Signaling Molecules and Their Roles in Plant–Microbe Interactions for Environmental Stress Resilience

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

Deadline for manuscript submissions: closed (15 December 2025) | Viewed by 5200

Special Issue Editor


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Guest Editor
Department of Biology, University of Louisiana Monore, Monroe, LA 71209, USA
Interests: plant stress tolerance; plant-microbe interactions

Special Issue Information

Dear Colleagues,

Plants are constantly challenged by a myriad of abiotic and biotic environmental stressors, posing significant challenges to ensure sustainable food security. Plants must elicit adequate adaptation responses to live under such stressful conditions, the majority of which are regulated and directed by several signaling molecules (SMs). SMs are at the core of plant cellular processes, producing signals critical for plant growth, development, and survival under stressful conditions. These SMs, which include phytohormones, reactive oxygen/nitrogen species, nitrogenous compounds, volatile compounds, small peptides, and gasotransmitters, orchestrate various intra-and inter-cellular communications for responding to environmental changes. Additionally, plants secrete these SMs to establish mutual relationships with the rhizosphere-associated microbes. Upon receiving plant-derived signals, microbes also produce a plethora of molecules and compounds, including antibiotics, certain proteins and peptides, volatile compounds, and quorum-sensing signals, which play significant roles in safeguarding plants from pathogens and environmental stresses. Effective interactions between plants and microbes can promote plant growth and stress resilience by triggering host responses at cellular and molecular levels. Thus, understanding the complexities of plant–microbe interactions may lead to novel ways of increasing plant survival and productivity while being ecologically benign. It is crucial to elucidate the molecular basis of SM-mediated plant–microbe interactions, and the functional roles of beneficial microbes to harness the potential of both plants and microbes to withstand environmental stress that adversely affects plant productivity. Our understanding of plant–microbe interactions and their importance for agricultural productivity have greatly advanced in recent years due to the advancement of genomics, proteomics, and metagenomics tools. However, how signaling molecules modulate the dialogues between plants and microbes, and how their mutual communication benefits plants are still far from being well characterized. In this Special Issue, we intend to collect novel findings elucidating the holistic mechanisms/pathways associated with signaling molecule-mediated plant–microbiome interactions for enhancing plant resilience to environmental stresses. The current Special Issue invites new findings in the following specific areas:

  1. Molecular mechanisms of signaling molecules in plant–microbe interactions.
  2. The role of the plant microbiome in the regulation of plant growth and development.
  3. Signaling molecules and their roles in microbe-mediated nutrient acquisition under stressful conditions.
  4. Crosstalk among signaling molecules in plant adaptation to environmental stresses.
  5. Integrated metabolomics, hormonomics, proteomics, and transcriptomics approaches to evaluate plant–microbe interactions for plant stress tolerance.
  6. Host-mediated microbial recruitment associated with abiotic stress resilience in plants.
  7. Genetic studies involving loss-of-function and gain-of-function for elucidating signaling molecules and pathways involved in symbiotic associations.
  8. The role of phytohormones in shaping microbiome for the improvement of plant stress tolerance.
  9. Identification of novel signaling molecules establishing plant–microbe interactions in a changing climate.
  10. Advances in biotechnological applications to improve plant–microbe symbiosis for sustainable agriculture.

We welcome the submission of research and review papers that will contribute to our understanding of this fascinating topic of plant–microbe interactions and aid in the development of plants that are more adaptable to changing environmental conditions. Authors are encouraged to consult with Guest Editors before submitting their manuscript(s) by sending an outline with the authors’ list.

Dr. Ahmad Humayun Kabir
Guest Editor

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Keywords

  • plant stress tolerance
  • plant-microbe interactions
  • abiotic and biotic stress
  • signaling molecules

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Published Papers (5 papers)

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Research

14 pages, 807 KB  
Article
Role of Stress Response Genes in Resistance and Germination of Bacillus subtilis Spores
by Paula Gómara, Emma Pinilla, Jorge Bellón and Elisa Gayán
Microorganisms 2026, 14(4), 805; https://doi.org/10.3390/microorganisms14040805 - 1 Apr 2026
Viewed by 505
Abstract
Bacterial adaptation to hostile environments depends on the coordinated expression of stress response genes. When adverse conditions persist and nutrients become limiting, sporulating species may initiate sporulation as a last-resort survival strategy. However, sporulation under such conditions may alter the resistance and germination [...] Read more.
Bacterial adaptation to hostile environments depends on the coordinated expression of stress response genes. When adverse conditions persist and nutrients become limiting, sporulating species may initiate sporulation as a last-resort survival strategy. However, sporulation under such conditions may alter the resistance and germination properties of the resulting spores. In this study, we investigated whether stress response regulators that facilitate vegetative cell adaptation to temperature and/or salinity changes during growth can influence the properties of Bacillus subtilis 168 spores. To this end, we examined the resistance and germination of mutant spores lacking key regulators of stress response pathways (SigB, SigW, SigX, Fur, HrcA, CtsR, and CssRS regulon), all produced under optimal sporulation conditions. The constitutive activation of the SigB-mediated general stress response, achieved through the deletion of its negative regulator RsbX, reduced spore heat resistance by 2.2-fold compared to the parental strain, while no effect was observed in vegetative cells. Additionally, ΔrsbX spores displayed both impaired nutrient-induced and CaDPA-induced germination. Collectively, these findings suggest that stress response regulators can influence spore behavior, although their effects may differ from those observed in vegetative cells. Full article
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27 pages, 5713 KB  
Article
Deciphering Molecular Pathways of Bletilla striata Seeds Symbiotic Germination with Tulasnella sp. bj1
by Yueyu Ye, Yucong Zhao, Ning Wang, Ruonan Tang, Zixin Huang, Shiqing Li, Meiya Li, Chunchun Zhang and Fusheng Jiang
Microorganisms 2026, 14(1), 174; https://doi.org/10.3390/microorganisms14010174 - 13 Jan 2026
Viewed by 723
Abstract
Orchid seed germination requires symbiotic association with mycorrhizal fungi that provide essential nutrients for germination and subsequent growth. Extensive research has elucidated the pivotal role of the mycorrhizal fungus Tulasnella sp. in the modulation of seed germination and growth processes in Bletilla striata [...] Read more.
Orchid seed germination requires symbiotic association with mycorrhizal fungi that provide essential nutrients for germination and subsequent growth. Extensive research has elucidated the pivotal role of the mycorrhizal fungus Tulasnella sp. in the modulation of seed germination and growth processes in Bletilla striata (Thunb.) Reiehb.f. However, the molecular mechanisms underlying this symbiosis remain poorly characterized. Our integrated transcriptomic-metabolomic analysis of symbiotic germination revealed that co-cultivation of Tulasnella sp. bj1 with B. striata seeds significantly downregulates the expression of plant-derived flavonoid biosynthetic genes, with flavonoid degradation potentially alleviating germination and growth inhibition. The bj1 strain modulates indoleacetic acid (IAA) biosynthesis in B. striata by upregulating the expression of plant-derived tryptophan decarboxylase (TDC) in the tryptophan pathway and hydrolytic enzymes (NtAMI) in the indoleacetamide pathway, with elevated IAA potentially contributing to seed germination and growth. Moreover, bj1 suppresses the jasmonic acid (JA) biosynthetic pathway of B. striata by downregulating key plant-derived biosynthetic genes, concurrently promoting the accumulation of 12-hydroxyjasmonic acid—a metabolite associated with plant immune regulation that may favor colonization and symbiotic establishment with B. striata seeds. Additionally, bj1 induces the expression of polysaccharide-degrading enzymes, potentially improving carbon source utilization to support protocorm development. In conclusion, bj1 modulates the immune response of B. striata seeds, facilitating the establishment of a symbiotic relationship. Subsequently, the germination and growth of B. striata seeds are enhanced through reduced flavonoid accumulation, increased IAA synthesis, and improved carbon source utilization. Consequently, this investigation provides a crucial foundation for elucidating mechanisms governing symbiotic germination in B. striata. Full article
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16 pages, 1339 KB  
Article
Cyclic di-GMP Modulation of Quorum Sensing and Its Impact on Type VI Secretion System Function in Sinorhizobium fredii
by Juan Aranda-Pérez, María del Carmen Sánchez-Aguilar, Ana María Cutiño-Gobea, Francisco Pérez-Montaño and Carlos Medina
Microorganisms 2025, 13(10), 2232; https://doi.org/10.3390/microorganisms13102232 - 24 Sep 2025
Cited by 2 | Viewed by 1459
Abstract
Effective rhizobium–legume symbiosis depends on multiple molecular signaling pathways, integrating not only classical nodulation factors and surface polysaccharides but also diverse protein secretion systems. Among them, the Type VI Secretion System (T6SS) has emerged as a key player, due to its dual roles [...] Read more.
Effective rhizobium–legume symbiosis depends on multiple molecular signaling pathways, integrating not only classical nodulation factors and surface polysaccharides but also diverse protein secretion systems. Among them, the Type VI Secretion System (T6SS) has emerged as a key player, due to its dual roles in interbacterial competition and interactions with eukaryotic hosts, though its contribution to symbiosis remains unclear. Key regulatory messengers, including the main autoinducer of the quorum sensing (QS) systems, the N-acyl homoserine lactones (AHLs), and the second messenger cyclic di-GMP (c-di-GMP), modulate the transition between motility and biofilm formation, especially in the context of bacteria interacting with eukaryotes, including rhizobia. While c-di-GMP’s impact on exopolysaccharide production in these organisms is well established, its influence on protein secretion systems, particularly in conjunction with QS, is largely unexplored. To contribute to the study of such interplay, we artificially increased intracellular c-di-GMP levels by overexpressing a heterologous diguanylate cyclase in three Sinorhizobium fredii strains of agronomic relevance. This engineering revealed strain-specific outcomes, since elevated c-di-GMP enhanced biofilm development in two strains, but reduced it in another. Furthermore, using β-galactosidase expression assays, we confirmed that both high c-di-GMP and/or AHL concentrations contribute to the transcriptional activation of T6SS. These results demonstrate a direct regulatory link between c-di-GMP, QS signals, and T6SS expression, shedding light on the multilayered control mechanisms that structure beneficial rhizobia–plant interactions. Full article
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20 pages, 4894 KB  
Article
Transcriptome Analysis of Chenopodium album in Response to Infection by Botrytis Strain HZ-011
by Haixia Zhu, Le Zhang, Yongqiang Ma and Lu Hou
Microorganisms 2025, 13(9), 2177; https://doi.org/10.3390/microorganisms13092177 - 18 Sep 2025
Viewed by 801
Abstract
This study conducted a transcriptome sequencing analysis of the interaction between Chenopodium album and Botrytis strain HZ-011 to identify genes involved in the response to fungal infections and elucidate the molecular mechanisms underlying the interaction. High-throughput RNA-seq technology was employed to analyze the [...] Read more.
This study conducted a transcriptome sequencing analysis of the interaction between Chenopodium album and Botrytis strain HZ-011 to identify genes involved in the response to fungal infections and elucidate the molecular mechanisms underlying the interaction. High-throughput RNA-seq technology was employed to analyze the transcriptomes of C. album leaves at 1, 4, and 5 days post-inoculation (dpi) with Botrytis strain HZ-011. The results revealed 11,645 differentially expressed genes (DEGs) at 1 dpi, including 7399 upregulated and 4246 downregulated genes; 11,285 DEGs at 4 dpi (7801 upregulated and 3484 downregulated); and 9976 DEGs at 5 dpi (7723 upregulated and 2253 downregulated). GO functional analysis indicated that downregulated DEGs were significantly enriched in chloroplast and plastid functional expression at 1, 4, and 5 dpi. Following infection by Botrytis strain HZ-011, downregulated genes were significantly enriched in pathways related to photosynthesis, including photosynthetic pathways, light-harvesting antenna proteins, and carotenoid biosynthesis. This suggests that the photosynthetic process in C. album was markedly inhibited, disrupting nutrient supply and leading to herbicidal effects. Notably, genes such as PSB28, PSBP, CAP10A, and CRTL-E-1 were significantly enriched in these pathways, indicating their potential roles in the herbicidal mechanism. These findings provide a foundation for understanding the herbicidal activity of strain HZ-011 and identifying potential targets for developing novel microbial herbicides. Full article
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18 pages, 11436 KB  
Article
Interaction of Potato Autophagy-Related StATG8 Family Proteins with Pathogen Effector and WRKY Transcription Factor in the Nucleus
by Sung Un Huh
Microorganisms 2025, 13(7), 1589; https://doi.org/10.3390/microorganisms13071589 - 5 Jul 2025
Cited by 2 | Viewed by 1202
Abstract
Autophagy is an essential eukaryotic catabolic process through which damaged or superfluous cellular components are degraded and recycled via the formation of double-membrane autophagosomes. In plants, autophagy-related genes (ATGs) are primarily expressed in the cytoplasm and are responsible for orchestrating distinct stages of [...] Read more.
Autophagy is an essential eukaryotic catabolic process through which damaged or superfluous cellular components are degraded and recycled via the formation of double-membrane autophagosomes. In plants, autophagy-related genes (ATGs) are primarily expressed in the cytoplasm and are responsible for orchestrating distinct stages of autophagosome biogenesis. Among these, ATG8 proteins, orthologous to the mammalian LC3 family, are conserved ubiquitin-like modifiers that serve as central hubs in selective autophagy regulation. Although ATG8 proteins are localized in both the cytoplasm and nucleus, their functions within the nucleus remain largely undefined. In the present study, the ATG8-interacting motif (AIM) was identified and functionally characterized in the potato ATG8 homolog (StATG8), demonstrating its capacity for selective target recognition. StATG8 was shown to form both homodimeric and heterodimeric complexes with other ATG8 isoforms, implying a broader regulatory potential within the ATG8 family. Notably, StATG8 was found to interact with the Ralstonia solanacearum type III effector PopP2, a nuclear-localized acetyltransferase, suggesting a possible role in effector recognition within the nucleus. In addition, interactions between StATG8 and transcription factors AtWRKY40 and AtWRKY60 were detected in both cytoplasmic autophagosomes and the nuclear compartment. These observations provide novel insights into the noncanonical, nucleus-associated roles of plant ATG8 proteins. The nuclear interactions with pathogen effectors and transcriptional regulators suggest that ATG8 may function beyond autophagic degradation, contributing to the regulation of nuclear signaling and plant immunity. These findings offer a foundational basis for further investigation into the functional diversification of ATG8 in plant cellular compartments. Full article
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