Soil Biology and Biochemistry

Decomposition of organic matter is a key process in soils contributing to carbon and nutrient cycling. To identify management strategies for agroecosystems that reduce nutrient losses while maximizing plant growth, it is important to understand which parameters determine decomposition rates. This study therefore investigated how the presence of winter wheat (Triticum aestivum var. Asory) affects decomposition in a controlled Ecotron setup with two soil types with varying organic matter content across three simulated climates (2013, 2068, 2085). Using the tea bag index, interstitial soil pore water analyses, microbial biomass quantification, bacterial and fungal gene abundance, and soil respiration measurements, we tested the hypotheses that plant exudates would enhance decomposition rate and microbial biomass, while plant nitrogen uptake would deplete soil nitrate, potentially mitigated by fertilization. Contrary to expectations, decomposition rates were lower in planted than in unplanted soils, suggesting resource competition between plants and microbes. No significant differences were observed in microbial biomass or respiration due to plant presence, and fertilization effects on nitrate or microbial mineralization were undetectable, likely due to rapid turnover of organic molecules including uptake by plants and microbes. Mechanistically, fungi and soil humidity were more important for decomposition than bacteria or temperature. The findings corroborate climate impacts on decomposition but also indicate microbial resilience and highlight the potential of management strategies like cover crops, adjusted planting dates and crop residual management which can contribute to healthy soils by sustaining carbon and nutrient cycling.

Soil organic matter (SOM) consists of diverse biochemical constituents, spanning a spectrum of chemical complexity, and the relative abundance of these substrates influences microbial metabolism and soil carbon persistence. However, mechanistic controls governing these processes and how they may be affected by environmental change remains incomplete. This study aims to assess (1) the molecular-level changes that occur across stages of root decomposition, from undecayed plant root litter to 1-year decomposed root litter, to mineral SOM and (2) how these changes are altered by anthropogenic nitrogen (N) deposition by using SOM biochemical and microbiome datasets and a long-term field experiment. N deposition did not significantly alter undecomposed or 1-year decomposed root litter, but did alter decomposing microbial communities and mineral SOM biochemical composition, specifically in lignin- and lipid-derived compounds. Taken together, this restructuring of microbial communities and alteration of SOM biochemistry likely contributed to the previously observed reduction in SOM decomposition.

Climate change is reshaping soil microbial communities, yet the impact of warming in bacterial-fungal interactions (BFIs) remains underexplored. We investigated whether heatwave temperature influence BFIs and the mechanism supporting the interaction. Using co-culture experiments with two bacterial and two fungal strains isolated from heathland soil, we compared mono- and co-cultures final abundances under ambient (18{degrees}C) and heatwave (25{degrees}C) soil temperatures. Our results revealed strongly asymmetric interactions, where fungi benefited by around 5% from bacterial presence, while bacterial abundance was inhibited by around 68%, regardless of temperature. Analyses of pH confirmed that acidification by fungi was probably the main cause of this inhibition. Moreover, warming did not affect the strength or direction of these interactions, though it slightly increased fungal abundance. These findings provide direct experimental evidence that fungi can impact bacteria via acidification, and that the interaction is unaffected by temperature. Understanding these mechanisms is crucial for improving predictions of microbial community dynamics and ecosystem functioning in warming environments.

Arctic winters are long and cold and have traditionally been considered a period of limited biological activity. However, the seasonal dynamics of microbial community composition and functional potential during winter remain poorly understood. Here, we investigated taxonomic (bacteria, fungi, archaea) and functional (fungal guilds and nitrogen cycling genes) dynamics throughout a full year at two Arctic tundra heath sites with contrasting snow regimes. A steep drop in microbial abundances in early to mid-winter, likely linked to freeze-thaw events, coincided with shifts in soil pH and elevated community turnover. Saprotrophic and root-associated fungi were more abundant in the cold-season, while inorganic nitrogen cycling groups were more abundant in summer and declined toward winter despite high bacterial abundance. This indicates sustained organic matter cycling during the winter and expanded inorganic nitrogen cycling in the summer. Functional gene ratios further suggested a higher early-winter nitrogen loss potential via nitrous oxide and greater late-winter nitrogen retention. Site-specific differences in snow regime altered the timing and magnitude of these dynamics. Together, our results demonstrate that winter represents a critical and dynamic period for microbial community restructuring with important implications for nitrogen turnover in Arctic tundra soils.

Northern peatlands store large carbon stocks but are sensitive to disturbance. Hydrology, vegetation, herbivory and snow conditions may affect the soil microorganisms driving methane (CH) and nitrous oxide (N2O) cycling. We investigated how reindeer exclusion and snow depth (increased and reduced relative to ambient) manipulations (ongoing for three seasons) influenced archaeal and bacterial communities in a boreal rich fen. Metagenomic (MG) and metatranscriptomic (MT) sequencing were combined with pore-water chemistry and CH flux measurements to link the microbiome to ecosystem processes. Microbial communities differed between outside and inside the exclosure. However, these patterns primarily reflected underlying hydrological variation. Slightly wetter inside plots showed higher expression of denitrification genes (norB, nosZ) and lower (nirS+nirK)/nosZ ratios, indicating greater potential for complete denitrification to N2 instead of N2O. Methane dynamics were mainly associated with vegetation: plots associated with Carex rostrata exhibited lower pmoA/mcrA ratios and elevated CH fluxes. Snow manipulations had subtle effects: reduced snow depth decreased the expression of taxa dependent on microbial interactions, while the effect to the investigated metabolic marker genes was small. Overall hydrology, leading to variations in redox conditions and nutrient availability, together with vegetation appeared as the primary drivers on microbial greenhouse gas processes in this peatland.

The soil microbiome is key to plant health and nutrient acquisition, and viruses likely play important but largely unknown roles in these processes. To interrogate bulk and rhizosphere soil viral biogeography, we collected samples over a tomato growing season in California from an experiment testing arbuscular mycorrhizal fungi (AMF) treatment. We generated 78 viromes, 16S rRNA gene, and ITS1 amplicon datasets, and 33 rhizosphere metatranscriptomes. Of 67,038 DNA viral species genomes (vOTUs), 25% were previously identified, predominantely in agricultural systems, suggesting habitat filtering and greater viral homogeneity across agricultural compared to natural soils globally. Rhizospheres had significantly higher DNA viral richness than bulk soils, whereas no significant richness differences were observed for other biota. 60% of vOTUs were shared between compartments, compared to only 21-23% of bacterial and fungal taxa. Although bulk soil viral biogeography resembled that of prokaryotes, with significant structuring by moisture content, greater virome similarity between high-moisture bulk soils and rhizospheres suggests that conditions with high host activity selected for similar viral communities. In rhizospheres, while bacterial and fungal communities differed most over time, DNA and RNA viral communities differed most by sampling location, matching prokaryotic transcriptional patterns and further implicating host activity in viral biogeography. Similarly, AMF treatment induced changes in the prokaryotic transcriptome but, across biota, only significantly affected DNA viral communities. Overall, results indicate strong viral responses to spatiotemporally localized conditions, with viral biogeography reflecting both dispersal opportunities (high between neighboring bulk and rhizosphere soils, low across fields) and selection via local host activity.

O_LIA productivity-driven higher nutrient demand of trees in diverse mixtures is frequently reported. Yet, it remains unclear how tree diversity influences microorganisms-plants interactions, in which microbes facilitate tree nutrient acquisition in exchange for carbon (C) to meet the resource demand of both. C_LIO_LIUsing a long-term tree diversity experiment in the subtropics, we assessed microbial investment in C-, nitrogen (N)-, and phosphorus (P)-acquiring enzymes in litter and mineral soil, testing the effects of tree species richness and mycorrhizal type (arbuscular (AM)- vs. ectomycorrhizal (EcM)-associated tree species). C_LIO_LIWith increasing tree species richness, microbial investment in C acquisition decreased, while investment in N and/or P acquisition increased in litter and in mineral soil. In mineral soil of AM-associated tree mixtures, ecoenzymatic stoichiometry revealed a shift from microbial investment in C toward P acquisition as tree species richness increased. C_LIO_LIOur findings suggest that tree diversity strengthens microbe-tree interactions in terms of C-for-nutrient exchange. This highlights the key role of soil microorganisms, particularly in AM symbiosis, shaping tree diversity-biogeochemical feedbacks. C_LI

Soil microbes support life on Earth by regulating the availability of nutrients in soils, yet we lack a fundamental, baseline knowledge of which fungi and bacteria are associated with specific soil nitrogen (N) cycling processes across ecosystems. We identified functional and taxonomic groups of fungi and bacteria that are associated with net ammonification and nitrification rates in soils from diverse ecosystems across the United States, including the environmental contexts where these relationships exist. To accomplish this, we co-analyzed soil, microbial, plant, and climatic data from 19 sites across the U.S. National Ecological Observatory Network (NEON). Distinct microbial groups were associated with net ammonification versus nitrification rates, highlighting the need to measure and model these two processes separately. The relative abundance of several microbial groups known for their N-decomposition abilities (i.e., Acidobacteriae, Bacteroidia, Saccharomycetes yeasts, ectomycorrhizal fungi) were positively associated with net ammonification rates across diverse environmental conditions. Meanwhile, pathogenic fungi, copiotrophic bacteria, and bacterial classes containing denitrifying bacteria were positively associated with net nitrification rates in many wet, hot, and high-N environments. These results deepen our understanding of soil microbiome ecology and represent a practical starting point to develop microbial-explicit biogeochemical cycling models at large spatial scales.

Plant species loss and nitrogen fertilization affect grassland biodiversity. However, their interactive effects on plant communities, soil properties, and the soil microbiome remain insufficiently understood. We analyzed how the removal of plant species, with and without urea addition, influenced plant diversity, soil properties, and soil bacterial communities in a Tibetan Plateau grassland. Continuous plant species removal and urea addition over seven years modified plant beta-diversity equally strong, while urea exerted a stronger negative effect on plant alpha-diversity. Both, plant species removal and urea addition caused soil acidification and an increase in NO2-/NO-, while dynamics in TOC, TON and TOC: TON were mainly driven by the growing season. Structural equation modeling identified soil acidification via urea addition as the most important indirect driver that negatively affected bacterial alpha-diversity and shifted bacterial beta-diversity. Urea addition also exerted direct negative effects on bacterial alpha- and beta-diversity, causing repression of oligotrophic (Acidobacteriota, Chloroflexota, Planctomycetota, Gemmatimonadota) and stimulation of copiotrophic (Bacillota, Bacteroidota, Pseudomonadota) bacterial taxa. Plant species removal caused slight increases in bacterial alpha-diversity, paralleled by less diverse but more even plant communities. We show that soil acidification by urea fertilization outweighs plant species loss in its negative effect on bacterial soil biodiversity in Tibetan grasslands.

Global change drivers are reshaping agroecosystems and their sustained functions worldwide. While soil microorganisms underpin the resilience of these systems, the individual and interactive effects of multiple anthropogenic stressors on microbial community structure and function using large-scale field experiments remain poorly understood. Here, we utilize a full-factorial field experiment in a subtropical agroecosystem to investigate how land-use intensity, cattle grazing intensity, and altered precipitation regimes interact to shape soil microbiomes. Combining microbiome sequencing with network analyses and functional bioinformatics, we evaluated effects of these drivers on prokaryotic and fungal diversity, composition, predicted functional profiles, and community structure. Land-use intensity emerged as the primary driver of microbial responses, explaining 25% and 13% of the total variation in community composition for prokaryotes and fungi, respectively. Compared to intensively managed pastures, semi-natural pastures had significantly different community composition for prokaryotes and fungi and exhibited 22% higher fungal diversity. Semi-natural pastures were enriched with decomposer-associated taxa and metabolic pathways related to energy and lipid metabolism indicating enhanced microbial activity. Surprisingly, intensively managed pastures showed higher network modularity but lower network richness, suggesting a trade-off between community compartmentalization and complexity under intensive land management. Grazing and precipitation manipulations induced core microbiome changes within land-use intensities but had no impact on overall community structure and no significant interactions with land-use. Together, these findings suggest that long-term land-use legacies exert a persistent influence on soil microbial community structure, function, and organization, shaping the context within which other global change drivers operate in subtropical agroecosystems.

Although rhizosphere microbiomes are known to enhance plants resistance to water stress, it is believed that only fungi actively contribute to the transport and uptake of water. We investigated the biomechanical impact of bacterial motility on water transport in soil by combining surface tension measurements and water infiltration experiments in soil microcosms. We observed that flagellar-based motility in Bacillus subtilis cells reduces the apparent surface tension of fluids by up to 15%. The effect reported depends on cell density and swimming speed, confirming its biomechanical origin, and was able to accelerate water infiltration and rewetting of soil. We conclude that Bacillus subtilis facilitates soil water transport through the deformation of air water interfaces in pores.

Microbial communities regulate carbon and nitrogen (N) cycling, yet their long-term responses to chronic global changes remain unclear. Using 12 years of grassland litter samples from the Loma Ridge Global Change Experiment in Irvine, California, we tested whether interactions between experimental drought and N deposition, and previously observed temporal variability are driven by background climatic conditions, including precipitation and temperature. Consistent with short-term studies, drought and N addition had relatively small effects on bacterial community composition compared to pronounced seasonal and interannual variability, with drought-by-year interactions explaining more variation than drought alone. Seasonal shifts were largely driven by short-term fluctuations in rainfall and temperature, whereas the substantial interannual variability in community composition was not captured by site-level climate metrics. Contrary to expectations, drought effects were influenced more by background temperature than precipitation, with the strongest effects observed in cooler years. Lastly, a bacterial taxons sensitivity to climate variability under ambient conditions did not predict its response to chronic drought. Together, our findings show that bacterial responses to drought are temporally dynamic and influenced by background temperature, underscoring the need for long-term longitudinal studies of soil microbial communities to better predict microbial responses under future global change. ImportanceMicrobial responses to global change, particularly drought and nitrogen addition, are often inferred from short-term studies (< 2 years), yet natural temporal variability may overshadow experimental effects. Using a 12-year dataset of grassland leaf litter communities, we show that temporal variability, both seasonal and interannual, exert a stronger influence on bacterial community composition than chronic drought or nitrogen deposition. These findings challenge assumptions about the magnitude of drought effects, particularly in naturally drought-affected ecosystem such as California grasslands and highlight the importance of long-term datasets for predicting microbial responses to climate change. By demonstrating that bacterial communities are strongly shaped by background climatic variability (baseline precipitation and temperature independent of imposed chronic treatments) and may be buffered to sustained drought, this work improves forecasts of ecosystem responses and informs the design of global change experiments and restoration strategies in future research studies.

Microbial communities can shift under drought in ways that enhance plant performance during drought ("microbe-mediated acclimation"). However, it is also possible for microbial communities to shift in ways that worsen the effects of drought ("mal-acclimation"). It is unclear how and where microbe-mediated acclimation vs. mal-acclimation occurs, or if there are types of soils or microbial communities that are more likely to harbor microbes that enhance plant acclimation and limit mal-acclimation. We tested for microbe-mediated plant acclimation/mal-acclimation to drought in soils from 21 maize farms in the midwestern United States, spanning a range of climate, soil types, and management practices. We first conditioned soil microbial communities to drought vs. well-watered conditions in a greenhouse and then tested for microbe-mediated acclimation by growing maize in soils inoculated with the conditioned microbial communities under drought and well-watered conditions. Drought-conditioned soils did not enhance plant performance under drought. In fact, one third of the farms exhibited mal-acclimation, especially under well-watered conditions where wet-conditioned soils reduced plant performance in well-watered contemporary conditions. Farm management practices, climate, soil texture, and microbial diversity generally did not predict when this microbe-mediated mal-acclimation occurred. Overall, these results suggest that in agricultural soils, microbes may frequently impede-rather than facilitate-plant acclimation to soil moisture levels. Open research statementThe plant and soil data used in this study are available via the Environmental Data Initiative repository at https://doi.org/10.6073/pasta/f4a0db3a076cf6d8cef908947f82736e. The bacterial and fungal amplicon sequence data are available via the European Nucleotide Archive under accessions PRJEB110071 and PRJEB109827, respectively.

Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied a genome-resolved stable isotope probing viromics (SIP-viromics) approach, combining H 18O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined metagenome assemblies. Only 22% of vOTUs exhibited significant 18O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76-5.15% of total virions per gram of soil, with viral loads ranging from 3.15 x 1010 to 6.59 x 1010 virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota--bacterial groups known to rapidly resuscitate following rewetting--suggesting that some viruses exhibit rapid turnover while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal host-associated patterns of lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance. ImportanceUnderstanding the persistence and production dynamics of soil viruses is critical for elucidating their roles in microbial community dynamics and nutrient cycling, yet these processes have remained largely uncharacterized due to methodological limitations. By integrating stable isotope probing with viromics, this study provides a robust framework for directly distinguishing newly produced from persistent virions in situ. Unlike conventional viromics, which only catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence under natural soil conditions. Our results demonstrate that most virions in a seasonally dry soil persisted through a rewetting event, with active replication limited to a minority of viral populations. Persistent virions were primarily linked to dominant bacterial groups, indicating that host ecophysiology and environmental stability strongly influence lytic infection. Collectively, these findings highlight viruses as long-term reservoirs of genetic material, capable of shaping microbial dynamics and ecosystem processes over time. This work establishes SIP-viromics as a powerful approach for studying virus-host interactions and their ecological significance in terrestrial environments.

Plant invasion can modify soil microbial communities and ecosystem processes through plant-soil feedbacks, yet it remains unclear whether these effects are expressed mainly through taxonomic turnover or through shifts in microbial function and interaction structure. We tested how soil legacy generated by the invasive Conyza bonariensis, the native Helminthotheca echioides, or unplanted control soil influenced short-term microbial responses to standardized amendments and plant-derived inputs. In Experiment 1, conditioned soils were amended with water, cellulose, or ammonium and analyzed for extracellular enzyme activity, qPCR-based gene abundance, bacterial community composition, and family-level co-occurrence networks. In Experiment 2, the same soil legacies were exposed to water, glucose, or sterile root exudates from native or invasive plants. Native- and invasive-conditioned soils differed significantly in composition, but they were not consistently distinguished by strong indicator taxa, indicating that legacy effects were expressed mainly through redistribution of shared taxa rather than community turnover. In contrast, functional responses were clearer: enzyme activity and nirS abundance showed strong soil-legacy dependence, and network analysis revealed that invasive-conditioned soil supported a denser, more positive, and more compact family-level association structure than native-conditioned soil. In Experiment 2, invasive root exudates produced stronger short-term functional-based differentiation among soil legacies than native exudates, especially for extracellular enzymes. Together, the two experiments show that plant invasion can leave a persistent belowground legacy that is expressed primarily through functional filtering and network rewiring of a broadly shared microbiome, rather than through major taxonomic turnover alone.

Interactions between amoebae and bacteria are increasingly viewed as key drivers of zoonotic pathogen emergence in rodent-dwelling burrows, yet the environmental factors shaping these interactions remain poorly understood. Here, we analyzed soil characteristics and used absolute quantitative high-throughput sequencing to assess microbial communities in active burrow, inactive burrow, and off-burrow soils across four rodent species (marmot, squirrel, gerbil, and vole) in the Hulunbuir grassland of Inner Mongolia, China. This study demonstrates that rodent activity creates chemically distinct soil microhabitats, with nitrate (NO --N) enrichment in active burrow soils consistently observed across rodent species. Elevated soil NO3--N was associated with reduced microbial phylogenetic diversity and reorganization of amoeba-co-occurring bacterial assemblages. Both absolute abundance-based correlations and functional prediction of co-occurring bacteria indicated that amoebae were primarily associated with nitrogen-cycling bacteria in off-burrow soils. In burrow soils, amoebae increasingly interacted with bacterial taxa associated with pathogenicity while retaining ties to nitrogen-cycling taxa. Structural equation modeling and mediation analysis revealed that NO3--N enrichment indirectly linked to increased infectious disease-related functional potential by amoeba-associated bacterial restructuring and coordinated shifts in nitrogen cycling, independent of changes in bacterial abundance. Together, our findings highlight the importance of rodent-driven soil heterogeneity in shaping amoeba-bacteria interactions and suggest that rodent-mediated NO --N enrichment may promote the emergence and persistence of potentially pathogenic bacteria, with broader implications for soil ecosystem functioning and disease-related processes in terrestrial ecosystems.

The contribution of soil chemistry to plant growth and resilience, including presence of phytohormones, is increasingly recognized. However, comprehensive characterization of soil phytohormones remains limited by chemical complexity of soil matrices, diversity and low- abundance of metabolites. To enable further discoveries we developed and validated performance of a liquid chromatography-mass spectrometry method with solid phase extraction, integrating targeted and untargeted hormonomic approaches for comprehensive soil phytohormone profiling. Method performance was evaluated for sixteen plant growth-regulating compounds and precursors, including abscisic acid, auxins, cytokinins, gibberellic acid, jasmonic acid, salicylic acid, karrikins, melatonin, serotonin, and tryptophan. The method demonstrated strong linearity (R{superscript 2} = 0.989-0.999), high sensitivity (limits of detection and quantification 0.1-50.2 and 1.4-167.3 pg on-column, respectively), and acceptable precision (1.3-9.6% intraday; 3.4-34.8% interday). Soil composition had a significant effect on recovery, with recovery being poor in some soils such as clay-rich soils; however, recovery for most phytohormones were within 20% of the matrix- adjusted spiked value. Validation results confirm that the method is suitable for use and was then used to quantify analytes in representative soil types. Integration of untargeted analysis expanded coverage to 250 additional putative phytohormones and hormone-related metabolites, revealing chemical signatures potentially associated with plant community composition. The method is robust across these soils spanning sandy, peat-rich, and clay-rich textures. This approach provides a versatile framework for investigating belowground phytohormone dynamics and their roles in plant physiology, resilience, and soil-plant feedbacks.

O_LICliffs are environmentally extreme yet biodiversity-rich ecosystems that harbour specialist plants, many endemic and threatened. Plant persistence in these nutrient-poor substrates may depend on tightly linked soil- and root-associated microbial communities, which remain poorly understood. These interactions may become increasingly important with the global expansion of recreational climbing. While physical climbing impacts on vegetation are documented, potential chemical effects, from the use of climbing chalk (magnesium carbonate), on soil properties and plant-associated microbiota remain unknown. C_LIO_LIWe sampled soils and roots beneath cliff-specialist and generalist plants, and unvegetated soils, across climbed and unclimbed routes in northern, central, and southern Spain. Soil physicochemical properties were quantified, fungal communities were characterized using ITS-metabarcoding, and structural equation modelling was used to disentangle direct and indirect effects. C_LIO_LIClimbing increased soil pH and altered soil chemical properties, driving shifts in fungal diversity and functional composition in soil and roots. The relative read abundance of root-associated symbiotrophic fungi declined, whereas arbuscular mycorrhizal fungi and pathogens increased in climbed cliffs. Overall effects were consistent, with cliff-specialist plants mediating nutrient and fungal shifts. C_LIO_LIur findings show that climbing can reshape cliff soil chemistry and fungal communities, with potential cascading consequences for plant functional performance, nutrient dynamics, and ecosystem resilience. C_LI

Photorhabdus bacteria are potent insect-killing microbes associated with entomopathogenic nematodes and offer opportunities for environmentally benign pest control. They can be applied as foliar sprays or soil drenches without their nematode vector, resulting in massive amounts of Photorhabdus cells and their (toxic) metabolites introduced into the soil. However, their effects beyond the target organisms are unknown. To fill this knowledge gap, we investigated the soil legacy effects of Photorhabdus cells and their metabolites on soil microbial communities, plant performance and resistance to herbivores. To this end, we first conditioned soils with i) mechanically killed (MK) or Photorhabdus-infected insect larvae, ii) aqueous extracts of MK or Photorhabdus-infected insect larvae, iii) cell-free Photorhabdus supernatants, iv) autoclaved soil complemented with live soil previously conditioned with MK or Photorhabdus-infected insect larvae. We then grew maize plants in these soils and measured plant biomass, profiled soil microbial communities and plant metabolites, and evaluated plant resistance against two pest insects Diabrotica balteata and Spodoptera frugiperda. We found that conditioned soils increased plant biomass by 10-26% relative to controls and significantly altered soil bacterial and nematode communities, and to a lesser extent, fungal communities. Re-inoculating conditioned soil microbiota into autoclaved soils recreated the plant growth-promoting effects, indicating microbial-mediated mechanisms. Additionally, plants grown in soils conditioned with Photorhabdus-infected insect cadavers were often more resistant to herbivorous insect attack, in a strain-specific manner. On average, D. balteata and S. frugiperda larvae gained 10-20% and 10-59% less weight, respectively, when fed on plants grown in conditioned soils than on plants grown in control soils. The plant metabolic profiles of plant leaves and roots also varied with resistance levels. We conclude that Photorhabdus metabolites modulate soil microbial communities towards a structure that enhances plant growth and triggers systemic responses against herbivores.

Viruses are key regulators of terrestrial carbon, nitrogen, and phosphorus cycling, yet how environmental perturbations structure viral activity remains poorly resolved. Rewetting of seasonally dry soils triggers rapid microbial and viral responses, but the relationships between virion-associated and transcriptionally active viral communities, and the role of phosphorus in these dynamics, remain unclear. Here, we integrated viromics, metatranscriptomics, environmental DNA (eDNA), and amplicon sequencing to track viral succession and virus-host interactions over three weeks following soil rewetting, with and without phosphorus amendment. We identified 13,840 viral populations (vOTUs), of which 3,803 were transcriptionally active, representing ongoing infections. Wet-up significantly altered virion and transcriptionally active viral communities, while phosphorus selectively influenced prokaryotic and transcriptionally active viral communities but not virion composition. Virus-host linkages were predicted for 32% of vOTUs, with transcriptionally active bacteriophages infecting Actinomycetota increasing under phosphorus amendment. Following wet-up, virion abundance decreased [~]3-fold while virocells increased [~]5-fold, indicating a shift from viral persistence in dry soils to active infection. Phosphorus further enhanced virocell abundance. eDNA captured rapid viral turnover and revealed transient dynamics not resolved by viromes or metatranscriptomes alone. Together, these results demonstrate that soil viral communities are structured by distinct but complementary molecular pools that operate over different ecological timescales. Wet-up activates a reservoir of persistent virions, while phosphorus availability regulates infection dynamics and host-virus coupling. These findings highlight viruses as dynamic drivers of microbial turnover and nutrient cycling following environmental perturbation, advancing a more predictive understanding of soil ecosystem responses to changing resource availability.