Vilchez, Juan Ignacio

Cheng R., Ke T., Gui F., Li J., Zhang X., Vílchez J.I., Matsumoto H.

Abstract Recent evidence highlights the potential of the plant microbiota to increase host plant disease resistance through the production of bioactive small molecules. However, the absence of comprehensive platforms for rapid access to this information hampers progress in the field. To address this gap, we developed the Disease Resistance-Shaping Small Molecules Database (drSMALL), a freely accessible and continuously updated resource that compiles profiles of microbial small molecules, which were experimentally evidenced to be associated with host disease resistance. drSMALL interlinks detailed information on microbial species, the small molecules they produce, host plants, and targeted pathogens, facilitating streamlined access to essential data. This initiative aims to advance the understanding of small molecules in disease resistance, filling a critical gap in data accessibility while fostering deeper exploration of sustainable agricultural practices. By leveraging the natural capabilities of plant microbiomes, drSMALL seeks to support innovative strategies for enhancing crop health and resilience against diseases.

Gil T., Romão I.R., Gomes J.D., Vergara-Diaz O., de Carvalho L.A., Sousa A., Kasa F., Teixeira R., Mateus S., Katamadze A., Pinheiro D.G., Vicente R., Vílchez J.I.

Maize, a vital crop for human nutrition, livestock, and industrial development, faces increasingly severe climatic conditions that hinder its production capacity along with other strategic crops. Novel treatments based on microorganisms have demonstrated efficiency in enhancing plant development and responding to stress. The use of bacteria isolated from seeds is a novel approach for biotreatment, as recent studies point to a co-evolution process for their presence in seeds. This approach hypothesize a pre-adaptation to its host, which may lead to increased efficiency. However, several aspects of this approach remain understudied. In this study, we aimed to evaluate the potential of native maize seed microbiota in comparison to that isolated from other species to mitigate drought stress. For this we characterized seedborne microbiota of a common productive maize variety in Portugal, to use it as biotreatment in other two varieties (sensitive and resistant to drought), selecting the strain Pseudomonas fulva MB as the most promising candidate. Stenotrophomonas maltophilia MS-M1 strain, isolated from wild alfalfa seeds and previously characterized as a drought-tolerant enhancer, served as a non-native control strain. . According to the data, both varieties of maize demonstrated enhanced vegetative growth when treated with both individual strains, as well with the consortium, with an increase in plant height of 5-7% in full and medium irrigation, and 50-55% when not irrigated. This trend was also observed in plant weight, which increased by 13-23%, even under no irrigation. In addition, production in both varieties was positively impacted by these treatments, based on the amount of grain produced (by weight). The drought-sensitive variety experienced a 17% increase under full irrigation, while the most tolerant variety experienced a 25-40% increase. Under medium irrigation level, the increase was about 15% in both varieties, while a 100% and 140% increase was observed in each variety, respectively, when no irrigation was applied. The results suggest that native strain the P. fulva MB was slightly more efficient treatment, as it outperformed the non-native strain in terms of productivity in both varieties. However, the differences were not solid enough along all parameters to consistently asses such difference. The consortium treatment only showed better performance under full or medium irrigation conditions for some production traits. These findings support the use of seed microbiota as very efficient biotreatments, suggesting than even non-native strains have a remarkable beneficial impact (interspecific), expanding the possible of use of this kind of bioinoculants. Further test are required to optimize the use of seed-isolated strains as better adapted or tailor-made solutions for agriculture.

Wu X., Yang Y., Wang M., Shao C., Morillas J.I., Yuan F., liu J., Zhang H.

Gil T., Rebelo Romão I., do Carmo Gomes J., Vergara-Diaz O., Amoroso Lopes de Carvalho L., Sousa A., Kasa F., Teixeira R., Mateus S., Katamadze A., Pinheiro D.G., Vicente R., Vílchez J.I.

Gil T., Teixeira R., Sousa A., d’Oliveira Palmeiro M.A., Cruz Coimbra de Matos A., Niza Costa M., Ferrer M.V., Rodrígues dos Santos A.S., Sequero López C., Rebelo Romão I., Vílchez J.I.

Saline and gypsic soils impede or condition the establishment of farms in many regions worldwide. Stress caused by the accumulation of sodium or calcium ions in the soil drastically limits plant growth and is a limiting factor in the production of many crops. For this reason, saline and gypsic soils were preferentially exploited for mineral extraction. However, nowadays, they can be a source of new biotechnological tools to help in the osmotic stress to which some crops are exposed. In these environments, despite being traditionally characterized by their low biodiversity, we can find well-adapted microbiota that may be able to interact with plants to deal with different environmental stresses. These mechanisms may consist of a very important contribution to the development of new osmotic stress-dealing bioinoculants. The present study sought to elucidate the diversity of the cultivable population of such environments and use them as regulators of soil nutrients and stress-relieving symbionts in plants under osmotic stress. Among the candidate strains selected to cover more scenarios, we found that the strains Stutzerimonas stutzeri A38 and Bacillus pumilus A49 were able to increase root size under osmotic stress in Medicago sativa and Medicago polymorpha plants. Moreover, Peribacillus frigoritolerans A70 and Bacillus licheniformis A46 also enhanced the performance in M. polymorpha, showing interesting potential for a future use in wasteland use for production to livestock feeding or other relevant industries.

Costa M.N., Gil T., Teixeira R., Santos A.S., Romão I.R., López C.S., Vílchez J.I.

During 2022, intense heat waves, together with particularly extreme dry conditions, created a propitious scenario for wildfires, resulting in the area of vegetation consumed in Europe doubling. Mediterranean countries have been particularly affected, reaching 293,155 hectares in Spain, the worst data in the last 15 years. The effects on the vegetation and the soil are devastating, so knowing the recovery factors is essential for after-fire management. Resilient microorganisms play a fundamental role in rapid nutrient recycling, soil structure, and plant colonization in fire-affected soils. In this present work, we have studied emergent microbial communities in the case of the Los Guájares (Granada, Spain) fire, one of the most extensive of the year, to evaluate their role in the recovery of soil and vegetation cover. We aim to discern which are the main actors in order to formulate a new treatment that helps in the ecosystem recovery. Thus, we have found the relevant loss in phosphorous and potassium solubilizers, as well as siderophores or biofilm producers. Here, we decided to use the strains Pseudomonas koreensis AC, Peribacillus frigoritolerans CB, Pseudomonas fluorescens DC, Paenibacillus lautus C, Bacillus toyonensis CD, and Paenarthrobacter nitroguajacolicus AI as a consortium, as they showed most of the capacities required in a regenerative treatment. On the other hand, the microcosm test showed an enhanced pattern of germination of the emerging model plant, Bituminaria bituminosa, as well as a more aggregated structure for soil. This new approach can create a relevant approach in order to recover fire-affected soils in the future.

Niza-Costa M., Rodríguez-dos Santos A.S., Rebelo-Romão I., Ferrer M.V., Sequero López C., Vílchez J.I.

Agricultural production is being affected by increasingly harsh conditions caused by climate change. The vast majority of crops suffer growth and yield declines due to a lack of water or intense heat. Hence, commercial legume crops suffer intense losses of production (20–80%). This situation is even more noticeable in plants used as fodder for animals, such as alfalfa and pitch trefoil, since their productivity is linked not only to the number of seeds produced, but also to the vegetative growth of the plant itself. Thus, we decided to study the microbiota associated with their seeds in different locations on the Iberian Peninsula, with the aim of identifying culturable bacteria strains that have adapted to harsh environments and that can be used as biotreatments to improve plant growth and resistance to stress. As potentially inherited microbiota, they may also represent a treatment with medium- and long-term adaptative effects. Hence, isolated strains showed no clear relationship with their geographical sampling location, but had about 50% internal similarity with their model plants. Moreover, out of the 51 strains isolated, about 80% were capable of producing biofilms; around 50% produced mid/high concentrations of auxins and grew notably in ACC medium; only 15% were characterized as xerotolerant, while more than 75% were able to sporulate; and finally, 65% produced siderophores and more than 40% produced compounds to solubilize phosphates. Thus, Paenibacillus amylolyticus BB B2-A, Paenibacillus xylanexedens MS M1-C, Paenibacillus pabuli BB Oeiras A, Stenotrophomonas maltophilia MS M1-B and Enterobacter hormaechei BB B2-C strains were tested as plant bioinoculants in lentil plants (Lens culinaris Medik.), showing promising results as future treatments to improve plant growth under stressful conditions.

Rodrigues-dos Santos A.S., Rebelo-Romão I., Zhang H., Vílchez J.I.

As a response to the current challenges in agriculture, the application of alternatives to a more sustainable management is required. Thus, biofertilizers begin to emerge as a reliable alternative to improve crop development and resistance to stresses. Among other effects on the plant, the use of beneficial strains may cause changes in their metabolic regulation, as in cell wall biogenesis and in nutrient/ion transportation, improving their growth process. Previous works showed that inoculation with the strain Priestia megaterium YC4-R4 effectively promoted vegetative growth of Arabidopsis thaliana Col-0 plants. Hence, the present work recorded a strain-mediated induction of several pathways of the central and secondary metabolism of the plant, as the induction of lipid, cellulose, phenol, and flavonoid biosynthesis, by using transcriptomic and biochemical analyses.

He D., Singh S.K., Peng L., Kaushal R., Vílchez J.I., Shao C., Wu X., Zheng S., Morcillo R.J., Paré P.W., Zhang H.

Lv S., Yang Y., Yu G., Peng L., Zheng S., Singh S.K., Vílchez J.I., Kaushal R., Zi H., Yi D., Wang Y., Luo S., Wu X., Zuo Z., Huang W., et. al.

Root microbiota is important for plant growth and fitness. Little is known about whether and how the assembly of root microbiota may be controlled by epigenetic regulation, which is crucial for gene transcription and genome stability. Here we show that dysfunction of the histone demethylase IBM1 (INCREASE IN BONSAI METHYLATION 1) in Arabidopsis thaliana substantially reshaped the root microbiota, with the majority of the significant amplicon sequence variants (ASVs) being decreased. Transcriptome analyses of plants grown in soil and in sterile growth medium jointly disclosed salicylic acid (SA)-mediated autoimmunity and production of the defense metabolite camalexin in the ibm1 mutants. Analyses of genome-wide histone modifications and DNA methylation highlighted epigenetic modifications permissive for transcription at several important defense regulators. Consistently, ibm1 mutants showed increased resistance to the pathogen Pseudomonas syringae DC3000 with stronger immune responses. In addition, ibm1 showed substantially impaired plant growth promotion in response to beneficial bacteria; the impairment was partially mimicked by exogenous application of SA to wild-type plants, and by a null mutation of AGP19 that is important for cell expansion and that is repressed with DNA hypermethylation in ibm1. IBM1-dependent epigenetic regulation imposes strong and broad impacts on plant-microbe interactions and thereby shapes the assembly of root microbiota.

He D., Singh S.K., Peng L., Kaushal R., Vílchez J.I., Shao C., Wu X., Zheng S., Morcillo R.J., Paré P.W., Zhang H.

Flavonoids are stress-inducible metabolites important for plant-microbe interactions. In contrast to their well-known function in initiating rhizobia nodulation in legumes, little is known about whether and how flavonoids may contribute to plant stress resistance through affecting non-nodulating bacteria. Here we show that flavonoids broadly contribute to the diversity of the Arabidopsis root microbiome and preferentially attract Aeromonadaceae, which included a cultivable Aeromonas sp. H1 that displayed flavonoid-induced chemotaxis with transcriptional enhancement of flagellum biogenesis and suppression of fumarate reduction for smooth swims. Strain H1 showed multiple plant-beneficial traits and enhanced plant dehydration resistance, which required flavonoids but not through a sudden “cry-for-help” upon stress. Strain H1 boosted dehydration-induced H2O2 accumulation in guard cells and stomatal closure, concomitant with synergistic induction of jasmonic acid-related regulators of plant dehydration resistance. These findings revealed a key role of flavonoids, and the underlying mechanism, in mediating plant-microbiome interactions including the bacteria-enhanced plant dehydration resistance.

Yang Y., Chen S., Wu X., Peng L., Vílchez J.I., Kaushal R., Liu X., Singh S.K., He D., Yuan F., Lv S., Morcillo R.J., Wang W., Huang W., Lei M., et. al.

Abstract Unlike microbe-associated molecular patterns (MAMPs) that are readily targeted by host immunity, microbial non-pathogenic factors (NPFs) appear negligible as they do not elicit defense. Little is known about whether and how NPFs may be monitored by hosts to control compatibility. Herein, a forward genetic screening isolated an Arabidopsis mutant with a loss of plant-rhizobacteria mutualism, leading to the disclosure of a plant latent defense response (LDR) to NPFs. The activation of LDR in the mutant, named rol1 for regulator of LDR 1, is triggered by several non-pathogenic volatile organic compounds and antagonizes plant compatibility with the beneficial bacterium Bacillus amyloliquefaciens GB03. The activation of LDR in rol1 is mediated through the prokaryotic pathway of chloroplastic lipid biosynthesis. The rol1 root microbiome showed a reduced proportion of the Bacillaceae family. We propose that, parallel to the forefront immunity to MAMPs, LDR to certain NPFs provides a hidden layer of defense for controlling compatibility with commensal or beneficial microbes.

Rebelo Romão I., Rodrigues dos Santos A.S., Velasco L., Martínez-Ferri E., Vilchez J.I., Manzanera M.

Droughts and high temperatures deeply affect crop production. The use of desiccation-tolerant (or xerotolerant) microorganisms able to protect plants from droughts represents a promising alternative. These xerotolerant microorganisms have previously been used to modulate plant responses and improve their tolerance to drought. In addition, these microorganisms could be stored and used in dry formats, which would improve their viability and resilience at a much lower cost than current market alternatives. In the present study we analyze the possibility of using strains of xerotolerant Actinobacteria in encapsulated format on seeds. Under this formulation, we carried out greenhouse with farming soil with maize plants. Under greenhouse conditions, the plants showed greater resistance to drought, as well as increased growth and production yield, but not as well in field trials. This alternative could represent a useful tool to improve water efficiency in crops for drought-affected areas or affected by water scarcity.

Morcillo R., Vílchez J., Zhang S., Kaushal R., He D., Zi H., Liu R., Niehaus K., Handa A., Zhang H.

Water deficit is one of the major constraints to crop production and food security worldwide. Some plant growth-promoting rhizobacteria (PGPR) strains are capable of increasing plant drought resistance. Knowledge about the mechanisms underlying bacteria-induced plant drought resistance is important for PGPR applications in agriculture. In this study, we show the drought stress-mitigating effects on tomato plants by the Bacillus megaterium strain TG1-E1, followed by the profiling of plant transcriptomic responses to TG1-E1 and the profiling of bacterial extracellular metabolites. Comparison between the transcriptomes of drought-stressed plants with and without TG1-E1 inoculation revealed bacteria-induced transcriptome reprograming, with highlights on differentially expressed genes belonging to the functional categories including transcription factors, signal transduction, and cell wall biogenesis and organization. Mass spectrometry-based analysis identified over 40 bacterial extracellular metabolites, including several important regulators or osmoprotectant precursors for increasing plant drought resistance. These results demonstrate the importance of plant transcriptional regulation and bacterial metabolites in PGPR-induced plant drought resistance.

Ignacio V., Yang Y., Yi D., Zhang H.

Liang H., Sun H., Shao C., Lv B., Zhu J., Cao W., Zhou J., Zhang Y.

Li X., Li H., Wang Q., Zhang S.

Huang W., Tan Z., Xiao Q., Liu X., Liu K., Li Z., Zhou X., Bai L., Luo K.

Abou Jaoudé R., Luziatelli F., Ficca A.G., Ruzzi M.

IntroductionSoil microbiome transplantation is a promising technique for enhancing plant holobiont response to abiotic and biotic stresses. However, the rapid assessment of microbiome-plant functional integration in short-term experiments remains a challenge.MethodsThis study investigates the potential of three evergreen sclerophyll species, Pistacia lentiscus (PL), Rosmarinus officinalis (RO), and Juniperus phoenicea (JP), to serve as a reservoir for microbial communities able to confer enhanced tolerance to drought in Salvia officinalis cultivated under water shortage, by analyzing biomass production, plant phenotype, plant ecophysiological responses, and leaf metabolome.ResultsOur results showed that the inoculation with the three rhizomicrobiomes did not enhance total plant biomass, while it significantly influenced plant architecture, ecophysiology, and metabolic responses. The inoculation with the JP rhizomicrobiome led to a significant increase in root biomass, resulting in smaller leaves and a higher leaf number. These morphological changes suggest improved water acquisition and thermoregulation strategies. Furthermore, distinct stomatal conductance patterns were observed in plants inoculated with microbiomes from PJ and PL, indicating altered responses to drought stress. The metabolome analysis demonstrated that rhizomicrobiome transplantation significantly influenced the leaf metabolome of S. officinalis. All three rhizomicrobiomes promoted the accumulation of phenolic compounds, terpenoids, and alkaloids, known to play crucial roles in plant defense and stress response. Five molecules (genkwanin, beta-ionone, sumatrol, beta-peltatin-A-methyl ester, and cinnamoyl-beta-D-glucoside) were commonly accumulated in leaves of inoculated sage, independently of the microbiome. Furthermore, unique metabolic alterations were observed depending on the specific inoculated rhizomicrobiome, highlighting the specialized nature of plant-microbe interactions and the possible use of these specific molecules as biomarkers to monitor the recruitment of beneficial microorganisms.DiscussionThis study provides compelling evidence that microbiome transplantation can induce phenotypic and metabolic changes in recipient plants, potentially enhancing their resilience to water scarcity. Our findings emphasize the importance of considering multiple factors, including biomass, physiology, and metabolomics, when evaluating the effectiveness of microbiome engineering for improving plant stress tolerance.

Kemen A., Kemen E.

Wang Y., Zhao D., Li Z., Zheng H., Li Y., Zheng Y., Zhang C.

ABSTRACTPlant growth‐promoting rhizobacteria (PGPR) are widely recognized for enhancing the absorption of mineral nutrients by crops. While Sphingobium species have been reported as PGPRs, their capacity to improve nitrogen use efficiency (NUE) and the underlying regulatory mechanisms are not yet fully understood. Here, a strain 41R9, isolated from the rhizosphere of N‐deficient rapeseed, was found to significantly enhance the growth performance of rapeseed under both low and normal N conditions. Genomic analysis revealed that strain 41R9 was closely related to Sphingobium yanoikuyae. 15N isotope tracer experiments confirmed that inoculation with strain 41R9 significantly boosted N uptake and translocation in rapeseed roots. Transcriptome profiling demonstrated that strain 41R9 directly upregulated N transporter genes (NRT2.5 and SLAH1/3), facilitating efficient N acquisition. Furthermore, strain 41R9 maintained jasmonic acid (JA) homoeostasis via JAZ‐mediated negative feedback, balancing defense responses and root development, thereby improving the plant's N acquisition capacity in the roots. Metabolomic and in vitro assays further demonstrated that strain 41R9 displayed strong chemotaxis towards kaempferol, a N‐deficiency‐induced root exudate, suggesting kaempferol might as a chemical effector for S. yanoikuyae recruitment. These findings advance our understanding of PGPR‐driven mechanisms in enhancing crop NUE and highlight the potential of harnessing PGPRs for sustainable agriculture.

Liu Y., Zhu J., Liu Z., Zhi Y., Mei C., Wang H.

The increasing emergence and dissemination of multidrug-resistant (MDR) bacterial pathogens have intensified the need for new antibiotics and alternative therapeutic strategies. Flavonoids, a diverse group of bioactive natural compounds found in plants, have shown significant promise as antibacterial agents. Flavonoids inhibit bacterial growth through various mechanisms, including disruption of cell wall synthesis, prevention of biofilm formation, disruption of cell membrane integrity, and inhibition of bacterial efflux pumps. These actions not only reduce bacterial viability but also enhance the efficacy of conventional antibiotics, offering a potential solution to antibiotic resistance. However, challenges such as poor bioavailability limit their clinical application. Recent advances in nanotechnology-based drug delivery systems, chemical modifications, and formulation techniques have shown promise in improving flavonoid bioavailability and therapeutic efficacy. This review evaluates the antibacterial mechanisms of flavonoids, explores their potential synergistic effects with antibiotics, and highlights strategies to overcome bioavailability issues. Our findings underscore the importance of continued research on flavonoids as promising candidates for innovative antibacterial therapies aimed at combating MDR bacterial infections.

Yang H., Kerner P., Liang X., Struhs E., Mirkouei A., You Y.

Abstract Biochar can enhance soil health and plant productivity, but the underlying mechanisms remain elusive. Here we tackled this question through the lens of the rhizosphere using wheat as a model plant. We examined the impact of four feedstocks (corn stover, cattle manure, pine sawdust, or wheat straw) and two application rates. Biochar modulated root metabolism, where amino acid metabolism was the most common, leading to cascade effects on a wide range of secondary metabolites, including many plant signaling molecules involved in plant–microbe interactions. All biochar treatments increased rhizosphere microbial diversity, altered community composition, enhanced microbial interactions, and resulted in potential functional changes. Increased Burkholderiales (denitrifying bacteria) abundance and decreased Thermoplasmata (archaeal methanogens) abundance could explain biochar’s widely reported effects of mitigating nitrous oxide and methane. Biochar enhanced positive correlations among microbes and network modularity, suggesting local adaptation through synergism and the formation of modules of functionally interrelated taxa. A diversity of keystone taxa from dominant and non-dominant phyla emerged, including those known to mediate methane, nitrogen, and sulfur cycling. Treatment-specific alterations also occurred, and biochar feedstock choice exerted greater influence than application rate. Wheat biochar at 0.25% showed the strongest and distinct modulating effects, resulting in orchestrated changes in root metabolome and rhizosphere microbiome, especially those relevant to plant–microbe interactions and plant growth promotion. Our work provides new insights into the potential of top-down rhizosphere microbiome engineering through biochar-based reprogramming of root-microbe interactions. Graphical Abstract

Sun R., Wang Y., Chen X., Deng X.

ABSTRACTPrior exposure of plants to a triggering factor can enhance their tolerance to more severe stressful events. Transcriptome reprogramming of metabolism and hormonal modulation processes in the resurrection plant Boea hygrometrica was observed during drought acclimation. However, the metabolic dynamics and underlying regulatory networks that modulate drought acclimation‐induced rapid desiccation tolerance (RDT) remain unexplored. Here, we performed an integrated transcriptome and metabolome analysis to investigate the phytohormone profiles and metabolic landscapes of B. hygrometrica during drought acclimation and dehydration stress. We identified a set of RDT acquisition‐associated biomarkers, including trans‐zeatin and some disaccharides (lactose, trehalose, sucrose, and isomaltulose). Exogenous application of lactose effectively enhanced the RDT of B. hygrometrica seedlings and improved drought tolerance in Arabidopsis, tobacco, maize, and wheat. In addition, transient overexpression of lactose‐associated transcription factors MYB330 and APETALA2 in B. hygrometrica can promote the RDT and transcription of drought acclimation‐inducible genes involved in calcium and ABA signalling and autophagy. In summary, our findings demonstrate that drought acclimation‐induced lactose accumulation facilitates the establishment of an “acclimated state”, leading to transcriptome reprogramming in response to rapid desiccation. These results will also pave the way for using RDT biomarkers to improve crop drought tolerance in an environmentally sustainable manner.

Espinosa-Palomeque B., Jiménez-Pérez O., Ramírez-Gottfried R.I., Preciado-Rangel P., Buendía-García A., Sifuentes G.Z., Sariñana-Navarrete M.A., Rivas-García T.

Biocontrol has emerged as an effective strategy for managing plant pathogens and pests. The use of plant growth-promoting rhizobacteria (PGPR) as biocontrol agents offers a sustainable alternative, enhancing plant morphology, biochemistry, physiology, and secondary metabolism. This study conducts a bibliometric analysis and systematic review of PGPR-based biocontrol research from 2019 to 2023, using the Web of Science (WoS) database. A total of 2823 publications were identified, with a significant increase in scientific output since 2019. Original research articles dominated the field, with India, China, the USA, and Pakistan leading in publication volume. Key contributors included Babalola (North-West University, South Africa), Kloepper (Auburn University, USA), and Shen (Nanjing Agricultural University, China), each with at least 25 publications. Co-authorship analysis revealed four major research networks centered in India, China, Brazil, and Canada. Bacillus and Pseudomonas were the most studied PGPR genera, recognized for their roles as bioinoculants, bioremediators, and biostimulants, mitigating the negative impacts of synthetic fertilizers and pesticides. This analysis underscores the growing global focus on PGPR-based biocontrol and its potential for sustainable agriculture. Strengthening international collaboration and accelerating applied research on PGPR formulations will be critical for optimizing their efficacy and scalability in real-world agricultural systems.

Li W., Wei J., Lei Y., Yang Z., Zhang S., Feng J., Li Y., Liu Y., Sheng H.

Sharma M., Devi S., Chand S.

Agoussar A., Tremblay J., Yergeau E.

AbstractManipulating microbial communities could increase crop resistance to environmental stressors such as drought. It is, however, not clear what would be the best approach to do so and what microbial traits are important. Here, we first compare multispecies inoculums created using different approaches. The only inoculum that increased wheat fresh biomass under drought was the one created from 25 isolates that had showed a capacity to grow under high osmolarity. We then looked at two potential mechanisms of action of this inoculum: 1) direct action, by sequencing and screening the genomes of the inoculated bacteria, 2) indirect action, by sequencing the 16S rRNA gene and ITS region of rhizosphere, root and leaves microbial communities. The microbes in the inoculum harbored many traits related to plant growth promoting, competition and water stress resistance. The inoculation also resulted in significant shifts in the microbial communities associated with wheat, including some microorganisms previously reported to improve plant drought resistance. We conclude that the inoculum studied here increased wheat growth because it potentially acted on two fronts: directly, through the traits it was selected for, and indirectly, through inducing shifts in the resident plant microbial communities.

Nicotra D., Mosca A., Dimaria G., Massimino M.E., Di Stabile M., La Bella E., Ghadamgahi F., Puglisi I., Vetukuri R.R., Catara V.

Climate change has reshaped global weather patterns and intensified extreme events, with drought and soil salinity negatively impacting the yield and quality of crop production. To mitigate the detrimental effects of drought stress, the introduction of beneficial plant growth-promoting rhizobacteria (PGPR) has proven to be a promising approach. In this study, we evaluated a synthetic microbial community (SynCom) comprising bacterial strains belonging to the species Bacillus velezensis, Pseudomonas simiae, P. salmasensis, Glutamicibacter halophytocola, and Leclercia sp., which have been demonstrated to promote tomato growth both individually and collectively. The SynCom and most of its individual bacterial strains were shown to mitigate the detrimental effects of polyethylene glycol (PEG)-induced drought stress in vitro in Arabidopsis thaliana seedlings, either by reducing alterations in xylem elements or promoting the formation of new xylem strands. In a greenhouse trial, soil drenching with the SynCom and two individual strains, B. velezensis PSE31B and P. salmasensis POE54, improved the water stress response in soilless-grown tomato plants under a 40% reduced irrigation regime. Additionally, bacterial treatments positively influenced the diversity of rhizosphere bacterial communities, with distinct changes in bacterial composition, which suggest a treatment-specific interplay between the introduced strains and the native microbiome. These findings highlight the potential of microbial consortia and individual PGPR strains as sustainable tools to improve plant resilience to abiotic stresses.

Bagum J., Banerjee D.

Today’s modern agriculture system is facing a major problem regarding the storage of foods after harvesting. These postharvest fungal infections negatively affect food security as more than 30% of food is getting wasted during postharvest operations. In this case, fungal pathogens are playing a major role behind these losses. So, they are needed to be controlled at the earliest. Synthetic fungicides can prevent these pathogens, but their toxicity toward humans, animals, and the environment is raising serious questions. The solitary solution could be green remedies like metabolites extracted from natural entities. Other than phytometabolites, microbial metabolites are also effective in controlling phytopathogens. Biocontrol agents are the good option against this problem as they are known to have fungicidal ability, mainly for protecting postharvest products like fruits, vegetables, and grains. Nowadays, secondary metabolites from untapped sources like endophytic fungi are acting as the rich hub for antimicrobial metabolites with multidomain utility in the field of agriculture. These metabolites are safe and are applied in the form of foliar/root spray. Endophytic fungi can also be a promising biocontrol agent as it protects the host plant from pest infection for its entire life cycle. So, inevitably endophytic fungi and their metabolites can prevent postharvest pathogens and become a permanent alternative to synthetic fungicides. This chapter extensively summarizes the role of endophytic fungi in preventing postharvest fungal diseases in cash crops.

Du Y., Han X., Tsuda K.

AbstractPlant pathogens cause plant diseases that significantly decrease crop yields, posing a serious threat to global food security. While plant disease resistance has traditionally been understood as the trait determined by the plant innate immune system and the pathogen virulence system, recent research underscores the pivotal role of the plant microbiome in disease resistance. Plant-associated microbiomes confer protection against pathogens through direct pathogen inhibition, resource competition, and activation of plant immune responses. Agricultural practices such as crop rotation, intercropping, disease-resistant breeding, biocontrol, and organic farming modulate plant microbiomes, thereby influencing disease resistance. This review synthesizes the latest advancements in understanding the intricate interactions among plants, pathogens, and microbiomes. We emphasize the need for in-depth mechanistic studies linking agricultural practices to microbiome dynamics and propose future research directions to leverage microbiomes for sustainable agriculture.

Fan X., Matsumoto H., Xu H., Fang H., Pan Q., Lv T., Zhan C., Feng X., Liu X., Su D., Fan M., Ma Z., Berg G., Li S., Cernava T., et. al.

Resident microbiota produces small molecules that influence the chemical microenvironments on leaves, but its signalling roles in pathogen defence are not yet well understood. Here we show that Aspergillus cvjetkovicii, enriched in rice leaf microbiota, subverts Rhizoctonia solani infections via small-molecule-mediated interspecies signalling. 2,4-Di-tert-butylphenol (2,4-DTBP), identified as a key signalling molecule within the Aspergillus-enriched microbiota, effectively neutralizes reactive oxygen species-dependent pathogenicity by switching off bZIP-activated AMT1 transcription in R. solani. Exogenous application of A. cvjetkovicii and 2,4-DTBP demonstrated varying degrees of protective effects against R. solani infection in diverse crops, including cucumber, maize, soybean and tomato. In rice field experiments, they reduced the R. solani-caused disease index to 19.7–32.2%, compared with 67.2–82.6% in the control group. Moreover, 2,4-DTBP showed activity against other rice phytopathogens, such as Fusarium fujikuroi. These findings reveal a defensive strategy against phytopathogens in the phyllosphere, highlighting the potential of symbiotic microbiota-driven neutralization of pathogenicity. Beneficial Aspergillus cvjetkovicii protects host plants against fungal diseases by inactivating pathogenicity-related gene transcription of phytopathogens via 2,4-DTBP signalling.

Ku Y., Liao Y., Chiou S., Lam H., Chan C.

SummaryThe reduction in crop yield caused by pathogens and pests presents a significant challenge to global food security. Genetic engineering, which aims to bolster plant defence mechanisms, emerges as a cost‐effective solution for disease control. However, this approach often incurs a growth penalty, known as the growth‐defence trade‐off. The precise molecular mechanisms governing this phenomenon are still not completely understood, but they generally fall under two main hypotheses: a “passive” redistribution of metabolic resources, or an “active” regulatory choice to optimize plant fitness. Despite the knowledge gaps, considerable practical endeavours are in the process of disentangling growth from defence. The plant microbiome, encompassing both above‐ and below‐ground components, plays a pivotal role in fostering plant growth and resilience to stresses. There is increasing evidence which indicates that plants maintain intimate associations with diverse, specifically selected microbial communities. Meta‐analyses have unveiled well‐coordinated, two‐way communications between plant shoots and roots, showcasing the capacity of plants to actively manage their microbiota for balancing growth with immunity, especially in response to pathogen incursions. This review centers on successes in making use of specific root‐associated microbes to mitigate the growth‐defence trade‐off, emphasizing pivotal advancements in unravelling the mechanisms behind plant growth and defence. These findings illuminate promising avenues for future research and practical applications.

Boo A., Toth T., Yu Q., Pfotenhauer A., Fields B.D., Lenaghan S.C., Stewart C.N., Voigt C.A.

AbstractPlants and microbes communicate to collaborate to stop pests, scavenge nutrients, and react to environmental change. Microbiota consisting of thousands of species interact with each other and plants using a large chemical language that is interpreted by complex regulatory networks. In this work, we develop modular interkingdom communication channels, enabling bacteria to convey environmental stimuli to plants. We introduce a “sender device” in Pseudomonas putida and Klebsiella pneumoniae, that produces the small molecule p-coumaroyl-homoserine lactone (pC-HSL) when the output of a sensor or circuit turns on. This molecule triggers a “receiver device” in the plant to activate gene expression. We validate this system in Arabidopsis thaliana and Solanum tuberosum (potato) grown hydroponically and in soil, demonstrating its modularity by swapping bacteria that process different stimuli, including IPTG, aTc and arsenic. Programmable communication channels between bacteria and plants will enable microbial sentinels to transmit information to crops and provide the building blocks for designing artificial consortia.

Zhan C., Wang M.

Plants regulate their microbiota to cope with diverse stresses. A recent study shows that rice maintains homeostasis of its phyllosphere microbiome through a secondary metabolite biosynthetic gene, which offers potential for harnessing microbiome-shaping genes in disease-resistance breeding.

Santos L.D., De Moura J.B., Lopes Filho L.C., Teixeira M.F., Peixoto J.D.

This research aims to identify the existence of legislative regulations for the production and use of bioinputs in the national territory, given the growing use of bioinputs as a sustainable alternative when compared to the use of pesticides. The objective is to analyze the conceptual and defining parameters of bioinputs, going into sustainable aspects and outlining an overview of the beneficial points when compared to pesticides. Based on the definitions presented, the study focuses on the following question: Are there laws in Brazil that regulate the use and manufacture of bioinputs in view of the exponential growth of the productive market? To answer the central question, the research makes use of the qualitative method that guided the search for bills in progress regarding the theme and enabled the analysis of the viability of the contents presented. As a result, the effectiveness of bioinputs as agents to combat pests is demonstrated, being an environmentally sustainable resource with demonstrated efficacy. Thus, with the demonstration of beneficial implications in management, a legislative gap is identified that permeates the production of bioinputs, including on-farm production, which reflects the lack of regulation regarding production, registration and especially supervision. Although the National Bioinputs Program is in force, laws need to be created from a regular legislative process aimed at regulating the sector that is in notorious growth, which demonstrates the need for the analysis of Bills 3668/21 and PL658/21, currently being processed in the Brazilian legislature.

Zeng Q., Zhao Y., Shen W., Han D., Yang M.

Gil T., Teixeira R., Sousa A., d’Oliveira Palmeiro M.A., Cruz Coimbra de Matos A., Niza Costa M., Ferrer M.V., Rodrígues dos Santos A.S., Sequero López C., Rebelo Romão I., Vílchez J.I.

Saline and gypsic soils impede or condition the establishment of farms in many regions worldwide. Stress caused by the accumulation of sodium or calcium ions in the soil drastically limits plant growth and is a limiting factor in the production of many crops. For this reason, saline and gypsic soils were preferentially exploited for mineral extraction. However, nowadays, they can be a source of new biotechnological tools to help in the osmotic stress to which some crops are exposed. In these environments, despite being traditionally characterized by their low biodiversity, we can find well-adapted microbiota that may be able to interact with plants to deal with different environmental stresses. These mechanisms may consist of a very important contribution to the development of new osmotic stress-dealing bioinoculants. The present study sought to elucidate the diversity of the cultivable population of such environments and use them as regulators of soil nutrients and stress-relieving symbionts in plants under osmotic stress. Among the candidate strains selected to cover more scenarios, we found that the strains Stutzerimonas stutzeri A38 and Bacillus pumilus A49 were able to increase root size under osmotic stress in Medicago sativa and Medicago polymorpha plants. Moreover, Peribacillus frigoritolerans A70 and Bacillus licheniformis A46 also enhanced the performance in M. polymorpha, showing interesting potential for a future use in wasteland use for production to livestock feeding or other relevant industries.

Wu X., Yang Y., Zhang H.

Medicinal plants are rich in secondary metabolites with beneficial pharmacological effects. The production of plant secondary metabolites is subjected to the influences by environmental factors including the plant-associated microbiome, which is crucial to the host's fitness and survival. As a result, research interests are increasing in exploiting microbial capacities for enhancing plant production of pharmacological metabolites. A growing body of recent research provides accumulating evidence in support of developing microbe-based tools for achieving this objective. This mini review presents brief summaries of recent studies on medicinal plants that demonstrate microbe-augmented production of pharmacological terpenoids, polyphenols, and alkaloids, followed by discussions on some key questions beyond the promising observations. Explicit molecular insights into the underlying mechanisms will enhance microbial applications for metabolic fortification in medicinal plants.

Benmrid B., Ghoulam C., Zeroual Y., Kouisni L., Bargaz A.

AbstractEnsuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions.

Liu X., Mei S., Salles J.F.

Microbial consortium inoculation has been proposed as a natural-based strategy to safeguard multiple ecosystem services. Still, its observed effects and comparisons to single-species inoculation have yet to be systematically quantified. In this global meta-analysis of 51 live-soil studies (carefully selected from a pool of 2149 studies), we compared the impact (mean and variability) of single-species and consortium inoculations on biofertilization and bioremediation. Our results showed that both single-species and consortium inoculations increased plant growth by 29 % and 48 %, respectively, and pollution remediation by 48 % and 80 %, respectively, compared with non-inoculated treatments. We revealed that the diversity of inoculants and the synergistic effect between frequently used inoculums (e.g., Bacillus and Pseudomonas) contributed to the effectiveness of consortium inoculation. Despite a reduction in efficacy in field settings compared to greenhouse results, consortium inoculation had a more significant overall advantage under various conditions. We recommend increasing original soil organic matter, available N, and P content and regulating soil pH to 6–7 to achieve a better inoculation effect. Overall, these findings support the use of microbial consortia for improved biofertilization and bioremediation in living soil and suggest perspectives for constructing and inoculating beneficial microbial consortia.

Ayaz M., Li C., Ali Q., Zhao W., Chi Y., Shafiq M., Ali F., Yu X., Yu Q., Zhao J., Yu J., Qi R., Huang W.

Plants are constantly exposed to various phytopathogens such as fungi, Oomycetes, nematodes, bacteria, and viruses. These pathogens can significantly reduce the productivity of important crops worldwide, with annual crop yield losses ranging from 20% to 40% caused by various pathogenic diseases. While the use of chemical pesticides has been effective at controlling multiple diseases in major crops, excessive use of synthetic chemicals has detrimental effects on the environment and human health, which discourages pesticide application in the agriculture sector. As a result, researchers worldwide have shifted their focus towards alternative eco-friendly strategies to prevent plant diseases. Biocontrol of phytopathogens is a less toxic and safer method that reduces the severity of various crop diseases. A variety of biological control agents (BCAs) are available for use, but further research is needed to identify potential microbes and their natural products with a broad-spectrum antagonistic activity to control crop diseases. This review aims to highlight the importance of biocontrol strategies for managing crop diseases. Furthermore, the role of beneficial microbes in controlling plant diseases and the current status of their biocontrol mechanisms will be summarized. The review will also cover the challenges and the need for the future development of biocontrol methods to ensure efficient crop disease management for sustainable agriculture.

Rai P.K., Rai A., Sharma N.K., Singh T., Kumar Y.

Sustainability and innovation are fundamental to any production system. Providing food to the increasing population is of paramount importance and is crtical to the global stability. However, the issue of food security is facing stiff challenge from continuously declining soil fertility and scarcity of fertile land. Our reliance on excessive use of toxic chemical fertilizers for increased yield is major concerns for environment and agriculture's future. Biofertilizers are gaining traction as a viable alternative to toxic chemical fertilizers, with a market potential of 3.8 billion dollars by 2025. Use of biofertilizer is natural mean to use live microorganisms to improve soil nutritional status by root surface area expansion, enhanced nutrient availability and acquisition (nitrogen fixation and phosphate solubilization), production of plant growth promoting substances and inhibition of plant pathogen growth, and combining all these. Despite being cost-effective and environmentally benign, constraints like inconsistent supplies and a lack of sufficient quality control is limiting the wide adoption or deployment of biofertilizers. To make them commercialy successful, we need to diversify resource base (i.e., identify and include more viable strains), create better manufacturing technology, and implement quality control procedures. Use of nanotechnology in biofertilizer sector via green synthesis or by nanocoating or encapsulation of beneficial microorganism using nanomaterials is a promising option. Bio-nanofertilizers increase nutrient use efficiency; diminishing nutrient losses, have multiple crop growth promoting activities and release of nutrients to rate compatible to plants demand. Adoption and popularization of bio-nanofertilizers require extensive field-testing, public awareness campaigns, capacity building of resource persons and stakeholders, adoptation of standard production processes, storage and application, as well as active participation of private organizations and enforcement of suitable legislation. Here, we discuss before-mentioned issues in light of available evidences and our experience with India system.

Ercole T.G., Kava V.M., Aluizio R., Pauletti V., Hungria M., Galli-Terasawa L.V.

Limiting factors for plant growth, such as low nutrient availability and intolerance to high salinity, may impair the production of several crops. Plant growth-promoting bacteria (PGPB) present a potential solution to mitigate these limitations by stimulating plant growth and development. This study aimed to identify the strains LGMB12, LGMB319, and LGMB426 (Bacillus velezensis) and LGMB417 (Stenotrophomonas maltophilia), and to assess single and co-inoculation effects of these bacteria on the growth promotion of maize (Zea mays L.) plants under normal conditions and in high salinity environments. These strains were identified through Bayesian inference multilocus analysis using 16 S rRNA, gyrA, recA, and rpoB genes. Antibiosis analysis revealed that the strains did not inhibit each other's growth. Thirteen inoculation conditions were tested in greenhouse experiments including controls, inoculation of each strain separately and in the six pairs of combinations to evaluate growth promotion and salinity tolerance, using 75 and 100 mM NaCl in the irrigation water. The results revealed that co-inoculation yielded the best outcomes, highlighting the synergistic effects of combining the strains. Overall, this study emphasizes the potential of co-inoculation with Bacillus velezensis and Stenotrophomonas maltophilia strains as a strategy to enhance plant growth and improve salinity tolerance in maize cultivation. Further investigations are warranted to explore their application as bioinputs in agricultural settings.

Rai D., Silveira M.L., Strauss S.L., Meyer J.L., Castellano-Hinojosa A., Kohmann M.M., Brandani C.B., Gerber S.

Prescribed burning is widely used land management strategy to reduce the risks of wildfire and to achieve a wide range of ecological, economic, and societal benefits. However, it can also affect carbon (C), nitrogen (N), and phosphorus (P) cycling with potential subsequent effects on soil microbial communities. This study examined the short-term effects of prescribed burning on soil chemical properties, potential enzyme activities, and bacterial and fungal community composition in native rangelands of Florida. Fire-induced responses were assessed immediately (2 days) and 2 to 3 months after a prescribed fire event. Soil pH, total C, and extractable NH4+ and P concentration declined after fire. Total N concentration increased 2 days after fire but returned to initial level 2 to 3 months after fire. Prescribed fire elicited no observable effects on soil total P and extractable Ca, K, Mg, Mn, Fe, and Al concentration. Reductions in potential beta glucosidase and N-acetyl glucosaminidase activity were observed 2 days after fire but returned at pre-fire levels after 2–3 months. Bacterial and fungal diversity and community composition at the phylum level showed no short-term changes. At the Order level, bacterial Desulfurellales increased while fungal Eurotiales and Pleosporales decreased 2 days after fire. Prescribed burning had minimal effect on soil microbial community composition in the short-term, probably due to limited effects of fire on soil heating and rapid post-fire vegetative recovery. Although the impacts of prescribed fire on soil properties have been widely acknowledged, this study is the first to document short-term fire-induced soil microbial responses in subtropical native rangelands of Florida. This work contributes to a wealth of evidence indicating limited impacts of prescribed fire on soil microbial community composition.