remain unclear^21,40. These results suggest lysogenic AMGs may influence host metabolism but remain poorly studied in polluted soils.

Soil as a system: physical and biological constraints

Soil complexity affects pollutant bioavailability and microbiota

Soils are heterogeneous abiotic–biotic ecosystems. Gravel, sand, silt, and clay form the matrix, with liquids and gases occupying pore spaces⁴¹. Spatial and temporal variation creates micro-niches restricting pollutant and microbial movement and generating resource pockets, some rapidly depleted and others persistent^42–44.

Pollutants such as PAHs, pesticides, and metal ions (e.g., Cd, Pb) adsorb to soil, limiting microbial biodegradation⁴⁵. Bioavailability varies with texture, pH, and pollutants: hydrocarbon remediation is ineffective in clay but successful in sand containing soils⁴⁶. Pollutant toxicity also reduces microbial abundance and diversity, leaving resistant taxa and altered physicochemical conditions that further inhibit microbial activity^47,48.

Soil properties impact phage interactions

For phage bioaugmentation in polluted soils, environmental interactions must support delivery and persistence. Soil texture affects viral retention and activity⁴⁹: phages adsorb strongly to clay via high surface area and hydrophobic interactions, limiting mobility^50,51. While restricting dispersal, this may help localize phage activity at pollutant hotspots.

pH and calcium influence DNA phage diversity and adsorption^52–55. In polluted soils, shifts in pH, ions, and microbial structure affect phage performance⁵⁶. Effective bioaugmentation requires accounting for local soil conditions; encapsulation, pH adjustment, or calcium addition can improve stability but may reduce mobility and host contact.

Phage bioaugmentation in context: potential and strategy

Phages may address microbial bioaugmentation limitations

Field bioremediation typically uses in situ methods (e.g., pH, oxygen, nutrient, or moisture adjustment) to stimulate native microbes^5,10. When indigenous activity is insufficient, bioaugmentation is applied, though each approach has limitations (Fig. 1).

Fig. 1. Key challenges of common bioaugmentation strategies in soil.

A Enzyme augmentation enables direct pollutant degradation but is limited by premature enzyme inactivation and lack of replication. B Bacterial augmentation introduces pollutant-degrading strains, but these face competition from native microbes and environmental stress. C Plasmid-mediated augmentation delivers degradation genes via donor cells, but conjugation requires close contact, and free plasmids degrade quickly. Created in BioRender. Romeo, N. (2026) https://BioRender.com/s718zum.

Bacterial and fungal bioaugmentation introduce live microbes pre-selected for their degradation capabilities. While effective in lab conditions, these often non-native strains can fail in complex soils due to competition and poor adaptability (Fig. 1B)^57,58. Enzyme and additive bioaugmentation deliver active compounds directly, enabling fast action even under stress, but they are transient, lack self-replication and can be prone to inactivation^57,59,60(Fig. 1A). Plasmid-mediated bioaugmentation attempts to spread catabolic traits via conjugation, a HGT mechanism⁶¹, but this requires close-cell contact. Extracellular plasmid DNA is also unstable and sensitive to soil properties, like moisture and texture^62–64(Fig. 1C).

These limitations highlight the need for adaptive, community-integrated strategies. Phage bioaugmentation can deliver AMGs to native bacteria, enhancing degradation without disrupting communities. Phage capsids protect DNA and enable wider dispersal than plasmids⁶⁵, while self-replication and horizontal gene transfer allow small inocula to produce large functional impacts.

Lateral transduction efficiently mobilizes large chromosomal regions, often exceeding plasmid and transposon transfer rates^66,67. With transduction occurring up to 10¹⁶ events per second globally⁶⁸, its evolutionary role is likely underestimated. CRISPR–Cas systems can also enhance transduction and may themselves spread via phages⁶⁸.

Although many phages have narrow host ranges⁶⁹, some evolve or can be engineered for broader tropism^70,71, enabling AMG delivery across diverse bacteria. Engineered phages can carry multiple genes improving pollutant bioavailability (e.g., biosurfactants) and multi-step degradation^5,72–75. This raises a key question: why use phages rather than engineer indigenous bacteria directly?

Compared with engineering native bacteria, phage strategies enhance multiple hosts via polyvalent infection, promoting functional redundancy in variable soils⁷⁶. Phages also offer scalable, host-specific AMG delivery with minimal off-target effects⁶⁹.

Phage infection delays resemble competition faced by introduced bacteria in bioaugmentation. Unlike engineered strains, phages amplify native microbial potential, enabling broader dissemination and ecological compatibility. Though direct comparisons are limited, phage bioaugmentation shows promise as a next-generation remediation tool.

Phage bioaugmentation strategy and feasibility

As phage bioaugmentation is not yet established, the following steps may guide application:

Site analysis: Determine pollutant composition, native microbial and phage communities, soil structure, and moisture content to inform phage delivery.

Phage selection and cultivation: Choose phages with bioremediation AMGs, considering (i) compatible hosts in the native microbiota, (ii) prior presence of related phages, and (iii) capacity to cultivate phage–host pairs. Polyvalent phages preferred.

Engineering phages: If native phages lack relevant AMGs, genome engineering, analogous to plasmid-mediated bioaugmentation, could introduce degradation genes to confer a selective advantage under pollutant pressure. However, the long-term stability of engineered inserts is a major hurdle, as phage genomes are subject to rapid mutation and selection during propagation and after release into complex soil environments.

Environmental delivery: Apply cultivated phages via injection or mixing. Emerging delivery strategies include immobilisation techniques such as encapsulation and embedding⁷⁷. Genetic release must be carefully regulated.

Monitoring: Track pollutant levels post-application. Ideally, the selective pressure maintaining AMGs will decline as remediation proceeds, leading to gene loss. Microcosm studies should estimate AMG persistence post-clean-up.

Phage bioaugmentation feasibility is supported by phage applications’ growing success in other complex microbiomes, including the human gut and agricultural systems. In clinical contexts, phage therapy is used to selectively target pathogenic bacteria without disrupting beneficial commensals, with successful outcomes reported in compassionate use cases and early-phase trials^78,79. In agriculture, lytic phages are deployed for biocontrol of bacterial plant pathogens, demonstrating target specificity and environmental persistence^80,81. These examples highlight efficient phage application in heterogeneous, multispecies environments, like conditions found in soils. While soils pose unique physicochemical challenges, documented phage ability to influence microbial composition and function across other domains supports phage bioaugmentation viability. Evidence of pollutant-degrading phage-encoded genes in soil further strengthens the case for application in environmental biotechnology.

Host and environmental factors may shape phage bioaugmentation outcomes

Optimising phage use in soil biotechnology requires understanding the factors influencing lytic versus lysogenic lifestyles, which is heavily shaped by host physiology and environmental conditions. Lytic infections limit the window for AMG expression, whereas lysogeny enables sustained gene delivery without host destruction. Lysogeny is more likely when hosts grow slowly, are nutrient-limited, or occur at high multiplicity of infection⁸². Supporting this, deeper soils, typically lower in nutrients and oxygen, harbour higher lysogenic fractions as total microbial abundance declines⁸³. However, the piggyback-the-winner model shows that lysogeny can emerge in dense, fast-growing populations^84–86. These coexisting strategies form a bimodal response tied to microbial density, which is relevant for polluted soils that are heterogeneous and host both stressed and metabolically active bacteria.

Abiotic stressors further modulate phage lifestyle. Soil moisture and temperature are key drivers: lysogeny increases in cold, dry, or low-nutrient environments, while moderate warming or increased moisture can reactivate lytic cycles^{20,40,87–90}. Since many polluted soils experience fluctuating or extreme temperatures (e.g., mine tailings, landfills, thawing permafrost), these shifts could alter engineered phages’ persistence and efficacy. Additionally, extreme heat or freeze-thaw events reduce overall phage viability²⁰.

In polluted environments where abiotic stressors like desiccation, salinity, or heavy metal toxicity co-occur, limiting microbial proliferation, these trends converge to favour lysogeny. This has important implications for soil bioaugmentation: lysogenic phages may offer stabler, long-term integration into microbial communities, enabling sustained metabolic enhancement of native degraders. Designing effective phage-based interventions therefore requires close attention to host ecology and soil conditions that influence viral dynamics.

Broader considerations: risks and future directions

Key research areas and challenges associated with phage bioaugmentation, spanning upstream preparation, field application, and downstream considerations, are summarised in Fig. 2. Introducing exogenous phages may risk displacing native degraders⁹¹, but lysogeny is usually host-specific and context-dependent, limiting broad disruption⁶⁹. Rather than replacing key bacteria, phage bioaugmentation aims to enhance compatible native taxa, increasing their selection advantage and preserving native microbial functions, supporting pollutant breakdown. Another concern is reversion to a lytic cycle, which could be mitigated through phage engineering for stable lysogeny and/or inhibited bursting. Integrated AMGs may also not persist if they provide little selective advantage. Approaches to predict such impacts would include microcosm experiments, machine learning, and advanced modelling, allowing for a comprehensive assessment of releasing such phages into a community^92,93.

Fig. 2. Conceptual overview of key research areas and challenges for phage bioaugmentation in soil bioremediation.

The figure highlights three interconnected stages: A upstream preparation, including isolation, propagation, and engineering of phages carrying bioremediation-relevant auxiliary metabolic genes; B field application challenges, where low gene expression, functional redundancy, environmental heterogeneity, and impacts on native microbial communities complicate experimental validation; and C downstream considerations, including genetic instability, gene loss, lytic reversion, and the need for robust regulatory and ecological risk assessments. Together, these stages illustrate critical knowledge gaps and research priorities for advancing phage-based soil bioremediation. Created in BioRender. Romeo, N. (2026) https://BioRender.com/s1wh4r2.

Another key concern is engineered phage genome stability following propagation and environmental release. Integrated AMGs may be lost or silenced if they impose metabolic costs or fail to confer sufficient selective advantage under site-specific conditions. To improve AMG retention, one strategy is linking target genes to functions that clearly enhance host fitness, allowing the engineered trait to persist under pollutant-driven selection pressures⁹⁴. In this context, pollutant presence itself may act as a stabilising force during lysogeny.

Additional approaches include minimising genetic payload size, integrating AMGs into conserved genomic regions, or coupling their expression to essential phage or host functions. Viral tools such as the T7 RNA polymerase system offers programmable, orthogonal gene expression that may improve functional robustness. This phage-derived, single-subunit polymerase enables strong, orthogonal gene activation from synthetic promoters, independent of host regulatory networks, but do not prevent mutational loss⁹⁵. Combining engineering strategies may significantly improve the stability, predictability, and effectiveness of soil phage bioaugmentation. The stability and persistence of engineered phages must be empirically validated through controlled propagation experiments and soil microcosms prior to any environmental application. Accordingly, engineered phage bioaugmentation should currently be viewed as an experimental and context-dependent approach, with naturally occurring or minimally modified phages likely to offer greater genetic stability in early-stage applications.

As these approaches advance, regulatory frameworks must evolve to assess ecological safety, genetic stability, and long-term impacts of releasing engineered phages into natural environments. Issues such as gene transfer potential, persistence, containment, and unintended effects on non-target organisms will need to be addressed through biosafety protocols and environmental risk assessments before field-scale deployment.

Conclusion

Outlook

Phage bioaugmentation offers a compelling new direction for environmental biotechnology, by harnessing the ecological roles of lysogenic phages to enhance microbial function in polluted soils. Through delivery of AMGs associated with stress tolerance and contaminant degradation, phages may strengthen native microbial communities and address limitations of conventional bioaugmentation. However, translation to practice requires deeper understanding of phage–host interactions, environmental controls on infection dynamics, and persistence of phage-derived functions in situ. Key knowledge gaps and technical challenges are summarised in Box 1 to define research priorities. Immediate efforts should focus on validating effective in-soil candidate phage, conducting controlled field experiments, and developing tools to monitor phage integration and AMG expression. As interest grows in using viruses as functional agents in terrestrial systems, careful consideration of biosafety, regulatory oversight, and unintended ecological impacts will be essential. With these safeguards in place, phage bioaugmentation could emerge as a precise and adaptive strategy for restoring polluted environments and promoting microbial resilience.

Box 1. Future directions and challenges in phage soil bioaugmentation.

Key Developments

• Soil phages carry AMGs related to nutrient metabolism, stress response, and pollutant breakdown.

• Transcriptomic evidence supports active expression of lysogenic AMGs in polluted environments.

• Metagenomic studies have functionally validated pollutant-degrading AMGs in some soil viral communities.

Outstanding Questions

• Are pollutant-degrading AMGs consistently expressed across soil types and microbial hosts?

• How stable are lysogenic phages and their AMGs in dynamic or heterogeneous soils?

• What host traits govern phage lifestyle choice (lytic vs. lysogenic) under pollution stress?

• Can we rationally design phage cocktails that integrate predictably into complex microbiomes?

• What are the long-term ecological consequences of introducing engineered or naturally enriched phages into soil?

Technical Challenges

• Isolation and culturing of relevant soil phages and bacterial hosts remain bottlenecks for functional testing. Detecting AMG functionality in situ is difficult due to low expression levels, host diversity, and gene redundancy.

• Environmental variables (e.g., pH, particle size, calcium, organic matter) impact phage stability and infection dynamics.

• Genetic instability of engineered phages: Rapid phage evolution may lead to mutation or loss of introduced AMGs during propagation or after release into soil.

• Lack of regulatory frameworks or safety guidelines for phage-based applications in open environments.

Author contributions

N.R. conceived the study, performed the literature review, developed the conceptual framework, wrote the manuscript and created the figures. E.H. and Q.Y provided conceptual guidance for figures and the manuscript. E.H., Q.Y., and J.M. edited, provided feedback, and approved the final manuscript.

Peer review

Peer review information

Communications Biology thanks Amechi Nwankwegu, Liao Hanpeng and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editors: Dr Eoin O’Gorman and Dr Ophelia Bu.

Competing interests

The authors declare no competing interests.