[This corrects the article DOI: 10.1016/j.crmicr.2022.100138.].

Cultural management practices in vineyards ( Vitis spp.) significantly influence soil quality. Nevertheless, the impact of these practices on soil quality within Chile's heritage vineyards remains largely unexplored. This study sought to assess the effects of two distinct management practices-organic and conventional-on soil quality in vineyards located in the Itata Valley, & Ntilde;uble Region. The investigation focused on microbiological variables, including microbial biomass, basal respiration, and enzymatic activities associated with the C, N, P, and S cycles, as well as chemical variables such as pH, organic matter, available nutrients, and total soil trace elements. Additionally, the study examined the influence of varying durations of organic management (2 to 11 yr) on soil quality parameters. Organic management was found to significantly enhance soil biological activity, as indicated by increased basal respiration, microbial biomass, and key enzymatic activities related to the C, N, P, and S cycles, with improvements ranging from two-to 3.2-fold (P < 0.05) compared to conventional management. Conversely, conventionally managed vineyards exhibited higher soil nutrient availability, including nitrate (58%) and sulfate (95%), than their organically managed counterparts. Soil quality has improved with extended periods of organic management. Over the span of 2 to 11 yr of organic management, there were significant increases in pH and Ca (P < 0.05), while Cd levels decreased by 25%. Consequently, organic management is superior for the sustainability of heritage vineyards, as it increases soil biological activity by up to 3.2-fold and reduces heavy metals such as Cd by 25% after 11 years of implementation.

Microbial biofilms are surface aggregates of microorganisms encapsulated within a self-secreted polymeric matrix. These aggregates grow, colonize, and thrive on various surfaces in diverse ecosystems, from terrestrial and aquatic to within the human body and on medical implants. Due to their compositional heterogeneity, biofilms exhibit varied physicochemical features, providing an arsenal of desirable properties. As symbiotic structures, microbial biofilms are important players in ecosystems, participating in nutrient replenishment, biogeochemical cycles, and soil structure stabilization. With such potential, especially in enhancing soil integrity and mitigating climate change, it is essential to study various aspects of these films’ structure, behavior, and interactions of the constituting microbial communities with soil. Although complex biofilm-soil interactions have been extensively studied, a comprehensive investigation integrating various aspects is still lacking. This review discusses different facets of microbial biofilms concerning microbial diversity, structural and compositional variations, influence on soil structure and aggregation, impact on soil fertility, and involvement in different biophysical processes. Furthermore, this review also highlights the impacts of climate change, challenges and limitations faced at different levels with respect to biofilms, and suggests the directions of future research on agricultural resources to address these limitations. The primary aim of this article is to emphasize how microbial biofilms benefit the resilience and sustainability of agricultural and food systems.

Global agriculture takes place in diverse environmental contexts that can impact its sustainable production. To assist in crop growth and development, strategies have been proposed to modify the microbiome, expecting positive outcomes from the plant–microbe–environment interaction. In this Topical Collection on “The Role of Plant Microbiome Engineering in Stressful Agriculture”, a set of articles has been gathered that explore various strategies—from in silico to experimental approaches—with the goal of proposing new paths toward sustainable production.

Pistachio (Pistacia vera L.) is among the most economically important nut crops worldwide. They are increasingly exposed to the environmental constraints associated with climate change, including drought, salinity, nutritional imbalances, and heightened disease pressure. These stressors compromise plant growth, physiological performance, nutrient acquisition, and orchard productivity, highlighting the need for sustainable strategies to enhance crop resilience. This review critically examines the current knowledge on the functional roles of arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) in pistachio production. Evidence indicates that AMF and PGPR contribute to plant performance through multiple complementary mechanisms, including improved nutrient mobilization and uptake, maintenance of ionic homeostasis, enhancement of water-use efficiency, stimulation of antioxidant defenses, modulation of stress-related signaling pathways, and suppression of phytopathogens. AMF primarily enhance phosphorus acquisition, water relations, and soil structural stability, whereas PGPR contribute to nutrient solubilization, biological control, and induction of plant defense responses. Despite promising experimental results, most studies have been conducted under controlled conditions, limiting the translation of microbial inoculation strategies to commercial orchards in the field. We identified the key knowledge gaps and research priorities required to improve the consistency, scalability, and field validation of microbiome-based approaches for sustainable pistachio production under increasingly challenging environmental conditions.

As food demand increases, agricultural practices have evolved, prompting increased exploration of sustainable ecological techniques and utilization of plant-associated microorganisms. In this context, plant fitness has been enhanced by plant growth-promoting microorganisms (PGPM), which stimulate growth through direct mechanisms, such as improved nutrient availability and phytohormone production, as well as indirect mechanisms, including protection against phytopathogens and suppression of soil-borne diseases. However, these innate capabilities of PGPM can be further improved through genomic modification or editing. This article reviews advances in the genomic engineering of plant-beneficial microorganisms as tools to enhance their positive effects on crop performance and environmental remediation. The genetic modification strategies analyzed here include random mutagenesis, targeted genome editing (such as CRISPR-Cas), gene over-expression, genome shuffling, RNA interference, metabolic pathway engineering, and synthetic biology approaches. These tools have enabled the optimization of functions, such as nitrogen fixation, phosphate solubilization, secondary metabolite production, biocontrol, stress tolerance, and bioremediation. However, we propose expanding the discussion of their regulation and use in various countries. Additionally, these modifications must be efficient and safe for the beneficial microbiota associated with the target crop, as well as for humans, animals, and the environment, all of which depend on sustainable agricultural practices.

World agriculture depends in part on the crop-associated microbiome for improved plant growth, health, and productivity. In particular, endophytic fungi (EF) with plant growth–promoting activities fulfill some of these roles and are central as bioinoculant agents. In the case of arbuscular mycorrhizal fungi (AMF), they form a symbiosis with their host plants, enhancing the uptake of water, phosphorus, nitrogen, and other micronutrients, while the plants provide them with photosynthates. This work reviews the differences in the colonization of internal plant niches between these beneficial fungi, as well as other distinctive ecological traits. It also explores mechanisms of seedborne vertical transmission in AMF and their classification. Genomic and transcriptomic advances in fungal endophytes are highlighted, shedding light on genes and expression profiles that define their lifestyle and plant associations. In addition, recent studies on their abilities to promote plant growth are analyzed, especially focusing on Trichoderma spp., Epichloë spp., Serendipita indica (formerly Piriformospora indica), and entomopathogens like Beauveria spp. and Metarhizium spp. Finally, the multiple interactions among EF, AMF, and other members of the plant microbiome—notably plant growth-promoting bacteria (PGPB)—are discussed, emphasizing how these organisms synergistically benefit the host. A deeper understanding of these fungi and their plant-beneficial effects should facilitate commercialization and help farmers achieve sustainable production, especially under challenges posed by global climate change.

Bioprospecting of plant growth-promoting bacteria enables the identification of beneficial microbial resources with significant potential for sustainable agricultural applications. In this context, strain TRQ48 was isolated from a commercial field of wheat (Triticum turgidum L. subsp. durum) located in the Yaqui Valley, Mexico, with the aim of exploring its plant growth-promoting potential. The draft genome sequence presented a genomic size of 2,777,016 bp, 32.5% G + C content, 665,763 bp N50, 2 L50, and 19 contigs. Taxonomic affiliation demonstrated that strain TRQ48 belonged to Mammaliicoccus sciuri. Genome annotation identified 2756 coding DNA sequences (CDS) distributed into 259 subsystems, highlighting CDS associated with iron acquisition and metabolism, stress response, and virulence, disease, and defense, among others. Metabolic assays reflect the strain’s capacity to produce siderophores and auxins, relating these positive traits to significantly (p ≤ 0.05) promote growth of wheat shoot length (7.09%) and root and shoot dry weight (75% and 18.43%) compared to uninoculated wheat plants. Biosafety testing indicated that the strain is susceptible to commonly used antibiotics and lacks clinically relevant resistance profiles, matching genomic analysis, which did not reveal any critical virulence factors. Thus, although the presented results show that M. sciuri TRQ48 is a promising beneficial biosafe strain, further studies are still needed to evaluate its performance under agro-ecosystems at commercial levels.

Trichoderma virens and plant growth-promoting bacteria (PGPB) are well-known agents that promote plant development and control pathogens. This study assessed the compatibility, biocontrol potential, and plant growth promotion of T. virens in combination with four PGPB strains (Pseudomonas fluorescens UM270, Rouxiella badensis SER3, Bacillus velezensis AF12, and Bacillus halotolerans AF23) against Fusarium brachygibbosum and Arabidopsis thaliana. The results showed that single inoculations significantly inhibited the growth of F. brachygibbosum by the 7th day of confrontation. However, co-inoculating T. virens with PGPB exhibited synergistic effects on the inhibition percentages for the consortia Tv + UM270 (48.94%), Tv + AF12 (67.04%), and Tv + SER3 (78.63%). Plant assays demonstrated that most microorganisms enhanced root development and plant height, with UM270 having the strongest beneficial effect. Expression analysis of T. virens effector genes (sm1, tvsep3, and tvhydii1) indicated early induction of tvhydii1 in the condition of Fb + AF12 at day 3, while sm1 was downregulated. No significant changes in the expression of these genes were detected during interaction with A. thaliana and PGPB. These findings demonstrate that T. virens-PGPB can simultaneously promote plant growth and suppress pathogens, with effector genes such as tvhydii1 contributing to these interactions, highlighting their potential for sustainable agriculture.

The rising global food demand requires boosting agricultural productivity without compromising environmental sustainability, especially in the face of intensive agrochemical use and soil degradation. Based on this, strain TRQ67 was isolated from wheat rhizosphere soil in the Yaqui Valley, Mexico, and characterized morphologically, biochemically, and genomically. Strain TRQ67 possesses a genome of 4.04 Mbp across 37 contigs with a G + C content of 46.3%, comprising 4127 coding DNA sequences (CDSs), and was identified as Bacillus velezensis through Overall Genome Relatedness Indices (OGRIs), including Average Nucleotide Identity (OrthoANI = 99.12%) and Genome-to-Genome Distance Calculator (Formula 2: 92.6%). The genome revealed key functional genes associated with auxin biosynthesis (trpABCDEF and yhcX), iron acquisition (dhbABF), nutrient solubilization (gabD, acnAB and pyc), stress response (clpCEPX and pspA), antifungal metabolite synthesis (srfAABCD, fenABCD and bmyABC), chemotaxis and motility (cheABCD, motAB, flgBCDEF, swrC), bacterial fitness (acoABR, acuABC and budABC), exopolysaccharide production (epsDEFHI), sporulation (spo0ABEF) and bioremediation. Predicted gene functions were supported by in vitro phenotypic assays; strain TRQ67 was able to solubilize phosphate (Solubilization Index of 4.1 ± 0.46), biosynthesize siderophores (Production Index of 1.70 ± 0.16), and produce indoles (6.52 ± 0.63 µg mL−1). Furthermore, this strain demonstrated antagonistic activity against phytopathogenic fungi Fusarium languescens and Bipolaris sorokiniana, resulting in reductions in fungal growth area of 87.33% and 89.28%, respectively. These antagonistic effects are consistent with the presence of Biosynthetic Gene Clusters (BGCs) encoding lipopeptides (surfactin and fengycin), polyketides (difficidin, bacillaene and macrolactin H), dipeptides (bacilysin) and siderophores (bacillibactin), as identified through antiSMASH analysis. Finally, the strain significantly improved root (27.63%) and shoot (5.82%) biomass in wheat plants under controlled conditions. These results highlight Bacillus velezensis TRQ67 as a promising microbial inoculant with plant growth promotion capabilities and potential antifungal activity against phytopathogenic fungi, as evidenced by strong in vitro antagonistic activity, supporting its further evaluation for sustainable agricultural practices.

The milpa is a Mesoamerican agroecological polyculture that faces productivity limitations due to environmental factors, and the use of plant growth-promoting rhizobacteria (PGPR) represents a promising strategy to mitigate these stressors. In this study, we evaluated the impact of a bioinoculant based on Pseudomonas fluorescens UM270, applied in liquid form and encapsulated in alginate beads, on the growth and production of Zea mays within a milpa system associated with Phaseolus vulgaris and Cucurbita spp. Both formulations improved maize growth, significantly enhancing chlorophyll content, plant height, root development, and biomass. The liquid bioinoculant increased maize yield by 35–37

Forest soils in industrialized coastal zones can experience chronic diffuse trace element (TE) exposure, yet how vegetation replacement influences soil microbial communities under these conditions remains poorly understood. This study compared soils from native sclerophyllous forests and exotic pine plantations in the Hualpén Peninsula Nature Sanctuary (Chile), located near an industrial complex characterized by oil refining, petrochemical, steel, and port activities. Twenty-two soil sites were evaluated for TE concentrations, contamination indices, physicochemical properties, microbial biomass, enzymatic activities, and bacterial community composition using 16S rRNA gene sequencing. Native forest soils contained 89% more organic matter (14.4% vs. 7.6%) and nearly twice the available N (53.6 vs. 26.2 mg kg-1) than plantation soils. These soils also exhibited greater respiration and microbial biomass carbon, whereas plantation soils showed higher metabolic quotients (qCO2), indicating lower microbial metabolic efficiency. Soil pH remained acidic in both systems (5.6-5.8). Mn and Zn were the most abundant elements, while contamination factors were highest for Pb, Cr, and Mn, indicating persistent trace element enrichment across the study area. Bacterial communities were dominated by Proteobacteria, Actinobacteriota, and Acidobacteriota, with native forest soils showing significantly higher Faith phylogenetic diversity (p = 0.041). Redundancy analysis revealed that bacterial community structure was more strongly associated with nutrient availability and microbial functional indicators than with trace element enrichment. However, Cr showed a significant secondary association (envfit r2 = 0.53, p = 0.032). Overall, the results indicate that variation in soil microbial functioning was more closely associated with vegetation type and related soil properties than with chronic trace element enrichment. These findings highlight the importance of considering land-use change, soil quality, and contamination together when evaluating microbial responses in industrially influenced forest ecosystems.

Pseudomonas fluorescens and its effect on blueberry (Vaccinium spp.) tolerance to phytopatogenic fungi Blueberry is a relative new crop in Mexico, it has been cultivated since the early 2000s; however, in the field it presents fruit worm, trips, and different diseases. This research shown the effect of in vitro inhibition of Pseudomonas fluorescens UM16, UM240, UM256, and UM270 strains against pathogenic fungi Phytophtora cinnamomi, Fusarium sp., and Phomopsis vaccinii, and the inoculation of Pseudomonas and fungi on blueberry (Vaccinium spp.) genotypes, Biloxi and UM811. The inhibition tests showed that the strains UM270, UM16, and UM256 inhibited Phytophtora cinnamomi, and Fusariu sp. by 34 and 30 % respectively, but not Phomopsis vaccinii. The Biloxi plants inoculated with the strains UM270, UM16+Phytophtora, and UM16+Phomopsis showed greater plant length with 91,6, 90,1 and 90,8 cm, respectively, greater dry root weight with 43,5 g (UM256+Phomopsis) and plant dry weight with 31,5 g, (UM16+Phomopsis), comparated with the UM811 genotype con45,3 cm (UM240+Fusarium), 43 g (UM240), and 15,1 g (UM240+Phomopsis), respectively, and the control plants of each genotype. The results showed that Pseudomonas strains used in this research can be a viable alternative in the control of Fusarium and Phytophtora root fungi , in blueberry crop.

The resident microbiota in agricultural soils strongly influences crop health and productivity. In this study, we evaluated the prokaryotic diversity of two clay soils with similar physicochemical characteristics but contrasting levels of maize (Zea mays L.) and wheat (Triticum aestivum L.) production using 16S rRNA gene sequencing. Yield records showed significant differences in grain production over five consecutive years. When comparing prokaryotic alpha diversity between the "non-productive" and "productive" soils, no major differences were found, and the abundance of ammonia-oxidizing archaea (AOA) and bacterial genera such as Arthrobacter, Neobacillus, and Microvirga remained consistent across soils. Analysis of the top 20 genera showing the greatest abundance shifts by compartment (bulk soil vs. rhizosphere) revealed that genera such as Priestia, Neobacillus, Sporosarcina, and Pontibacter decreased in the rhizosphere of the non-productive soil, while in the productive soil, these genera remained unchanged. In the non-productive soil, genera such as Flavisobacter decreased in abundance in the rhizosphere, whereas Arthrobacter increased. Principal coordinates analysis (PCoA) showed no clear clustering by compartment (bulk vs. rhizosphere), but two distinct clusters emerged when grouping by soil type (productive vs. non-productive). Interaction networks varied by soil type: non-productive soils showed positive Candidatus-Bacillus and negative Massilia links, while productive soils were dominated by Flavisolibacter and negative Pontibacter. Across soils, Rhizobium-Bradyrhizobium associations were positive, whereas Neobacillus and Priestia were negative. These findings highlight that a few potential beneficial microbiota and their interactions may be key drivers of soil productivity, representing targets for microbiome-based agricultural management.

Fire, whether occurring on the surface or underground, significantly influences soil microbial dynamics by reshaping community composition, functional diversity and overall soil and plant health. This review examines the effects of fire on soil-beneficial microbial communities, with particular attention to how surface and underground fires drive shifts in microbial diversity and functional roles within the agroecosystems. These changes impact key processes such as nutrient cycling, soil physicochemical structure and organic matter decomposition, ultimately affecting crop production. Bacterial groups such as Firmicutes and Actinobacteria often increase in abundance following fire events, while others lacking survival strategies tend to decline. Resilient fungal groups, including Ascomycota (such as Aspergillus, Penicillium and Trichoderma), frequently play pivotal roles during the recovery process. Fire can also enhance microbial metabolic activity, particularly in pathways involved in organic matter degradation, leading to short-term increases in nutrient availability that support plant regrowth. Finally, the review discusses the molecular responses of microbes to fire and outlines perspectives for better understanding this type of stress and how it affects the beneficial soil microbiota in agricultural edaphic systems.

Abstract Plant growth-promoting bacterial endophytes represent a sustainable strategy for enhancing agricultural productivity while reducing reliance on synthetic fertilizers and pesticides. This study focused on the genomic and functional characterization of two endophytic bacterial strains, R11F and R19M, isolated from bean and maize roots, respectively. Comparative analyses based on 16S rRNA gene sequences, average nucleotide identity (ANI), and genome-to-genome distance calculations (GGDC) classified both isolates as Pseudomonas palleroniana . Comparative genomic analyses revealed highly conserved genomes containing genes associated with plant colonization, phosphate solubilization, stress adaptation, heavy metal resistance, and hydrocarbon degradation. Genome mining further identified 17 and 18 biosynthetic gene clusters (BGCs) in R11F and R19M, respectively, including non-ribosomal peptide synthetases (NRPS), pyoverdine, NRP-metallophores, RiPP-like compounds, arylpolyenes, β-lactones, terpenes, NAGGN, and hydrogen cyanide. Strain-specific BGCs associated with syringomycin and viscosin biosynthesis were identified in R11F, whereas R19M harbored clusters related to asplenin and kolossin biosynthesis. In vitro assays confirmed indole production, phosphate solubilization, and siderophore production, as well as the ability of both strains to grow in nitrogen-free medium. Both strains significantly inhibited the growth of Fusarium oxysporum , Phytophthora cinnamomi , and Colletotrichum gloeosporioides . Furthermore, plant inoculation assays demonstrated host-dependent growth promotion, with R11F showing the most consistent improvements in plant growth parameters in tomato, wheat, and lentil. Overall, the integration of comparative genomics and experimental validation demonstrates that P. palleroniana R11F and R19M possess complementary traits associated with plant growth promotion, pathogen suppression, saline stress adaptation, and bioremediation.

ABSTRACT Climate change‐mediated abiotic stresses limit crop performance, and plant responses are increasingly recognized as emergent properties of the coupling between soil, plants, and microbiomes rather than inherent plant characteristics. This review synthesizes mechanistic evidence from 2020 to 2025 on how rhizosphere microbiota contribute to crop stress adaptation within climate‐smart agriculture. We combined ecological theory with biochemical and physiological investigations to demonstrate how microbial community assembly, functional redundancy, network organization, and cropping‐system legacy interact with soil conditions to shape stress‐mitigating microbial pathways. Microbes employ these pathways, including phytohormone modulation, osmolyte and exopolysaccharide synthesis, volatile‐mediated signaling, and nutrient‐transforming metabolites, to influence plant performance under stress. Instead of considering microbiome interventions as universally transferable solutions, we highlight the constraints on microbial establishment and functioning imposed by soil structure, nutrient stoichiometry, moisture regime, host genotype, and legacy‐conditioned soil ecological contexts. We critically examine existing rhizosphere engineering approaches, including synthetic communities and inoculants, soil amendments, and microbiome‐based plant breeding, and highlight clear evidence of causation, inconsistencies, and unresolved outcomes. Particular emphasis is placed on emerging evidence that prior cropping systems, especially legume‐inclusive rotations, function as ecological conditioning mechanisms that influence microbial recruitment, amendment responsiveness, and intervention persistence. Based on this synthesis, we identify key knowledge gaps and focus on mechanistic research required to enhance the predictability, monitoring, and scalability of microbiome‐based strategies. Overall, we advance the concept of crop resilience as a property of coupled soil‐microbiome systems, and argue that climate‐smart agriculture requires predictable, scalable, and mechanistically grounded microbiome‐based approaches.