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Plant Microbiome and Host Tolerance to Biotic and Abiotic Stresses

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: closed (31 January 2024) | Viewed by 15353

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Prof. Dr. Nathalie Vaillant-Gaveau

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Research Unit Induced Resistance and Plant Bioprotection, University of Reims, EA 4707 USC INRAe 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France
Interests: physiology; ecophysiology; photosynthesis; carbon metabolism

Prof. Dr. Essaid Ait Barka

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Research Unit Induced Resistance and Plant Bioprotection, University of Reims, EA 4707 USC INRAe 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France
Interests: plant-microbe interaction; stress physiology plants responses to biotic and abiotic stress; crop protection; biological control
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Dr. Cédric Jacquard

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Prof. Dr. Rachid Lahlali

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Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Km 10, BP S/40, Meknès 50001, Morocco
Interests: plant–microbe interaction; mycology; crop protection; biological control; horticultural crops
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Worldwide agriculture is facing a transition process toward more sustainable production, which involves a decrease in chemical inputs and the preservation of microbiomes’ richness and biodiversity. Rhizosphere interactions are based on complex exchanges within a diverse community of microorganisms, which compete and interact with each other and with the plant root. Plant-associated microbes can impact plant growth by synthetizing and releasing secondary metabolites that can either reduce or prevent the harmful impacts of phytopathogenic organisms in the rhizosphere and/or by facilitating the availability or uptake of some nutrients from the root environment. Plants can modulate both the level and type of molecules that they exude and, based on the knowledge that different root exudates select for different types of bacteria, these plants might therefore modulate their microbiomes.

Recent reports have revealed that plants exposed to a specific abiotic stress or biotic stress have evolved a “cry-for-help” approach to recruit beneficial soil microorganisms to reduce damages caused by these stresses. As beneficial soil microbes can help plants to overcome different stresses and improve plant growth, it is crucial for plants to recruit, activate, and assemble protective microbiomes by adjusting their exudates to select specific consortia.

The present issue will present the state of the art of research in plant microbiome and host tolerance to biotic and abiotic stresses by addressing fundamental questions on functions and mechanisms involved when plants are subjected to (a)biotic stress and how these processes are impacted/amplified by microbiome or affect the composition of rhizosphere microbial communities.

We invite researchers to submit regular research papers, reviews, communications, and short notes that are intended to meet the following or related topics:

Plant immunity;
Plant resilience;
Rhizosphere plant-microbe interactions;
Chemical signaling and communication by microbes;
Gene regulation and genomic regulatory analysis;
Chemistry of microbial recruitment by roots of plants under stress;
Root exudate chemistry;
Metagenomics, metatranscriptomics, proteomic and metabolomics analysis;
Signal transduction during the induction of acquired resistance.

Prof. Dr. Nathalie Vaillant-Gaveau
Prof. Dr. Essaid Ait Barka
Dr. Cédric Jacquard
Prof. Dr. Rachid Lahlali
Guest Editors

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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. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

plant immunity
signaling pathways
rhizosphere microbial communities
engineering microbiota

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Published Papers (7 papers)

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Research

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20 pages, 4489 KiB

Open AccessArticle

Substrate Matters: Ionic Silver Alters Lettuce Growth, Nutrient Uptake, and Root Microbiome in a Hydroponics System

by LaShelle Spencer, Blake Costine, Tesia Irwin, Anirudha Dixit, Cory Spern, Angie Diaz, Brittney Lozzi, Wenyan Li, Christina Khodadad, Trent Smith, Raymond Wheeler and Aubrie O’Rourke

Microorganisms 2024, 12(3), 515; https://doi.org/10.3390/microorganisms12030515 - 4 Mar 2024

Viewed by 2241

Abstract

Ionic silver (Ag⁺) is being investigated as a residual biocide for use in NASA spacecraft potable water systems on future crewed missions. This water will be used to irrigate future spaceflight crop production systems. We have evaluated the impact of three concentrations (31 ppb, 125 ppb, and 500 ppb) of ionic silver biocide solutions on lettuce in an arcillite (calcinated clay particle substrate) and hydroponic (substrate-less) growth setup after 28 days. Lettuce plant growth was reduced in the hydroponic samples treated with 31 ppb silver and severely stunted for samples treated at 125 ppb and 500 ppb silver. No growth defects were observed in arcillite-grown lettuce. Silver was detectable in the hydroponic-grown lettuce leaves at each concentration but was not detected in the arcillite-grown lettuce leaves. Specifically, when 125 ppb silver water was applied to a hydroponics tray, Ag⁺ was detected at an average amount of 7 μg/g (dry weight) in lettuce leaves. The increase in Ag⁺ corresponded with a decrease in several essential elements in the lettuce tissue (Ca, K, P, S). In the arcillite growth setup, silver did not impact the plant root zone microbiome in terms of alpha diversity and relative abundance between treatments and control. However, with increasing silver concentration, the alpha diversity increased in lettuce root samples and in the water from the hydroponics tray samples. The genera in the hydroponic root and water samples were similar across the silver concentrations but displayed different relative abundances. This suggests that ionic silver was acting as a selective pressure for the microbes that colonize the hydroponic water. The surviving microbes likely utilized exudates from the stunted plant roots as a carbon source. Analysis of the root-associated microbiomes in response to silver showed enrichment of metagenomic pathways associated with alternate carbon source utilization, fatty-acid synthesis, and the ppGpp (guanosine 3′-diphosphate 5′-diphosphate) stringent response global regulatory system that operates under conditions of environmental stress. Nutrient solutions containing Ag⁺ in concentrations greater than 31 ppb in hydroponic systems lacking cation-exchange capacity can severely impact crop production due to stunting of plant growth. Full article

(This article belongs to the Special Issue Plant Microbiome and Host Tolerance to Biotic and Abiotic Stresses)

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15 pages, 5150 KiB

Open AccessArticle

Divergent Fungal Community Dynamics of Thuja sutchuenensis in Arid Environments

by Youwei Zuo, Lingxiang Yang, Qian Wang, Benchao Zhu, Changying Xia, Huan Zhang, Wenqiao Li, Zhe Zhang and Hongping Deng

Microorganisms 2024, 12(3), 446; https://doi.org/10.3390/microorganisms12030446 - 22 Feb 2024

Viewed by 1157

Abstract

Thuja sutchuenensis Franch., an endangered species sparsely distributed in the mountainous and arid regions of southwest China, faces the critical challenge of adapting to these harsh conditions. Understanding the plant’s strategies for survival and the precise roles played by soil fungal communities in this adaptation remains an area of limited knowledge. Our investigation centers on the fungal communities associated with T. sutchuenensis and their interactions with soil water content. Notably, we identified unique fungal communities in the low soil moisture group, and these communities exhibited lower coverage but higher phylogenetic diversity (PD), Chao1, and Shannon indices compared to other groups. Network analysis revealed a modular structure within the fungal communities, with key hub nodes identified, particularly in the arid group. This group demonstrated higher levels of soil saprotrophs and ectomycorrhizal fungi and a reduced presence of plant pathogens. Linear discriminant analysis highlighted the significance of genera such as Russula, Myxotrichaceae, and Sebacina, emphasizing their roles in supporting the plant in arid environments. Random forest analysis indicated that soil moisture content emerged as the primary driver in determining fungal composition and diversity and contributed to the variables of several fungal genera. Collectively, this study provides valuable insights into the fungal communities associated with T. sutchuenensis, shedding light on their adaptation to extreme arid conditions. Full article

(This article belongs to the Special Issue Plant Microbiome and Host Tolerance to Biotic and Abiotic Stresses)

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15 pages, 2974 KiB

Open AccessArticle

Effects of NaHCO₃ Stress on Black Locust (Robinia pseudoacacia L.) Physiology, Biochemistry, and Rhizosphere Bacterial Communities

by Lulu Liu, Yu Chen, Liwen Zhang, Xueqi Bi, Fanjuan Meng and Qiuxiang Luo

Microorganisms 2023, 11(12), 2941; https://doi.org/10.3390/microorganisms11122941 - 8 Dec 2023

Viewed by 1250

Abstract

Soil salinization has become an ecological and environmental problem that cannot be ignored. Tetraploid black locust (Robinia pseudoacacia L.) is a leguminous tree with characteristics of drought and saline-alkali tolerance. Rhizosphere bacteria are the primary functional microorganisms within the plant root system, and they play a crucial role in regulating plant growth and enhancing stress tolerance. However, there is still a lack of research on the effect of saline-alkali stress on the bacterial community structure in the rhizosphere of black locusts. In this study, we applied 0, 50, 100, and 150 mM NaHCO₃ stress to diploid (2×) and tetraploid (4×) black locusts for 16 days. We used 16S rDNA sequencing to investigate the changes in the rhizosphere bacterial communities. Furthermore, we evaluated soil enzyme activity and plant physiological characteristics to explore the response of rhizosphere bacteria to NaHCO₃ stress. The results demonstrated that the 4× plant exhibited superior alkali resistance compared to its 2× plant counterpart under NaHCO₃ stress. Simultaneously, it was observed that low concentrations of NaHCO₃ stress notably increased the abundance of rhizosphere bacteria in both plant types, while reducing their diversity. The impact of stress on the rhizosphere bacterial community weakened as the stress concentration increased. The application of NaHCO₃ stress caused a significant change in the composition of the bacterial community in the rhizosphere. Additionally, alkaline salt stress influences the diversity of rhizosphere bacterial communities, which are linked to soil enzyme activities. These data will help us better understand the relationship between the dominant rhizosphere bacterial community and black locust. They will also provide a reference for further improving the alkali resistance of black locust by enhancing the soil bacterial community. Full article

(This article belongs to the Special Issue Plant Microbiome and Host Tolerance to Biotic and Abiotic Stresses)

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14 pages, 3965 KiB

Open AccessArticle

Organic Farming Allows Balanced Fungal and Oomycetes Communities

by Bora Nam, Hyo Jung Lee and Young-Joon Choi

Microorganisms 2023, 11(5), 1307; https://doi.org/10.3390/microorganisms11051307 - 17 May 2023

Cited by 1 | Viewed by 2009

Abstract

Conventional and organic farming systems affect soils differently, thereby influencing microbial diversity and composition. Organic farming, which relies on natural processes, biodiversity, and cycles adapted to local conditions, is generally known to improve soil texture and alleviate microbial diversity loss compared with that of conventional farming, which uses synthetic inputs such as chemical fertilisers, pesticides, and herbicides. Although they affect the health and productivity of host plants, the community dynamics of fungi and fungi-like oomycetes (under Chromista) in organic farmland are poorly understood. The present study aimed to determine the differences in the diversity and composition of fungi and oomycetes inhabiting organic and conventional farm soils using culture-based DNA barcoding and culture-independent environmental DNA (eDNA) metabarcoding. Four tomato farms with different farming practices were selected and investigated: mature pure organic (MPO) via non-pesticide and organic fertiliser, mature integrated organic (MIO) via non-pesticide and chemical fertiliser, mature conventional chemical (MCC) via both pesticide and chemical fertiliser, and young conventional chemical (YCC). Culture-based analysis revealed that different genera were dominant on the four farms: Linnemannia in MPO, Mucor in MIO, and Globisporangium in MCC and YCC. eDNA metabarcoding demonstrated that the fungal richness and diversity on the MPO farm were higher than that on other farms. Both conventional farms exhibited simpler fungal and oomycete network structures with lower phylogenetic diversity. Interestingly, a high richness of oomycetes was shown in YCC; in which, Globisporangium, a potential pathogenic group on tomato plants, was abundantly observed. Our findings indicate that organic farming enhances fungal and oomycete diversity, which may provide robust support for maintaining healthy and sustainable agricultural practices. This study contributes to our knowledge on the positive effects of organic farming on crop microbiomes and provides essential information for maintaining biological diversity. Full article

(This article belongs to the Special Issue Plant Microbiome and Host Tolerance to Biotic and Abiotic Stresses)

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13 pages, 3446 KiB

Open AccessArticle

Influence of Plant Growth-Promoting Rhizobacteria on the Formation of Apoplastic Barriers and Uptake of Water and Potassium by Wheat Plants

by Zarina Akhtyamova, Elena Martynenko, Tatiana Arkhipova, Oksana Seldimirova, Ilshat Galin, Andrey Belimov, Lidiya Vysotskaya and Guzel Kudoyarova

Microorganisms 2023, 11(5), 1227; https://doi.org/10.3390/microorganisms11051227 - 6 May 2023

Cited by 7 | Viewed by 2308

Abstract

The formation of apoplastic barriers is important for controlling the uptake of water and ions by plants, thereby influencing plant growth. However, the effects of plant growth-promoting bacteria on the formation of apoplastic barriers, and the relationship between these effects and the ability of bacteria to influence the content of hormones in plants, have not been sufficiently studied. The content of cytokinins, auxins and potassium, characteristics of water relations, deposition of lignin and suberin and the formation of Casparian bands in the root endodermis of durum wheat (Triticum durum Desf.) plants were evaluated after the introduction of the cytokinin-producing bacterium Bacillus subtilis IB-22 or the auxin-producing bacterium Pseudomonas mandelii IB-Ki14 into their rhizosphere. The experiments were carried out in laboratory conditions in pots with agrochernozem at an optimal level of illumination and watering. Both strains increased shoot biomass, leaf area and chlorophyll content in leaves. Bacteria enhanced the formation of apoplastic barriers, which were most pronounced when plants were treated with P. mandelii IB-Ki14. At the same time, P. mandelii IB-Ki14 caused no decrease in the hydraulic conductivity, while inoculation with B. subtilis IB-22, increased hydraulic conductivity. Cell wall lignification reduced the potassium content in the roots, but did not affect its content in the shoots of plants inoculated with P. mandelii IB-Ki14. Inoculation with B. subtilis IB-22 did not change the potassium content in the roots, but increased it in the shoots. Full article

(This article belongs to the Special Issue Plant Microbiome and Host Tolerance to Biotic and Abiotic Stresses)

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16 pages, 4922 KiB

Open AccessArticle

Rhizobacterial Colonization and Management of Bacterial Speck Pathogen in Tomato by Pseudomonas spp.

by Mohsen M. Elsharkawy, Amr A. Khedr, Farid Mehiar, Elsayed M. El-Kady, Khairiah Mubarak Alwutayd and Said I. Behiry

Microorganisms 2023, 11(5), 1103; https://doi.org/10.3390/microorganisms11051103 - 23 Apr 2023

Cited by 4 | Viewed by 1833

Abstract

Plants and soil microorganisms interact at every stage of growth. Pseudomonas spp. are highly regarded for their ability to increase crop production and protection from diseases. The aim of this study is to understand the mechanisms of the rhizobacterial colonization of tomato roots via chemotaxis assay and the activation of tomato resistance against the pathogenic bacterium, Pseudomonas syringae pv. tomato DC3000 (Pst). The capillary assay was used to evaluate the chemotaxis response of PGPRs (plant growth-promoting rhizobacteria). The activities of defense enzymes and the expressions of PR (pathogenesis-related) genes were measured using real-time qPCR. Chemotactic responses to malic and citric acids (the most important root exudates found in different plant species) at low concentrations varied substantially among the rhizobacterial isolates (63 species). Beneficial isolates including Pseudomonas resinovorans A5, P. vranovensis A30, P. resinovorans A28, P. umsongensis O26, P. stutzeri N42, and P. putida T15 reacted well to different concentrations of root exudates. P. putida T15 demonstrated the most potent anti-Pst activity. At three and six days after inoculation, the greatest levels of polyphenol oxidase and peroxidase activity were reported in the A5 and T15 groups. In tomato, transcript levels of four PR (pathogenesis-related) genes were elevated by rhizobacterial treatments. PGPR isolates alone or in combination with BABA (β-amino butyric acid) up-regulated the transcriptions of PR1, PR2, LOX, and PAL genes. Treatments with N42 and T15 resulted in the greatest improvements in tomato growth and yield traits. In conclusion, the results explain the mechanisms of rhizobacterial colonization for the improved management of Pst. Rhizobacterial isolates play a role in tomato’s resistance to Pst via salicylic acid and jasmonic acid pathways. Full article

(This article belongs to the Special Issue Plant Microbiome and Host Tolerance to Biotic and Abiotic Stresses)

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22 pages, 6336 KiB

Open AccessReview

Mass Spectral Imaging to Map Plant–Microbe Interactions

by Gabriel D. Parker, Luke Hanley and Xiao-Ying Yu

Microorganisms 2023, 11(8), 2045; https://doi.org/10.3390/microorganisms11082045 - 9 Aug 2023

Cited by 3 | Viewed by 2715

Abstract

Plant–microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms. Full article

(This article belongs to the Special Issue Plant Microbiome and Host Tolerance to Biotic and Abiotic Stresses)

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