Ecosystem consequences of introducing plant growth promoting rhizobacteria to managed systems and potential legacy effects

Early inoculation and bacterial community assembly in plants: A review

The relationship between plants and early colonizing microbes is crucial for regulating agricultural ecosystems. Recent evidence strongly suggests that by introducing beneficial microbes during the seed or seedling stages, the diversity and assembly structure of the plant-related microbial community during later plant development can be altered, recruiting beneficial bacteria to enhance plant protection. However, the mechanisms of community assembly and their effects on plant growth are still not fully understood. To deepen our understanding of the importance of early inoculation for improving plant performance, this review comprehensively summarizes recent research advancements on the effects of early introduction on plant growth and adaptability. The mechanisms and ecological significance of early inoculation in the assembly of plant-related bacterial communities are discussed, with particular emphasis on the importance of seed endophytes, plant growth-promoting rhizobacteria (PGPR), and synthetic microbial consortia as microbial inoculants in enhancing plant health and productivity. Additionally, this review proposes a new strategy: sequential inoculation during the seed and seedling stages, aiming to maximize the effects of microbes.

Optimization of compound bacterial inoculant enhances soil nutrients and bacterial community richness in alpine grassland

Grassland degradation results in nutrient loss and ecosystem function impairment, making it crucial to explore green and effective restoration technologies. In this study, three strains (Acinetobacter calcoaceticus J1, Pseudomonas piscium J5, Bacillus subtilis Y3) isolated from alpine grassland, and mixed in equal volume (VJ1:VJ5:VY3 = 1:1:1) to prepare the compound bacteria. The fermentation medium and conditions of the compound bacteria were optimized, then pot and field experiments were conducted to validate the application of the optimized compound bacterial inoculant. The optimal conditions were: soluble starch 2.62 g L-1, yeast extract 20.26 g L-1, KCl 5.01 g L-1, pH 6.0, incubated at 25 °C for 48 h, with 20 % liquid volume, 3 % inoculation ratio, and 200 r·min-1. Under these conditions, the number of viable bacteria was 128.47 times higher than before optimization. The obtained compound bacterial inoculant resulted in a significant increase of 34.24 %, 52.61 %, 57.74 %, 62.50 %, and 53.92 % in the height, total root length, root surface area, volume, and branch number of Elymus nutans, with better effects than the single bacterial. The field experiment revealed that the compound bacterial inoculant could significantly increase above-ground biomass (10.63 %), organic matter (16.99 %), available nitrogen (12.58 %), total nitrogen, and phosphorus (15.79 % and 11.54 %). This study has developed an environmentally friendly compound bacterial inoculant (G1), that accelerates soil nutrient cycling by reducing soil pH and increasing the richness of the bacterial community, thus restoring degraded grassland. This result realized the principle of "near-natural restoration" of degraded alpine grassland and provided a new biological restoration technology for the degraded alpine grassland.

Arbuscular mycorrhizal fungi build a bridge for soybeans to recruit Pseudomonas putida

The assembly of the rhizosphere microbiome determines its functionality for plant fitness. Although the interactions between arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) play important roles in plant growth and disease resistance, research on the division of labor among the members of the symbionts formed among plants, AMF, and PGPR, as well as the flow of carbon sources, is still insufficient. To address the above questions, we used soybean (Glycine max), Funneliformis mosseae, and Pseudomonas putida KT2440 as research subjects to establish rhizobiont interactions and to elucidate the signal exchange and division of labor among these components. Funneliformis mosseae can attract P. putida KT2440 by secreting cysteine as a signaling molecule and can promote the colonization of P. putida KT2440 in the soybean rhizosphere. Colonized P. putida KT2440 can stimulate the l-tryptophan secretion of the host plant and can lead to the upregulation of genes involved in converting methyl-indole-3-acetic acid (Me-IAA) into IAA in response to l-tryptophan stimulation. Collectively, we decipher the tripartite mechanism of rhizosphere microbial community assembly via cross-kingdom interactions.

The effects of introduced biocontrol microbes on root and flower surface microbiomes of strawberry grown in coir substrate in a polythene tunnel

AIMS

Biocontrol of plant diseases is a key component of sustainable agriculture. Augmented introduction of biocontrol microbes may affect the resident phytobiome, potentially leading to unintended consequences. We studied the effects of three biocontrol microbes (Gliocladium catenulatum, Trichoderma asperellum, and Bacillus subtilis) on communities of living microbes on table-top strawberries grown in coir bags in a polythene tunnel.

METHODS AND RESULTS

Gliocladium catenulatum and T. asperellum were applied to roots via drenching soon after planting, and G. catenulatum and B. subtilis were sprayed onto flowers. To profile communities of living microbes, we treated samples with PMAxx™ before DNA extraction. Flower and root epiphytes were profiled by amplicon and shot-gun sequencing, respectively. Applying the three microbes led to significant increases in their relative abundance on both flowers and roots. The two introduced fungal taxa (G. catenulatum and T. asperellum) appeared to affect mainly fungal microbiome components, whereas the introduced bacterial taxon (B. subtilis) mainly affected bacterial microbiome components. The effects of introduced biocontrol microbes on the resident microbiome were more profound and long-lasting on roots than on flowers.

CONCLUSIONS

Introduced microbes can persist better on roots than on flowers. Although the applied microbes led to significant changes in the overall microbial composition, their effects on individual taxa groups were limited. Introduced microbes appeared to have only largely affected microbial communities in the same kingdom.

Enhancing multi-season wheat yield through plant growth-promoting rhizobacteria using consortium and individual isolate applications

In recent decades, there has been a growing interest in harnessing plant growth-promoting rhizobacteria (PGPR) as a possible mechanism to mitigate the environmental impact of conventional agricultural practices and promote sustainable agricultural production. This study investigated the transferability of promising PGPR research from maize to another Poaceae cereal crop, wheat. This multi-seasonal study evaluated the wheat grain yield effect of Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29) when applied i. individually, ii. as a consortium with Bacillus safensis (S7), and iii. at a 75% reduced fertilizer rate. Whole genome sequencing allowed annotation of genes linked to plant growth promotion, providing potential genomic explanations for the observed in-field findings. Application of the consortium compared to a commercial PGPR showed significantly increased wheat yield by 30.71%, and 25.03%, respectively, in season one, and 63.92% and 58.45%, respectively, under reduced fertilizer rates in season two. Individual application of T19 and T29 showed varying results, with T19 increasing wheat yield by 9.33% and 16.22% during seasons three and four but a substantial reduction (33.39%) during season five. T29 exhibited yield increases during season three (9.31%) and five (5.61%) but led to a significant reduction (21.15%) in season four. Genomic analysis unveiled a spectrum of plant growth-promoting genes including those associated with ammonification, phosphate solubilization, ethylene, siderophore, catalase, and superoxide dismutase production. These findings offer valuable insights into the mechanisms behind observed field results, with potential implications for advancing sustainable agriculture and crop productivity in evolving agricultural landscapes.

Halotolerant phosphate solubilizing bacteria isolated from arid area in Tunisia improve P status and photosynthetic activity of cultivated barley under P shortage

Forty-seven (47) bacterial strains were isolated from soil of Gabes (an arid region in southern Tunisia) and were screened for their ability to produce Indole-3-Acetic Acid (IAA) and to solubilize phosphate (P). The characterization and molecular identification of the most successful P-solubilizing bacteria (PSB) were then carried out. When grown on suitable artificial media, the most salt-tolerant strains also showed the highest P solubilization capacity (up to 126.8 μg ml-1 of released phosphorus after 7 day incubation) and the strongest ability to produce IAA (up to 101.86 μg ml-1 after 3 day incubation). Overall, bacterial isolates displayed a different tolerance to varying pH, temperatures, and salinity. The molecular identification revealed that 11 strains belonged to three genera: Bacillus, Pseudomonas and Mesorhizobium. Inoculation of barley with P-solubilizing bacteria under tricalcium phosphate-induced P shortage significantly improved plant growth (biomass, shoot height, and root length) together with increasing total chlorophyll contents and photosynthetic activity. This was concomitant with (i) higher P uptake and translocation and (ii) increased phosphorus absorption and utilization efficiencies (PAE and PUE), which is indicative of a better plant P nutrition under P scarcity. Taken together, we provide strong arguments showing that bacteria native to extreme environments display PSB potential making them promising candidates to mitigate low Pi availability for crop plants.

Emerging eco-friendly technologies for remediation of Per- and poly-fluoroalkyl substances (PFAS) in water and wastewater: A pathway to environmental sustainability

Per- and polyfluoroalkyl substances (PFAS) are rampant, toxic contaminants from anthropogenic sources, called forever chemicals for their recalcitrance. Although banned in several parts of the world for public health implications, including liver, kidney, and testicular diseases, PFAS are abundant in water sources due to easy dispersion. With chemical properties resulting from strong hydrophobic bonds, they defile many physicochemical removal methods. Though adsorption processes such as granular activated carbon (GAC) are widely used, they are marred by several limitations, including cost and secondary contamination. Thus, eco-friendly methods involving a synergy of the removal principles have been preferred for ease of use, cost-effectiveness, and near-zero effect on the environment. We present novel eco-friendly methods as the solution to PFAS remediation towards environmental sustainability. Current eco-friendly methods of PFAS removal from water sources, including electrocoagulation, membrane/filtration, adsorption, and phytoremediation methods, were highlighted, although with limitations. Novel eco-friendly methods such as microbial fuel cells, photoelectrical cells, and plasma treatment offer solutions to PFAS remediation and are quite efficient in terms of cost, result, and environmental sustainability. Overall, the successful integration of eco-friendly techniques in a seamless manner ensures the desired result. We also present a balanced position on the ecosystem impact of these ecofriendly methods, noting the successes towards environmental sustainability while exposing the gaps for further research.

Drought-tolerant rhizobacteria with predicted functional traits enhanced wheat growth and P uptake under moderate drought and low P-availability

This study aims to investigate the effect of isolated drought-tolerant rhizobacteria, spanning various groups, such as nitrogen-fixing bacteria (NFB), phosphate solubilizing bacteria (PSB), and other plant growth promoting rhizobacteria (PGPR), on the growth of wheat (Triticum durum) plants, focusing on various morphological and physiological responses under moderate drought and low-P availability. Among 343 rhizobacterial morphotypes, 16 exhibited tolerance to NaCl and PEG-6000. These included 8 PSB, 4 NFB, and 4 osmotolerant-PGPR groups, distributed across 14 different genera. Biochemical characterization showcased diverse PGP capabilities, particularly in P solubilization. The dynamic responses of drought-tolerant PSB to salt and PEG-6000-induced drought stress involved variations in organic acid (OA) secretion, with specific acids, including palmitic, lactic, and stearic, playing crucial roles in enhancing available P fractions. Inoculation with rhizobacteria significantly increased both shoot (SDW) and root (RDW) dry weights of wheat plants, as well as rhizosphere available P. PSB11 (Arthrobacter oryzae) emerged as the most effective strain, plausibly due to its positive impact on root morphological traits (length, surface, and volume). Other isolates, PSB10 (Priestia flexa), PSB13 (Bacillus haynesii), and particularly PGPR2 (Arthrobacter pascens) significantly increased shoot P content (up to 68.91 %), with a 2-fold increase in chlorophyll content. The correlation analysis highlighted positive associations between SDW, shoot P content, chlorophyll content index (CCI), and leaf area. Additionally, a negative correlation emerged between microbial biomass P and root morphophysiological parameters. This pattern could be explained by reduced competition between plants and rhizobacteria for accessible P, as indicated by low microbial biomass P and strong plant growth. Our investigation reveals the potential of drought-tolerant rhizobacteria in enhancing wheat resilience to moderate drought and low-P conditions. This is demonstrated through exceptional performance in influencing root architecture, P utilization efficiency, and overall plant physiological parameters. Beyond these outcomes, the innovative isolation procedure employed, targeting rhizobacteria from diverse groups, opens new avenues for targeted isolation techniques. This unique approach contributes to the novelty of our study, offering promising prospects for targeted bioinoculants in mitigating the challenges of drought and P deficiency in wheat cultivation.

Fungal endophyte promotes plant growth and disease resistance of Arachis hypogaea L. by reshaping the core root microbiome under monocropping conditions

Fungal endophytes play critical roles in helping plants adapt to adverse environmental conditions. The root endophyte Phomopsis liquidambaris can promote the growth and disease control of peanut plants grown under monocropping systems; however, how such beneficial traits are produced is largely unknown. Since the plant endophytic microbiome is directly linked to plant growth and health, and the composition of which has been found to be potentially influenced by microbial inoculants, this study aims to clarify the roles of root endophytic bacterial communities in P. liquidambaris-mediated plant fitness enhancement under monocropping conditions. Here, we found that P. liquidambaris inoculation induced significant changes in the root bacterial community: enriching some beneficial bacteria such as Bradyrhizobium sp. and Streptomyces sp. in the roots, and improving the core microbial-based interaction network. Next, we assembled and simplified a synthetic community (SynII) based on P. liquidambaris-derived key taxa, including Bacillus sp. HB1, Bacillus sp. HB9, Burkholderia sp. MB7, Pseudomonas sp. MB2, Streptomyces sp. MB6, and Bradyrhizobium sp. MB15. Furthermore, the application of the simplified synthetic community suppressed root rot caused by Fusarium oxysporum, promoted plant growth, and increased peanut yields under continuous monocropping conditions. The resistance of synII to F. oxysporum is related to the increased activity of defense enzymes. In addition, synII application significantly increased shoot and root biomass, and yield by 35.56%, 81.19%, and 34.31%, respectively. Collectively, our results suggest that the reshaping of root core microbiota plays an important role in the probiotic-mediated adaptability of plants under adverse environments.

Microbial Catabolic Activity: Methods, Pertinence, and Potential Interest for Improving Microbial Inoculant Efficiency

Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to assess soil microbial function potential. For its measure, several methods are available including multi-substrate-induced respiration (MSIR) measurement which allow to estimate functional diversity using selected carbon substrates targeting specific biochemical pathways. In this review, the techniques used to measure soil MCA are described and compared with respect to their accuracy and practical use. Particularly the efficiency of MSIR-based approaches as soil microbial function indicators was discussed by (i) showing their sensitivity to different agricultural practices including tillage, amendments, and cropping systems and (ii) by investigating their relationship with soil enzyme activities and some soil chemical properties (pH, soil organic carbon, cation exchange capacity). We highlighted the potential of these MSIR-based MCA measurements to improve microbial inoculant composition and to determine their potential effects on soil microbial functions. Finally, we have proposed ideas for improving MCA measurement notably through the use of molecular tools and stable isotope probing which can be combined with classic MSIR methods. Graphical abstract describing the interrelation between the different parts and the concepts developed in the review.

Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems

Ensuring 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.

Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review

The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome.

Comparative Genomics and Physiological Investigations Supported Multifaceted Plant Growth-Promoting Activities in Two Hypericum perforatum L.-Associated Plant Growth-Promoting Rhizobacteria for Microbe-Assisted Cultivation

Plants are no longer considered standalone entities; instead, they harbor a diverse community of plant growth-promoting rhizobacteria (PGPR) that aid them in nutrient acquisition and can also deliver resilience. Host plants recognize PGPR in a strain-specific manner; therefore, introducing untargeted PGPR might produce unsatisfactory crop yields. Consequently, to develop a microbe-assisted Hypericum perforatum L. cultivation technique, 31 rhizobacteria were isolated from the plant's high-altitude Indian western Himalayan natural habitat and in vitro characterized for multiple plant growth-promoting attributes. Among 31 rhizobacterial isolates, 26 produced 0.59 to 85.29 μg mL-1 indole-3-acetic acid and solubilized 15.77 to 71.43 μg mL-1 inorganic phosphate; 21 produced 63.12 to 99.92% siderophore units, and 15 exhibited 103.60 to 1,296.42 nmol α-ketobutyrate mg-1 protein h-1 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity. Based on superior plant growth-promoting attributes, eight statistically significant multifarious PGPR were further evaluated for an in planta plant growth-promotion assay under poly greenhouse conditions. Plants treated with Kosakonia cowanii HypNH10 and Rahnella variigena HypNH18 showed, by significant amounts, the highest photosynthetic pigments and performance, eventually leading to the highest biomass accumulation. Comparative genome analysis and comprehensive genome mining unraveled their unique genetic features, such as adaptation to the host plant's immune system and specialized metabolites. Moreover, the strains harbor several functional genes regulating direct and indirect plant growth-promotion mechanisms through nutrient acquisition, phytohormone production, and stress alleviation. In essence, the current study endorsed strains HypNH10 and HypNH18 as cogent candidates for microbe-assisted H. perforatum cultivation by highlighting their exclusive genomic signatures, which suggest their unison, compatibility, and multifaceted beneficial interactions with their host and support the excellent plant growth-promotion performance observed in the greenhouse trial. IMPORTANCE Hypericum perforatum L. (St. John's wort) herbal preparations are among the top-selling products to treat depression worldwide. A significant portion of the overall Hypericum supply is sourced through wild collection, prompting a rapid decline in their natural stands. Crop cultivation seems lucrative, although cultivable land and its existing rhizomicrobiome are well suited for traditional crops, and its sudden introduction can create soil microbiome dysbiosis. Also, the conventional plant domestication procedures with increased reliance on agrochemicals can reduce the diversity of the associated rhizomicrobiome and plants' ability to interact with plant growth-promoting microorganisms, leading to unsatisfactory crop production alongside harmful environmental effects. Cultivating H. perforatum with crop-associated beneficial rhizobacteria can reconcile such concerns. Based on a combinatorial in vitro, in vivo plant growth-promotion assay and in silico prediction of plant growth-promoting traits, here we recommend two H. perforatum-associated PGPR, Kosakonia cowanii HypNH10 and Rahnella variigena HypNH18, to extrapolate as functional bioinoculants for H. perforatum sustainable cultivation.

Deciphering Plant-Insect-Microorganism Signals for Sustainable Crop Production

Agricultural crop productivity relies on the application of chemical pesticides to reduce pest and pathogen damage. However, chemical pesticides also pose a range of ecological, environmental and economic penalties. This includes the development of pesticide resistance by insect pests and pathogens, rendering pesticides less effective. Alternative sustainable crop protection tools should therefore be considered. Semiochemicals are signalling molecules produced by organisms, including plants, microbes, and animals, which cause behavioural or developmental changes in receiving organisms. Manipulating semiochemicals could provide a more sustainable approach to the management of insect pests and pathogens across crops. Here, we review the role of semiochemicals in the interaction between plants, insects and microbes, including examples of how they have been applied to agricultural systems. We highlight future research priorities to be considered for semiochemicals to be credible alternatives to the application of chemical pesticides.

Organic pulses and bacterial invasion alleviated by the resilience of soil microbial community

Biogas slurry is a nutrient-rich secondary product of livestock feces digestion which is recycled as a crop plantation fertilizer and provides exogenous microbes to the soil. However, the effects of biogas slurry microbes on the soil resident community remain unknown. In this study, we examined the ecological consequences of long-term biogas slurry pulse on the soil resident community and found that it promoted crop yield and altered soil characteristics. The soil microbial ecosystem was altered as a result of organic amendments due to the exogenous input of microbes and nutrients. Nevertheless, the soil resident communities were highly resilient to long-term organic pulses, as evidenced by community diversity and composition. The two dominant bacterial species in biogas slurry were Sterolibacterium and Clostridium. Notably, the abundance of Clostridium in biogas slurry increased following long-term amendments, while other species such as GP1 and Subdivision3_genera_incertae_sedis decreased; which was consistent with the results of module-eigengene analysis. Long-term organic pulses shifted the balance of microbial community assembly from stochastic to deterministic processes. Overall, our findings indicated that organic pulses accompanied with bacterial invasion could be alleviated by the resilience of soil microbial communities, thereby emphasizing the importance of microbiota assemblage and network architecture.

Fusarium equiseti-inoculation altered rhizosphere soil microbial community, potentially driving perennial ryegrass growth and salt tolerance

Fusarium equiseti is an effective plant growth-promoting fungi that induce systemic disease resistance in plants. However, the role of F. equiseti in regulating salt stress response and the underlying mechanisms remain largely unknown. Here, we investigated the effect of F. equiseti Z7 strain on the growth and salt stress response in perennial ryegrass. Additionally, the role of Z7 in regulating the abundance, composition, and structure of native microbial communities in the rhizosphere soil was determined. We observed that Z7 could produce indole-3-acetic acid (IAA) and siderophores. Hence, Z7 inoculation further enhanced plant growth and salt tolerance in perennial ryegrass. Inoculating Z7 increased K⁺ and decreased Na⁺ in plant tissues. Z7 inoculation also enhanced soil quality by reducing soluble salt and increasing available phosphorus. Moreover, inoculating Z7 altered the compositions of bacterial and fungal communities in the rhizosphere soil. For instance, beneficial bacterial genera, such as Flavobacterium, Enterobacter, Agrobacterium, and Burkholderiales were dominantly enriched in Z7-inoculated soil. Interestingly, the relative abundance of these genera showed significantly positive correlations with the fresh weight of perennial ryegrass. Our results demonstrate that Z7 could remarkably promote plant growth and salt tolerance by regulating ion homeostasis in plant tissues and microbial communities in the rhizosphere soil. This study provides a scientific foundation for applying microbes to improve plant growth under extreme salt stress conditions.

The positive effects of mineral-solubilizing microbial inoculants on asymbiotic nitrogen fixation of abandoned mine soils are driven by keystone phylotype

Toward the restoration of the increasing numbers of abandoned mines across China, external-soil spray seeding technologies have become more extensively utilized. However, considerable challenges remain that seriously hamper the effectiveness of these technologies, such as inadequate nutrient availability for plants. Previous studies have shown that mineral-solubilizing microbial inoculants can increase the nodules of legumes. However, their effects on symbiotic nitrogen fixation (SNF), asymbiotic nitrogen fixation (ANF), and diazotrophic communities remain unknown. Further, research into the application of functional microorganisms for the restoration of abandoned mines has been conducted either in greenhouses, or their application in the field has been too brief. Thus, we established a four-year field experiment in an abandoned mine and quantified the SNF, ANF, and diazotrophic communities. To the best of our knowledge, this study is the first to describe the long-term application of specific functional microorganisms for the remediation of abandoned mine sites in the field. We revealed that mineral-solubilizing microbial inoculants significantly increased the soil ANF rate and SNF content. There was no significant correlation between the diazotrophic alpha diversity and soil ANF rate; however, there were strong positive associations between the relative abundance and biodiversity of keystone phylotype (module #5) within ecological clusters and the ANF rate. Molecular ecological networks indicated that microbial inoculants increased network complexity and stability. Moreover, the inoculants significantly enhanced the deterministic ratio of diazotrophic communities. Furthermore, homogeneous selection predominantly mediated the assembly of soil diazotrophic communities. It was concluded that mineral-solubilizing microorganisms played a critical role in maintaining and enhancing nitrogen, which offers a new solution with great potential for the restoration of ecosystems at abandoned mine sites.

Lectin Receptor-like Kinase Signaling during Engineered Ectomycorrhiza Colonization

Mutualistic association can improve a plant’s health and productivity. G-type lectin receptor-like kinase (PtLecRLK1) is a susceptibility factor in Populus trichocarpa that permits root colonization by a beneficial fungus, Laccaria bicolor. Engineering PtLecRLK1 also permits L. bicolor root colonization in non-host plants similar to Populus trichocarpa. The intracellular signaling reprogramed by PtLecRLK1 upon recognition of L. bicolor to allow for the development and maintenance of symbiosis is yet to be determined. In this study, phosphoproteomics was utilized to identify phosphorylation-based relevant signaling pathways associated with PtLecRLK1 recognition of L. bicolor in transgenic switchgrass roots. Our finding shows that PtLecRLK1 in transgenic plants modifies the chitin-triggered plant defense and MAPK signaling along with a significant adjustment in phytohormone signaling, ROS balance, endocytosis, cytoskeleton movement, and proteasomal degradation in order to facilitate the establishment and maintenance of L. bicolor colonization. Moreover, protein–protein interaction data implicate a cGMP-dependent protein kinase as a potential substrate of PtLecRLK1.

Impact of Plant-Beneficial Bacterial Inocula on the Resident Bacteriome: Current Knowledge and Future Perspectives

The inoculation of plant growth-promoting bacteria (PGPB) as biofertilizers is one of the most efficient and sustainable strategies of rhizosphere manipulation leading to increased plant biomass and yield and improved plant health, as well as the ameliorated nutritional value of fruits and edible seeds. During the last decades, exciting, but heterogeneous, results have been obtained growing PGPB inoculated plants under controlled, stressful, and open field conditions. On the other hand, the possible impact of the PGPB deliberate release on the resident microbiota has been less explored and the little available information is contradictory. This review aims at filling this gap: after a brief description of the main mechanisms used by PGPB, we focus our attention on the process of PGPB selection and formulation and we provide some information on the EU regulation for microbial inocula. Then, the concept of PGPB inocula as a tool for rhizosphere engineering is introduced and the possible impact of bacterial inoculant on native bacterial communities is discussed, focusing on those bacterial species that are included in the EU regulation and on other promising bacterial species that are not yet included in the EU regulation.

The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont

Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant–microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant–microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.