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Interaction between Plants, Microorganisms, and Soils in Different Ecosystems

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (20 December 2022) | Viewed by 50775

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Special Issue Editors

Prof. Dr. Anna Gałązka

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Guest Editor

Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Puławy, Poland
Interests: microbiome and mycobiome of soil and plant rhizosphere; endorhizosphere; next generation sequencing; soil and plant biodiversity
Special Issues, Collections and Topics in MDPI journals

Dr. Łukasz Pawlik

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Guest Editor

Institute of Earth Sciences, Faculty of Natural Sciences, University of Silesia, ul. Bedzinska 60, 41-200 Sosnowiec, Poland
Interests: forest disturbance; windstorm; machine learning; biomorphodynamics; geohazards

Special Issue Information

Dear Colleagues,

Plants are colonised by an extremely high number of organisms, which can reach cell density much greater than the number of cells in the plant itself. In addition, the number of genes of microorganisms inhabiting the rhizosphere significantly exceeds the number of plant genes. Plants act as a link between communities of microorganisms, insects, and other invertebrate and vertebrate animals occurring both above and below the soil surface. In the natural environment, abiotic and biotic factors have an indirect or direct impact on plants. The root system of a plant works like a factory that produces a huge amount of chemicals to communicate effectively with the microorganisms around it. At the same time, micro-organisms can use these compounds as an energy source. The variety of microorganisms associated with plant roots is enormous, amounting to tens of thousands of species. This complex microbial community, also called the second plant genome, is essential for plant health and productivity. Over the last few years, there has been significant progress in research into the structure and dynamics of the microbial sphere of the rhizosphere. It has been proven that plants shape the composition of microorganisms by synthesizing root secretions. On the other hand, microorganisms play a key role in the functioning of plants through their positive impact on their growth and development. In general, rhizosphere microorganisms promote plant growth directly by providing plants with minerals such as nitrogen and phosphorus and by synthesizing growth regulators, as well as indirectly, by inhibiting the development of various plant pathogens. Researchers use novel technologies including next-generation sequencing, the use of soil profiling and microprobes for genomics, transcriptomics and metabolomics studies to conduct informative studies in the soil rhizosphere, and the role of plants and microorganisms in these interactions.

This Special Issue intends to improve our understanding of the “Interaction between the Plant Rhizosphere and Soil Organisms”. Submissions could consist of research on topics including but not limited to:

Diversity of soil microorganisms;
Soil microorganisms in forest ecosystems;
Rhizosphere diversity;
Interaction between plants and their microbial communities;
Functions of rhizosphere microorganisms;
Microorganisms synthesizing plant growth regulators;
Biological plant protection;
Genetic diversity among soil microbial communities;
Novel bioactive compound isolation and identification in plants and soil.

We would like to take this opportunity to welcome the submission of research articles, reviews, as well as technical notes and communications, on these related topics.

Prof. Dr. Anna Gałązka
Dr. Łukasz Pawlik
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

microbiome and mycobiome of soil and tree rhizosphere
mycorrhizal fungi
next-generation sequencing
soil and tree biodiversity
interaction between plants and microorganisms

Published Papers (11 papers)

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11 pages, 1613 KiB

Open AccessArticle

The Antifungal Effect of Pyroligneous Acid on the Phytopathogenic Fungus Botrytis cinerea

by Giorgia Pertile and Magdalena Frąc

Int. J. Mol. Sci. 2023, 24(4), 3080; https://doi.org/10.3390/ijms24043080 - 04 Feb 2023

Cited by 2 | Viewed by 2032

Abstract

In recent years, climate change has intensified harsh periods of rain alternating with periods of drought, leading to an increase in the presence of phytopathogenic fungi. In this study, we want to analyse the antifungal properties of pyroligneous acid against the fungal phytopathogen Botrytis cinerea. Through the inhibition test, we observed that the application of different dilutions of pyroligneous acid rarefied the growth of the fungal mycelium. Furthermore, we have seen through the metabolic profile that B. cinerea is not able to use pyroligneous acid as a resource or even grow in close contact with this resource. Moreover, we observed that the pre-incubation of the fungus in pyroligneous acid leads to a reduction in biomass production. These results give us hope for the possible use of this natural substance as a possible substance to protect plantations from pathogen attacks. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems)

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24 pages, 6360 KiB

Open AccessArticle

The Impact of Permethrin and Cypermethrin on Plants, Soil Enzyme Activity, and Microbial Communities

by Agata Borowik, Jadwiga Wyszkowska, Magdalena Zaborowska and Jan Kucharski

Int. J. Mol. Sci. 2023, 24(3), 2892; https://doi.org/10.3390/ijms24032892 - 02 Feb 2023

Cited by 12 | Viewed by 5717

Abstract

Pyrethroids are insecticides most commonly used for insect control to boost agricultural production. The aim of the present research was to determine the effect of permethrin and cypermethrin on cultured and non-cultivated bacteria and fungi and on the activity of soil enzymes, as well as to determine the usefulness of Zea mays in mitigating the adverse effects of the tested pyrethroids on the soil microbiome. The analyses were carried out in the samples of both soil not sown with any plant and soil sown with Zea mays. Permethrin and cypermethrin were found to stimulate the multiplication of cultured organotrophic bacteria (on average by 38.3%) and actinomycetes (on average by 80.2%), and to inhibit fungi growth (on average by 31.7%) and the enzymatic activity of the soil, reducing the soil biochemical fertility index (BA) by 27.7%. They also modified the number of operational taxonomic units (OTUs) of the Actinobacteria and Proteobacteria phyla and the Ascomycota and Basidiomycota phyla. The pressure of permethrin and cypermethrin was tolerated well by the bacteria Sphingomonas (clone 3214512, 1052559, 237613, 1048605) and Bacillus (clone New.ReferenceOTU111, 593219, 578257), and by the fungi Penicillium (SH1533734.08FU, SH1692798.08FU) and Trichocladium (SH1615601.08FU). Both insecticides disturbed the growth and yielding of Zea mays, as a result of which its yield and leaf greenness index decreased. The cultivation of Zea mays had a positive effect on both soil enzymes and soil microorganisms and mitigated the anomalies caused by the tested insecticides in the microbiome and activity of soil enzymes. Permethrin decreased the yield of its aerial parts by 37.9% and its roots by 33.9%, whereas respective decreases caused by cypermethrin reached 16.8% and 4.3%. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems)

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18 pages, 41893 KiB

Open AccessArticle

Phenol and Polyaromatic Hydrocarbons Are Stronger Drivers Than Host Plant Species in Shaping the Arbuscular Mycorrhizal Fungal Component of the Mycorrhizosphere

by Monika Malicka, Franco Magurno and Zofia Piotrowska-Seget

Int. J. Mol. Sci. 2022, 23(20), 12585; https://doi.org/10.3390/ijms232012585 - 20 Oct 2022

Cited by 2 | Viewed by 1519

Abstract

Changes in soil microbial communities in response to hydrocarbon pollution are critical indicators of disturbed ecosystem conditions. A core component of these communities that is functionally adjusted to the life-history traits of the host and environmental factors consists of arbuscular mycorrhizal fungi (AMF). AMF communities associated with Poa trivialis and Phragmites australis growing at a phenol and polynuclear aromatic hydrocarbon (PAH)-contaminated site and at an uncontaminated site were compared based on LSU rDNA sequencing. Dissimilarities in species composition and community structures indicated soil pollution as the main factor negatively affecting the AMF diversity. The AMF communities at the contaminated site were dominated by fungal generalists (Rhizophagus, Funneliformis, Claroideoglomus, Paraglomus) with wide ecological tolerance. At the control site, the AMF communities were characterized by higher taxonomic and functional diversity than those exposed to the contamination. The host plant identity was the main driver distinguishing the two AMF metacommunities. The AMF communities at the uncontaminated site were represented by Polonospora, Paraglomus, Oehlia, Nanoglomus, Rhizoglomus, Dominikia, and Microdominikia. Polonosporaceae and Paraglomeraceae were particularly dominant in the Ph. australis mycorrhizosphere. The high abundance of early diverging AMF could be due to the use of primers able to detect lineages such as Paraglomeracae that have not been recognized by previously used 18S rDNA primers. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems)

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20 pages, 4517 KiB

Open AccessArticle

Effects of Rhizosphere Bacteria on Strawberry Plants (Fragaria × ananassa Duch.) under Water Deficit

by Dominika Paliwoda, Grzegorz Mikiciuk, Małgorzata Mikiciuk, Anna Kisiel, Lidia Sas-Paszt and Tymoteusz Miller

Int. J. Mol. Sci. 2022, 23(18), 10449; https://doi.org/10.3390/ijms231810449 - 09 Sep 2022

Cited by 7 | Viewed by 1800

Abstract

Due to the observed climate warming, water deficiency in soil is currently one of the most important stressors limiting the size and quality of plant crops. Drought stress causes a number of morphological, physiological, and biochemical changes in plants, limiting their growth, development, and yield. Innovative methods of inducing resistance and protecting plants against stressors include the inoculation of crops with beneficial microorganisms isolated from the rhizosphere of the plant species to which they are to be applied. The aim of the present study was to evaluate 12 different strains of rhizosphere bacteria of the genera Pantoea, Bacillus, Azotobacter, and Pseudomonas by using them to inoculate strawberry plants and assessing their impact on mitigating the negative effects of drought stress. Bacterial populations were assessed by estimates of their size based on bacterial counts in the growth substrate and with bioassays for plant growth-promoting traits. The physiological condition of strawberry plants was determined based on the parameters of chlorophyll fluorescence. The usefulness of the test methods used to assess the influence of plant inoculation with rhizosphere bacteria on the response of plants growing under water deficit was also evaluated. A two-factor experiment was performed in a complete randomization design. The first experimental factor was the inoculation of plant roots with rhizosphere bacteria. The second experimental factor was the different moisture content of the growth substrate. The water potential was maintained at −10 to −15 kPa under control conditions, and at −40 to −45 kPa under the conditions of water deficit in the substrate. The tests on strawberry plants showed that the highest sensitivity to water deficiency, and thus the greatest usefulness for characterizing water stress, was demonstrated by the following indices of chlorophyll “a” fluorescence: F_M, F_V, F_V/F_M, PI, and Area. Based on the assessment of the condition of the photosynthetic apparatus and the analysis of chlorophyll “a” fluorescence indices, including hierarchical cluster analysis, the following strains of rhizosphere bacteria were found to have favorable effects on strawberry plants under water deficit: the Bacillus sp. strains DLGB2 and DKB26 and the Pantoea sp. strains DKB63, DKB70, DKB68, DKB64, and DKB65. In the tests, these strains of Bacillus sp. exhibited a common trait—the ability to produce siderophores, while those of Pantoea sp. were notable for phosphate mobilization and ACCD activity. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems)

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17 pages, 1584 KiB

Open AccessArticle

Microbial Community, Metabolic Potential and Seasonality of Endosphere Microbiota Associated with Leaves of the Bioenergy Tree Paulownia elongata × fortunei

by Małgorzata Woźniak, Anna Gałązka, Anna Marzec-Grządziel and Magdalena Frąc

Int. J. Mol. Sci. 2022, 23(16), 8978; https://doi.org/10.3390/ijms23168978 - 11 Aug 2022

Viewed by 1787

Abstract

The microbial structure and metabolic function of plant-associated endophytes play a key role in the ecology of various environments, including trees. Here, the structure and functional profiles of the endophytic bacterial community, associated with Paulownia elongata × fortunei, in correlation with seasonality, were evaluated using Biolog EcoPlates. Biolog EcoPlates was used to analyse the functional diversity of the microbiome. The total communities of leaf endophyte communities were investigated using 16S rRNA V5–V7 region amplicon deep sequencing via Illumina MiSeq. Community level physiological profiling (CLPP) analysis by the Biolog EcoPlate™ assay revealed that the carboxylic acids (19.67–36.18%) and amino acids (23.95–35.66%) were preferred by all by all communities, whereas amines and amides (0.38–9.46%) were least used. Seasonal differences in substrate use were also found. Based on the sequencing data, mainly phyla Proteobacteria (18.4–97.1%) and Actinobacteria (2.29–78.7%) were identified. A core microbiome could be found in leaf-associated endophytic communities in trees growing in different locations. This work demonstrates the application of Biolog EcoPlates in studies of the functional diversity of microbial communities in a niche other than soil and shows how it can be applied to the functional analyses of endomicrobiomes. This research can contribute to the popularisation of Biolog EcoPlates for the functional analysis of the endomicrobiome. This study confirms that the analysis of the structure and function of the plant endophytic microbiome plays a key role in the health control and the development of management strategies on bioenergy tree plantations. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems)

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19 pages, 3512 KiB

Open AccessArticle

Soil and Soilless Tomato Cultivation Promote Different Microbial Communities That Provide New Models for Future Crop Interventions

by Alice Anzalone, Alexandros Mosca, Giulio Dimaria, Daniele Nicotra, Matilde Tessitori, Grete Francesca Privitera, Alfredo Pulvirenti, Cherubino Leonardi and Vittoria Catara

Int. J. Mol. Sci. 2022, 23(15), 8820; https://doi.org/10.3390/ijms23158820 - 08 Aug 2022

Cited by 12 | Viewed by 3797

Abstract

The cultivation of soilless tomato in greenhouses has increased considerably, but little is known about the assembly of the root microbiome compared to plants grown in soil. To obtain such information, we constructed an assay in which we traced the bacterial and fungal communities by amplicon-based metagenomics during the cultivation chain from nursery to greenhouse. In the greenhouse, the plants were transplanted either into agricultural soil or into coconut fiber bags (soilless). At the phylum level, bacterial and fungal communities were primarily constituted in all microhabitats by Proteobacteria and Ascomycota, respectively. The results showed that the tomato rhizosphere microbiome was shaped by the substrate or soil in which the plants were grown. The microbiome was different particularly in terms of the bacterial communities. In agriculture, enrichment has been observed in putative biological control bacteria of the genera Pseudomonas and Bacillus and in potential phytopathogenic fungi. Overall, the study describes the different shaping of microbial communities in the two cultivation methods. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems)

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17 pages, 3295 KiB

Open AccessArticle

Response of Poplar and Associated Fungal Endophytic Communities to a PAH Contamination Gradient

by Lilian Gréau, Damien Blaudez, Dimitri Heintz, Julie Zumsteg, David Billet and Aurélie Cébron

Int. J. Mol. Sci. 2022, 23(11), 5909; https://doi.org/10.3390/ijms23115909 - 25 May 2022

Cited by 4 | Viewed by 1591

Abstract

Microbial populations associated to poplar are well described in non-contaminated and metal-contaminated environments but more poorly in the context of polycyclic aromatic hydrocarbon (PAH) contamination. This study aimed to understand how a gradient of phenanthrene (PHE) contamination affects poplar growth and the fungal microbiome in both soil and plant endosphere (roots, stems and leaves). Plant growth and fitness parameters indicated that the growth of Populus canadensis was impaired when PHE concentration increased above 400 mg kg⁻¹. Values of alpha-diversity indicators of fungal diversity and richness were not affected by the PHE gradient. The PHE contamination had a stronger impact on the fungal community composition in the soil and root compartments compared to that of the aboveground organs. Most of the indicator species whose relative abundance was correlated with PHE contamination decreased along the gradient indicating a toxic effect of PHE on these fungal OTUs (Operational Taxonomic Units). However, the relative abundance of some OTUs such as Cadophora, Alternaria and Aspergillus, potentially linked to PHE degradation or being plant-beneficial taxa, increased along the gradient. Finally, this study allowed a deeper understanding of the dual response of plant and fungal communities in the case of a soil PAH contamination gradient leading to new perspectives on fungal assisted phytoremediation. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems)

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25 pages, 7237 KiB

Open AccessArticle

Biodiversity and Metabolic Potential of Bacteria in Bulk Soil from the Peri-Root Zone of Black Alder (Alnus glutinosa), Silver Birch (Betula pendula) and Scots Pine (Pinus sylvestris)

by Anna Gałązka, Anna Marzec-Grządziel, Milan Varsadiya, Jacek Niedźwiecki, Karolina Gawryjołek, Karolina Furtak, Marcin Przybyś and Jarosław Grządziel

Int. J. Mol. Sci. 2022, 23(5), 2633; https://doi.org/10.3390/ijms23052633 - 27 Feb 2022

Cited by 7 | Viewed by 2165

Abstract

The formation of specific features of forest habitats is determined by the physical, chemical, and biological properties of the soil. The aim of the study was to determine the structural and functional biodiversity of soil microorganisms inhabiting the bulk soil from the peri-root zone of three tree species: Alnus glutinosa, Betula pendula, and Pinus sylvestris. Soil samples were collected from a semi-deciduous forest located in an area belonging to the Agricultural Experimental Station IUNG-PIB in Osiny, Poland. The basic chemical and biological parameters of soils were determined, as well as the structural diversity of bacteria (16S ribosomal RNA (rRNA) sequencing) and the metabolic profile of microorganisms (Biolog EcoPlates). The bulk soils collected from peri-root zone of A. glutinosa were characterized by the highest enzymatic activities. Moreover, the highest metabolic activities on EcoPlates were observed in bulk soil collected in the proximity of the root system the A. glutinosa and B. pendula. In turn, the bulk soil collected from peri-root zone of P. sylvestris had much lower biological activity and a lower metabolic potential. The most metabolized compounds were L-phenylalanine, L-asparagine, D-mannitol, and gamma-hydroxy-butyric acid. The highest values of the diversity indicators were in the soils collected in the proximity of the root system of A. glutinosa and B. pendula. The bulk soil collected from P. sylvestris peri-root zone was characterized by the lowest Shannon’s diversity index. In turn, the evenness index (E) was the highest in soils collected from the P. sylvestris, which indicated significantly lower diversity in these soils. The most abundant classes of bacteria in all samples were Actinobacteria, Acidobacteria_Gp1, and Alphaproteobacteria. The classes Bacilli, Thermoleophilia, Betaproteobacteria, and Subdivision3 were dominant in the B. pendula bulk soil. Streptosporangiales was the most significantly enriched order in the B. pendula soil compared with the A. glutinosa and P. sylvestris. There was a significantly higher mean proportion of aerobic nitrite oxidation, nitrate reduction, sulphate respiration, and sulfur compound respiration in the bulk soil of peri-root zone of A. glutinosa. Our research confirms that the evaluation of soil biodiversity and metabolic potential of bacteria can be of great assistance in a quality and health control tool in the soils of forested areas and in the forest production. Identification of bacteria that promote plant growth and have a high biotechnological potential can be assume a substantial improvement in the ecosystem and use of the forest land. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems)

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26 pages, 6861 KiB

Open AccessArticle

Bisphenol A—A Dangerous Pollutant Distorting the Biological Properties of Soil

by Magdalena Zaborowska, Jadwiga Wyszkowska, Agata Borowik and Jan Kucharski

Int. J. Mol. Sci. 2021, 22(23), 12753; https://doi.org/10.3390/ijms222312753 - 25 Nov 2021

Cited by 22 | Viewed by 2691

Abstract

Bisphenol A (BPA), with its wide array of products and applications, is currently one of the most commonly produced chemicals in the world. A narrow pool of data on BPA–microorganism–plant interaction mechanisms has stimulated the following research, the aim of which has been to determine the response of the soil microbiome and crop plants, as well as the activity of soil enzymes exposed to BPA pressure. A range of disturbances was assessed, based on the activity of seven soil enzymes, an abundance of five groups of microorganisms, and the structural diversity of the soil microbiome. The condition of the soil was verified by determining the values of the indices: colony development (CD), ecophysiological diversity (EP), the Shannon–Weaver index, and the Simpson index, tolerance of soil enzymes, microorganisms and plants (TI_BPA), biochemical soil fertility (BA₂₁), the ratio of the mass of aerial parts to the mass of plant roots (PR), and the leaf greenness index: Soil and Plant Analysis Development (SPAD). The data brought into sharp focus the adverse effects of BPA on the abundance and ecophysiological diversity of fungi. A change in the structural composition of bacteria was noted. Bisphenol A had a more beneficial effect on the Proteobacteria than on bacteria from the phyla Actinobacteria or Bacteroidetes. The microbiome of the soil exposed to BPA was numerously represented by bacteria from the genus Sphingomonas. In this object pool, the highest fungal OTU richness was achieved by the genus Penicillium, a representative of the phylum Ascomycota. A dose of 1000 mg BPA kg⁻¹ d.m. of soil depressed the activity of dehydrogenases, urease, acid phosphatase and β-glucosidase, while increasing that of alkaline phosphatase and arylsulfatase. Spring oilseed rape and maize responded significantly negatively to the soil contamination with BPA. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems)

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Review

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28 pages, 1845 KiB

Open AccessReview

Trichoderma: The Current Status of Its Application in Agriculture for the Biocontrol of Fungal Phytopathogens and Stimulation of Plant Growth

by Renata Tyśkiewicz, Artur Nowak, Ewa Ozimek and Jolanta Jaroszuk-Ściseł

Int. J. Mol. Sci. 2022, 23(4), 2329; https://doi.org/10.3390/ijms23042329 - 19 Feb 2022

Cited by 147 | Viewed by 21605

Abstract

Rhizosphere filamentous fungi of the genus Trichoderma, a dominant component of various soil ecosystem mycobiomes, are characterized by the ability to colonize plant roots. Detailed knowledge of the properties of Trichoderma, including metabolic activity and the type of interaction with plants and other microorganisms, can ensure its effective use in agriculture. The growing interest in the application of Trichoderma results from their direct and indirect biocontrol potential against a wide range of soil phytopathogens. They act through various complex mechanisms, such as mycoparasitism, the degradation of pathogen cell walls, competition for nutrients and space, and induction of plant resistance. With the constant exposure of plants to a variety of pathogens, especially filamentous fungi, and the increased resistance of pathogens to chemical pesticides, the main challenge is to develop biological protection alternatives. Among non-pathogenic microorganisms, Trichoderma seems to be the best candidate for use in green technologies due to its wide biofertilization and biostimulatory potential. Most of the species from the genus Trichoderma belong to the plant growth-promoting fungi that produce phytohormones and the 1-aminocyclopropane-1-carboxylate (ACC) deaminase enzyme. In the present review, the current status of Trichoderma is gathered, which is especially relevant in plant growth stimulation and the biocontrol of fungal phytopathogens. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems)

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17 pages, 1491 KiB

Open AccessReview

Abiotic Stress and Belowground Microbiome: The Potential of Omics Approaches

by Marco Sandrini, Luca Nerva, Fabiano Sillo, Raffaella Balestrini, Walter Chitarra and Elisa Zampieri

Int. J. Mol. Sci. 2022, 23(3), 1091; https://doi.org/10.3390/ijms23031091 - 19 Jan 2022

Cited by 22 | Viewed by 4145

Abstract

Nowadays, the worldwide agriculture is experiencing a transition process toward more sustainable production, which requires the reduction of chemical inputs and the preservation of microbiomes’ richness and biodiversity. Plants are no longer considered as standalone entities, and the future of agriculture should be grounded on the study of plant-associated microorganisms and all their potentiality. Moreover, due to the climate change scenario and the resulting rising incidence of abiotic stresses, an innovative and environmentally friendly technique in agroecosystem management is required to support plants in facing hostile environments. Plant-associated microorganisms have shown a great attitude as a promising tool to improve agriculture sustainability and to deal with harsh environments. Several studies were carried out in recent years looking for some beneficial plant-associated microbes and, on the basis of them, it is evident that Actinomycetes and arbuscular mycorrhizal fungi (AMF) have shown a considerable number of positive effects on plants’ fitness and health. Given the potential of these microorganisms and the effects of climate change, this review will be focused on their ability to support the plant during the interaction with abiotic stresses and on multi-omics techniques which can support researchers in unearthing the hidden world of plant–microbiome interactions. These associated microorganisms can increase plants’ endurance of abiotic stresses through several mechanisms, such as growth-promoting traits or priming-mediated stress tolerance. Using a multi-omics approach, it will be possible to deepen these mechanisms and the dynamic of belowground microbiomes, gaining fundamental information to exploit them as staunch allies and innovative weapons against crop abiotic enemies threatening crops in the ongoing global climate change context. Full article

(This article belongs to the Special Issue Interaction between Plants, Microorganisms, and Soils in Different Ecosystems)

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