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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. [ABSTRACT FROM AUTHOR]

The complex interplay among plants, microbes, and the environment strongly affects productivity of vegetation ecosystems; however, determining causal relationships among various factors in these systems remains challenging. To address this issue, this study aimed to evaluate the potential of a data analytical framework called empirical dynamic modeling, which identifies causal links and directions solely from time series data. By cultivating duckweed, a promising aquatic plant for biomass production and wastewater treatment, we obtained a 63-day time series data of plant productivity, microbial community structure, wastewater treatment performance, and environmental factors. We confirmed that empirical dynamic modeling can identify the correct causal directions among temperature, light intensity and plant growth, solely from time series data. Extending the analysis to microbial community data suggested that the bacterial family Comamonadaceae positively affects host duckweed growth and nitrogen removal. Additionally, the predicted abundance of bacterial genes relevant to xenobiotics biodegradation was shown to have a positive effect on organic pollutant removal, supporting the significant role of bacterial metabolism in phytoremediation performance. These results demonstrate the effectiveness of empirical dynamic modeling in uncovering causal relationships within vegetation ecosystems, which are difficult to examine comprehensively through conventional experiment-based approaches., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Hidehiro Ishizawa reports financial support was provided by Japan Society for the Promotion of Science. Hidehiro Ishizawa reports financial support was provided by Kurita Water and Environment Foundation. Michihiko Ike reports financial support was provided by Science and Technology Research Partnership for Sustainable Development. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Programmed cell death occurring during plant development (dPCD) is a fundamental process integral for plant growth and reproduction. Here, we investigate the connection between developmentally controlled PCD and fungal accommodation in Arabidopsis thaliana roots, focusing on the root cap-specific transcription factor ANAC033/SOMBRERO (SMB) and the senescence-associated nuclease BFN1. Mutations of both dPCD regulators increase colonization by the beneficial fungus Serendipita indica , primarily in the differentiation zone. smb-3 mutants additionally exhibit hypercolonization around the meristematic zone and a delay of S. indica -induced root-growth promotion. This demonstrates that root cap dPCD and rapid post-mortem clearance of cellular corpses represent a physical defense mechanism restricting microbial invasion of the root. Additionally, reporter lines and transcriptional analysis revealed that BFN1 expression is downregulated during S. indica colonization in mature root epidermal cells, suggesting a transcriptional control mechanism that facilitates the accommodation of beneficial microbes in the roots., Competing Interests: NC, EL, CD, DV, MN, AZ No competing interests declared, (© 2024, Charura, Llamas et al.)

Heterotrophic microbes rely on host-derived carbon sources for their growth and survival. Depriving pathogens of plant carbon is therefore a promising strategy for protecting plants from disease and reducing yield losses. Importantly, this carbon starvation-mediated resistance is expected to be more broad-spectrum and durable than race-specific R-gene-mediated resistance. Although sugars are well characterized as major carbon sources for bacteria, emerging evidence suggests that plant-derived lipids are likely to be an essential carbon source for some fungal microbes, particularly biotrophs. Here, we comprehensively discuss the dual roles of carbon sources (mainly sugars and lipids) and their transport processes in immune signalling and microbial nutrition. We summarize recent findings revealing the crucial roles of lipids as susceptibility factors at all stages of pathogen infection. In particular, we discuss the potential pathways by which lipids and other plant carbon sources are delivered to biotrophs, including protein-mediated transport, vesicle trafficking and autophagy. Finally, we highlight knowledge gaps and offer suggestions for clarifying the mechanisms that underlie nutrient uptake by biotrophs, providing guidance for future research on the application of carbon starvation-mediated resistance., (© 2024 The Author(s). Plant, Cell & Environment published by John Wiley & Sons Ltd.)

In this study, we investigated the effects of wheat root exudates on soil bacterial communities in the watermelon rhizosphere using quantitative PCR and Illumina MiSeq sequencing. The qPCR results showed that wheat root exudates significantly increased the abundance of total bacteria, Pseudomonas, Bacillus and Streptomyces spp. Illumina MiSeq sequencing results showed that wheat root exudates significantly changed the bacterial community structure and composition. These results indicated that plant root exudates play a role in plant-to-plant signalling, strongly affect the microbial community composition.

IntroductionDrought has become more prevalent due to dramatic climate change worldwide. Consequently, the most compatible fungal communities collaborate to boost plant development and ecophysiological responses under environmental constraints. However, little is known about the specific interactions between non-host plants and endophytic fungal symbionts that produce growth-promoting and stress-alleviating hormones during water deficits.MethodsThe current research was rationalized and aimed at exploring the influence of the newly isolated, drought-resistant, ACC deaminase enzyme-producing endophytic fungi Trichoderma gamsii (TP), Fusarium proliferatum (TR), and its consortium (TP+TR) from a xerophytic plant Carthamus oxycantha L. on Moringa oleifera L. grown under water deficit induced by PEG-8000 (8% osmoticum solution).ResultsThe current findings revealed that the co-inoculation promoted a significant enhancement in growth traits such as dry weight (217%), fresh weight (123%), root length (65%), shoot length (53%), carotenoids (87%), and chlorophyll content (76%) in comparison to control plants under water deficit. Total soluble sugars (0.56%), proteins (132%), lipids (43%), flavonoids (52%), phenols (34%), proline (55%), GA3 (86%), IAA (35%), AsA (170%), SA (87%), were also induced, while H2O2 (-45%), ABA (-60%) and ACC level (-77%) was decreased by co-inoculation of TP and TR in M. oleifera plants, compared with the non-inoculated plants under water deficit. The co-inoculum (TP+TR) also induced the antioxidant potential and enzyme activities POX (325%), CAT activity (166%), and AsA (21%), along with a lesser decrease (-2%) in water potential in M. oleifera plants with co-inoculation under water deficit compared with non-inoculated control. The molecular analysis for gene expression unraveled the reduced expression of ethylene biosynthesis and signaling-related genes up to an optimal level, with an induction of antioxidant enzymatic genes by endophytic co-inoculation in M. oleifera plants under water deficit, suggesting their role in drought stress tolerance as an essential regulatory function.ConclusionThe finding may alert scientists to consider the impacts of optimal reduction of ethylene and induction of antioxidant potential on drought stress tolerance in M. oleifera. Hence, the present study supports the use of compatible endophytic fungi to build a bipartite mutualistic symbiosis in M. oleifera non-host plants to mitigate the negative impacts of water scarcity in arid regions throughout the world.

In this work we compiled information on current and emerging microbial-based fertilization practices, especially the use of cell-free microbial culture filtrates (CFs), to promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identified limitations to bring microbial CFs to the market as biostimulants. In nature, plants act as metaorganisms, hosting microorganisms that communicate with the plants by exchanging semiochemicals through the phytosphere. Such symbiotic interactions are of high importance not only for plant yield and quality, but also for functioning of the soil microbiota. One environmentally sustainable practice to increasing crop productivity and/or protecting plants from (a)biotic stresses while reducing the excessive and inappropriate application of agrochemicals is based on the use of inoculants of beneficial microorganisms. However, this technology has a number of limitations, including inconsistencies in the field, specific growth requirements and host compatibility. Beneficial microorganisms release diffusible substances that promote plant growth and enhance yield and stress tolerance. Recently, evidence has been provided that this capacity also extends to phytopathogens. Consistently, soil application of microbial cell-free culture filtrates (CFs) has been found to promote growth and enhance the yield of horticultural crops. Recent studies have shown that the response of plants to soil application of microbial CFs is associated with strong proliferation of the resident beneficial soil microbiota. Therefore, the use of microbial CFs to enhance both crop yield and stress tolerance, and to activate beneficial soil microbiota could be a safe, efficient and environmentally friendly approach to minimize shortfalls related to the technology of microbial inoculation. In this review, we compile information on microbial CFs and the main constituents (especially volatile compounds) that promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identify challenges and limitations for their use as biostimulants to bring them to the market and we propose remedial actions and give suggestions for future work.

This research focused on cadmium (Cd), which negatively affects plant growth and auxin hemostasis. In plants, many processes are indirectly controlled through the expression of certain genes due to the secretion of bacterial auxin, as indole-3-acetic acid (IAA) acts as a reciprocal signaling molecule in plant–microbe interaction. The aim of current studies was to investigate responsible genes in rice for plant–microbe interaction and lateral root development due to the involvement of several metabolic pathways. Studies revealed that GH3-2 interacts with endogenous IAA in a homeostasis manner without directly providing IAA. In rice, indole-3-pyruvate decarboxylase (IPDC) transgenic lines showed a 40% increase in lateral roots. Auxin levels and YUCCA (auxin biosynthesis gene) expression were monitored in osaux1 mutant lines inoculated with Bacillus cereus exposed to Cd. The results showed an increase in root hairs (RHs) and lateral root density, changes in auxin levels, and expression of the YUCCA gene. B. cereus normalizes the oxidative stress caused by Cd due to the accumulation of O2− and H2O2 in osaux1 mutant lines. Furthermore, the inoculation of B. cereus increases DR5:GUS expression, indicating that bacterial species have a positive role in auxin regulation. Thus, the current study suggests that B. cereus and IPDC transgenic lines increase the RH development in rice by interacting with IAA synthetase genes in the host plant, alleviating Cd toxicity and enhancing plant defense mechanisms.

The microbiome of soil has a fundamental role in maintaining the health of soil and plants. While the diversity of microbes is one of the most important factors in the environment, little is known about the effects of elevation on the microbiome and the impact of the affected microbiome on plants. The main goal of this study is to expand our knowledge of what happens to the soil bacterial community along an altitudinal gradient and investigate their possibly different impacts on plant growth. Bacteria from soils at various altitudes have been isolated, characterized, and identified by Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) to determine the effects of an elevational gradient on the microbiome and plant growth. Furthermore, their effects have been investigated by isolates assessment on maize, wheat, and canola. Based on our results, higher altitude results in a higher diversity of the microbiome and lower bacteria biomass. Bacillus cereus is found in abundance in arid and semi-arid samples. Interestingly, enhanced diversity in higher altitudes shows similarity in response to environmental stress and tolerates these factors well. Furthermore, the inoculation of these bacteria could enhance the overall growth of plants. We prove that bacterial communities could change their biomass and diversity in response to altitude changes. These indicate evolutionary pressure as these bacteria could tolerate stress factors well and have a better relationship with plants.

Ensuring food and nutritional security, it is crucial to use chemicals in agriculture to boost yields and protect the crops against biotic and abiotic perturbations. Conversely, excessive use of chemicals has led to many deleterious effects on the environment like pollution of soil, water, and air; loss of soil fertility; and development of pest resistance, and is now posing serious threats to biodiversity. Therefore, farming systems need to be upgraded towards the use of biological agents to retain agricultural and environmental sustainability. Plants exhibit a huge and varied niche for endophytic microorganisms inside the planta, resulting in a closer association between them. Endophytic microorganisms play pivotal roles in plant physiological and morphological characteristics, including growth promotion, survival, and fitness. Their mechanism of action includes both direct and indirect, such as mineral phosphate solubilization, fixating nitrogen, synthesis of auxins, production of siderophore, and various phytohormones. Medicinal and aromatic plants (MAPs) hold a crucial position worldwide for their valued essential oils and several phytopharmaceutically important bioactive compounds since ancient times; conversely, owing to the high demand for natural products, commercial cultivation of MAPs is on the upswing. Furthermore, the vulnerability to various pests and diseases enforces noteworthy production restraints that affect both crop yield and quality. Efforts have been made towards enhancing yields of plant crude drugs by improving crop varieties, cell cultures, transgenic plants, etc., but these are highly cost-demanding and time-consuming measures. Thus, it is essential to evolve efficient, eco-friendly, cost-effective simpler approaches for improvement in the yield and health of the plants. Harnessing endophytic microorganisms as biostimulants can be an effective and alternative step. This review summarizes the concept of endophytes, their multidimensional interaction inside the host plant, and the salient benefits associated with endophytic microorganisms in MAPs. [ABSTRACT FROM AUTHOR]

Plant roots are colonized by a multitude of microbial taxa that dynamically influence plant health. Plant-microbe interactions at the root-soil interface occur at the micro-scale and are affected by variation in root phenotypes. Different root phenotypes can have distinct impacts on physical and chemical gradients at the root-soil interface, leading to heterogeneous microhabitats for microbial colonization. Microbes that influence plant physiology will establish across these heterogeneous microhabitats, and, therefore, exploiting variation in root phenotypes can allow for targeted manipulation of plant-associated microbes. In this mini-review, we discuss how changes in root anatomy and architecture can influence resource availability and the spatial configuration of microbial microhabitats. We then propose research priorities that integrate root phenotypes and microbial microhabitats for advancing the manipulation of root-associated microbiomes. We foresee the yet-unexplored potential to harness diverse root phenotypes as a new level of precision in microbiome management in plant-root systems. [ABSTRACT FROM AUTHOR]

Plants must balance both beneficial (symbiotic) and pathogenic challenges from microorganisms, the former benefitting the plant and agriculture and the latter causing disease and economic harm. Plant innate immunity describes a highly conserved set of defense mechanisms that play pivotal roles in sensing immunogenic signals associated with both symbiotic and pathogenic microbes and subsequent downstream activation of signaling effector networks that protect the plant. An intriguing question is how the innate immune system distinguishes "friends" from "foes". Here, we summarize recent advances in our understanding of the role and spectrum of innate immunity in recognizing and responding to different microbes. In addition, we also review some of the strategies used by microbes to manipulate plant signaling pathways and thus evade immunity, with emphasis on the use of effector proteins and micro-RNAs (miRNAs). Furthermore, we discuss potential questions that need addressing to advance the field of plant–microbe interactions. [ABSTRACT FROM AUTHOR]

Entomopathogenic fungi (EF) provide a potent biocontrol tool; also, their endophytic behavior has broadened their contribution to integrated pest management (IPM) and crop production. In this work, Beauveria bassiana and Metarhizium brunneum were applied to bread wheat (Triticum aestivum) seedlings to elucidate how fungal colonization influences plant growth and the relative expression of 24 genes involved in hormonal syntheses and plant immune mechanisms. A preliminary assay was used to determine the time needed for fungal colonization and assess its effect on wheat growth. Then, plant material collected at various times after inoculation (viz., 2, 8, 20, and 36 h and 9 and 15 days) was used to investigate gene expression by quantitative reverse transcription PCR (RT-qPCR). During the colonization time, B. bassiana and M. brunneum caused strong downregulation of most genes associated with plant immunity and the synthesis of hormones like auxin, cytokinin, and gibberellin. This effect was concomitant with a slowdown of endophytic-colonization-related plant growth until 19 days postinoculation (dpi). However, the wheat started to recover at 15 dpi, simultaneously with upregulation of auxin- and gibberellin-related genes. The results suggest that the EF trigger induced systemic resistance rather than acquired systemic resistance during early plant-microbe cross talk in wheat. Also, they confirm that the hormone and immune responses of wheat triggered by EF inoculation influenced plant growth, which can be useful with a view to optimizing management of these microorganisms for sustainable agriculture. [ABSTRACT FROM AUTHOR]

Major crops such as corn, wheat, and rice can benefit from interactions with various plant growth-promoting bacteria (PGPB). Naturally, several studies have investigated the primary mechanisms by which these PGPB promote plant growth. These mechanisms involve biological nitrogen fixation, phytohormone synthesis, protection against biotic and abiotic stresses, etc. Decades of genetic and biochemical studies in the legume-rhizobia symbiosis and arbuscular mycorrhizal symbiosis have identified a few key plant and microbial signals regulating these symbioses. Furthermore, genetic studies in legumes have identified the host genetic pathways controlling these symbioses. But, the same depth of information does not exist for the interactions between host plants and PGPB. For instance, our knowledge of the host genes and the pathways involved in these interactions is very poor. However, some transcriptomic studies have investigated the regulation of gene expression in host plants during these interactions in recent years. In this review, we discuss some of the major findings from these studies and discuss what lies ahead. Identifying the genetic pathway(s) regulating these plant-PGPB interactions will be important as we explore ways to improve crop production sustainably. [ABSTRACT FROM AUTHOR]

Change in global climate has started to show its effect in the form of extremes of temperatures and water scarcity which is bound to impact adversely the global food security in near future. In the current review we discuss the impact of drought on plants and highlight the ability of endophytes, microbes that inhabit the plants asymptomatically, to confer stress tolerance to their host. For this we first describe the symbiotic association between plant and the endophytes and then focus on the molecular and physiological strategies/mechanisms adopted by these endophytes to confer stress tolerance. These include root alteration, osmotic adjustment, ROS scavenging, detoxification, production of phytohormones, and promoting plant growth under adverse conditions. The review further elaborates on how omics-based techniques have advanced our understanding of molecular basis of endophyte mediated drought tolerance of host plant. Detailed analysis of whole genome sequences of endophytes followed by comparative genomics facilitates in identification of genes involved in endophyte-host interaction while functional genomics further unveils the microbial targets that can be exploited for enhancing the stress tolerance of the host. Thus, an amalgamation of endophytes with other sustainable agricultural practices seems to be an appeasing approach to produce climate-resilient crops. [ABSTRACT FROM AUTHOR]

Although it is becoming widely appreciated that microbes can enhance plant tolerance to environmental stress, the nature of microbial mediation of exposure responses is not well understood. We addressed this deficit by examining whether microbial mediation of plant responses to elevated salinity is contingent on the environment and factors intrinsic to the host. We evaluated the influence of contrasting environmental conditions relative to host genotype, provenance and evolution by conducting a common‐garden experiment utilizing ancestral and descendant cohorts of Schoenoplectus americanus genotypes recovered from two 100+ year coastal marsh seed banks. We compared S. americanus productivity and trait variation as well as associated endophytic microbial communities according to plant genotype, provenance, and age cohort under high and low salinity stress with and without native soil inoculation. The magnitude and direction of microbial mediation of S. americanus responses to elevated salinity varied according to individual genotype, provenance, as well as temporal shifts in genotypic variation and G × E (gene by environment) interactions. Relationships differed between plant traits and the structure of endosphere communities. Our findings indicate that plant‐microbe associations and microbial mediation of plant stress are not only context‐dependent but also dynamic. Our results additionally suggest that evolution can shape the fate of marsh ecosystems by altering how microbes confer plant tolerance to pressures linked to global change. [ABSTRACT FROM AUTHOR]

Abiotic stresses are the most significant factors reducing agricultural productivity. Plants face extreme environmental conditions that may affect their biological mechanisms, thereby influencing their growth and development. Microorganisms possess substantial metabolites that aid in helping plants mitigate abiotic stresses. Plants' interaction with microbes constitutes a diversified ecosystem, as sometimes both the partners share a mutualistic relationship. Endophytes, plant-growth-promoting rhizobacteria (PGPRs), and arbuscular mycorrhizal fungi (AMFs) are examples of microorganisms that play an essential role in alleviating abiotic stresses and, hence, improving plant growth. The plant–microbe interaction leads to the modulation of complex mechanisms in the plant cellular system. Moreover, the residing microbial flora also inhibits the phytopathogens, therefore, it becomes part of plants' innate defense system. Keeping in view the growing environmental concerns, it is important to identify the role of the plant microbiome in the transportation of nutrients to maintain sustainable production. Furthermore, it is important to identify the factors enabling plants to recruit beneficial microbial species and how to deal with the potential pathogens. Therefore, this review aims to summarize the impacts of various abiotic stressors on agricultural productivity and the role of beneficial microorganisms in mitigating the negative effects of abiotic stresses. The literature review also shows that the beneficial microbes, including PGPRs, AMFs, and endophytes, adopt various mechanisms for ameliorating the negative effects of various stresses. It has been observed that biochar and microbes, either individually or in combination, can play a significant role in maintaining plant growth under stress conditions. Although conventional inoculation of beneficial microbes mitigates abiotic stresses and enhances productivity, the advancement in genetic engineering would help transfer specific genes from the microbes to plants to aid in abiotic stress mitigation. [ABSTRACT FROM AUTHOR]

Plants interact with diverse microbial communities and share complex relationships with each other. The intimate association between microbes and their host mutually benefit each other and provide stability against various biotic and abiotic stresses to plants. Endophytes are heterogeneous groups of microbes that live inside the host tissue without showing any apparent sign of infection. However, their functional attributes such as nutrient acquisition, phytohormone modulation, synthesis of bioactive compounds, and antioxidant enzymes of endophytes are similar to the other rhizospheric microorganisms. Nevertheless, their higher colonization efficacy and stability against abiotic stress make them superior to other microorganisms. In recent studies, the potential role of endophytes in bioprospecting has been broadly reported. However, the molecular aspect of host–endophyte interactions is still unclear. In this study, we have briefly discussed the endophyte biology, colonization efficacy and diversity pattern of endophytes. In addition, it also summarizes the molecular aspect of plant–endophyte interaction in biotic stress management. [ABSTRACT FROM AUTHOR]

Drought stress is one of the most severe abiotic stresses affecting soil fertility and plant health, and due to climate change, it is destined to increase even further, becoming a serious threat to crop production. An efficient, eco-friendly alternative is the use of plant growth-promoting bacteria (PGPB), which can promote plant fitness through direct and indirect approaches, protecting plants from biotic and abiotic stresses. The present study aims to identify bacterial consortia to promote Spinacia oleracea L. cv Matador's seed germination and protect its seedlings from drought stress. Eight PGPB strains belonging to the Bacillus, Azotobacter, and Pseudomonas genera, previously characterized in physiological conditions, were analyzed under water-shortage conditions, and a germination bioassay was carried out by biopriming S. oleracea seeds with either individual strains or consortia. The consortia of B. amyloliquefaciens RHF6, B. amyloliquefaciens LMG9814, and B. sp. AGS84 displayed the capacity to positively affect seed germination and seedlings' radical development in both standard and drought conditions, ameliorating the plants' growth rate compared to the untreated ones. These results sustain using PGPB consortia as a valid ameliorating water stress strategy in the agro-industrial field. [ABSTRACT FROM AUTHOR]

Global climate change has imposed harsh environmental conditions such as drought. Naturally, the most compatible fungal consortia operate synergistically to enhance plant growth and ecophysiological responses against abiotic strains. Yet, little is known about the interactions between phytohormone-producing endophytic fungal symbionts and plant growth under drought stress. The existing research was rationalized to recognize the role of newly isolated drought-resistant, antioxidant-rich endophytic fungal consortia hosting a xerophytic plant, Carthamus oxycantha L., inoculated to Moringa oleifera L. grown under drought stress of 8% PEG (polyethylene glycol-8000). Under drought stress, the combined inoculation of endophytic strain Microdochium majus (WA), Meyerozyma guilliermondi (TG), and Aspergillus aculeatus (TL3) exhibited a significant improvement in growth attributes such as shoot fresh weight (1.71-fold), shoot length (0.86-fold), root length (0.65-fold), dry weight (2.18-fold), total chlorophyll (0.46-fold), and carotenoids (0.87-fold) in comparison to control (8% PEG). Primary and secondary metabolites were also increased in M. oleifera inoculated with endophytic consortia, under drought stress, such as proteins (1.3-fold), sugars (0.58-fold), lipids (0.41-fold), phenols (0.36-fold), flavonoids (0.52-fold), proline (0.6-fold), indole acetic acid (IAA) (4.5-fold), gibberellic acid (GA) (0.7-fold), salicylic acid (SA) (0.8-fold), ascorbic acid (ASA) (1.85-fold), while abscisic acid (ABA) level was decreased (−0.61-fold) in comparison to the control (8% PEG). Under drought stress, combined inoculation (WA, TG, TL3) also promoted the antioxidant activities of enzymes such as ascorbate peroxidase (APX) (3.5-fold), catalase (CAT) activity (1.7-fold), and increased the total antioxidant capacity (TAC) (0.78-fold) with reduced reactive oxygen species (ROS) such as H2O2 production (−0.4-fold), compared to control (8% PEG), and stomatal aperture was larger (3.5-fold) with a lesser decrease (−0.02-fold) in water potential. Moreover, combined inoculation (WA, TG, TL3) up regulated the expression of MolHSF3, MolHSF19, and MolAPX genes in M. oleifera under drought stress, compared to the control (8% PEG), is suggestive of an important regulatory role for drought stress tolerance governed by fungal endophytes. The current research supports the exploitation of the compatible endophytic fungi for establishing the tripartite mutualistic symbiosis in M. oleifera to alleviate the adverse effects of drought stress through strong antioxidant activities. [ABSTRACT FROM AUTHOR]

Soil microbial biomass is critical for biogeochemical cycling and serves as precursor for carbon (C) sequestration. The anthropogenic nitrogen (N) input has profoundly changed the pool of soil microbial biomass. However, traditional N deposition simulation experiments have been exclusively conducted through infrequent N addition, which may have caused biased effects on soil microbial biomass compared with those under the natural and continuous N deposition. Convincing data are still scarce about how the different N addition frequencies affect soil microbial biomass. By independently manipulating the frequencies (2 times vs. 12 times N addition yr–1) and the rates (0–50 g N m−2 yr−1) of N addition, our study aimed to examine the response of soil microbial biomass C (MBC) to different N addition frequencies with increasing N addition rates. Soil MBC gradually decreased with increasing N addition rates under both N addition frequencies, while the soil MBC decreased more at low frequency of N addition, suggesting that traditional studies have possibly overestimated the effects of N deposition on soil microbial biomass. The greater soil microbial biomass loss with low N frequency resulted from the intensified soil acidification, higher soil inorganic N, stronger soil C and N imbalance, less net primary production allocated to belowground and lower fungi to bacteria ratio. To reliably predict the effects of atmospheric N deposition on soil microbial functioning and C cycling of grassland ecosystems in future studies, it is necessary to employ both the dosage and the frequency of N addition. [ABSTRACT FROM AUTHOR]

In the United Arab Emirates (UAE), sudden decline syndrome (SDS) is one of the major fungal diseases caused by Fusarium solani affecting date palm plantations. To minimize the impact of the causal agent of SDS on date palm, native actinobacterial strains isolated from rhizosphere soils of healthy date palm plants were characterized according to their antifungal activities against F. solani DSM 106836 (Fs). Based on their in vitro abilities, two promising biocontrol agents (BCAs), namely Streptomyces tendae UAE1 (St) and Streptomyces violaceoruber UAE1 (Sv), were selected for the production of antifungal compounds and cell wall degrading enzymes (CWDEs), albeit their variations in synthesizing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD). Although both isolates showed antagonism when applied 7 days before the pathogen in the greenhouse experiments, the ACCDproducing Sv was relatively superior in its efficacy against SDS over the non-ACCD-producing St. This was evident from the symptoms of SDS in diseased date palm seedlings which were greatly reduced by Sv compared to St. On a scale of 5.0, the estimated disease severity indices in Fs-diseased seedlings were significantly (P < 0.05) reduced from 4.8 to 1.5 and 0.5 by St and Sv, respectively. Thus, the number of conidia of Fs recovered from plants pre-treated with both BCAs was comparable, but significantly (P < 0.05) reduced compared to plants without any BCA treatment. In addition, a significant (P < 0.05) decrease in ACC levels of both the root and shoot tissues was detected in Sv + Fs seedlings to almost similar levels of healthy seedlings. However, in planta ACC levels highly increased in seedlings grown in soils infested with the pathogen alone or amended with St prior to F. solani infestation (St + Fs). This suggests a major role of ACCD production in relieving the stress of date palm seedlings infected with F. solani, thus supporting the integrated preventive disease management programs against this pathogen. This is the first report of effective rhizosphere actinobacterial BCAs to provide protection against SDS on date palm, and to help increase agricultural productivity in a more sustainable manner in the UAE and the other arid regions. [ABSTRACT FROM AUTHOR]

Arsenic (As) is a toxic metalloid that is present in natural surroundings in many forms with severe consequences to sustainable agriculture and human health. Plant growth-promoting Rhizobia have been found involved in the induction of plant tolerance under various biotic and abiotic stresses. An endofungal Rhizobium species associated with arbuscular mycorrhizal fungi (AMF) Serendipita indica deploy beneficial role in the promotion of plant growth and tolerance against various biotic and abiotic stresses. In the current study, we have determined the role of endofungal Rhizobium species in protection of host plant growth under As stress. We observed that endofungal Rhizobium species strain Si001 tolerate AsV up to 25 mM and its inoculation enhances tomato seed germination and seedling growth. A hyper-colonization of Rhizobium species Si001 in tomato roots was observed under As stress and results in modulation of GSH and proline content with reduced ROS. Rhizobium species Si001 colonization in host plant recovered pigment contents (chlorophyll-a and chlorophyll-b up to 189.5% and 192%, respectively), photosynthesis (157%), and water use efficiency (166%) compared to As-treated plants. Interestingly, bacterial colonization results in 40% increased As accumulation in the root, while a reduction in As translocation from root to shoot up to 89% was observed as compared to As treated plants. In conclusion, endofungal Rhizobium species Si001 association with the host plant may improve plant health and tolerance against As stress with reduced As accumulation in the crop produce. [ABSTRACT FROM AUTHOR]

European grapevine is a complex holobiont composed of two plant genomes, that of the scion (Vitis vinifera L.) and the rootstock (Vitis spp.), and a multitude of microbial genomes that collectively form the microbiome. The grapevine microbiome has been extensively described over the last decade, primarily using metabarcoding approaches. Unfortunately, metabarcoding data alone provide little information on microbial functions and outcomes of plant-microbe interactions. Here we review knowledge about the microorganisms that have a demonstrated influence, positive or negative, on the performance of the grapevine holobiont. Our review encompasses bacteria, filamentous fungi, yeasts, oomycetes and viruses. It covers aboveground and belowground microorganisms, including arbuscular mycorrhizal and ectomycorrhizal fungi. We focus on taxa and functions that protect the plant against pathogens and pests, promote growth, increase tolerance to abiotic stresses and highlight those involved in disease and decline. As the outcomes of plant-microbe interactions are labile, we examine the dynamics and functions of grapevine-microbiome interactions over both the plant lifetime and the plant evolutionary history, beginning with plant domestication. Based on the knowledge and gaps we identify, we suggest field sampling designs, culture-based experiments, molecular tools and theoretical analysis methods, including shotgun metagenomics and network models, that could be used in future research to uncover and leverage the full functional potential of the grapevine microbiome. [ABSTRACT FROM AUTHOR]

Single or combined plant growth-promoting bacteria (PGPB) strains were widely applied as microbial agents in cadmium (Cd) phytoextraction since they could promote plant growth and facilitate Cd uptake. However, the distinct functional effects between single and combined inoculants have not yet been elucidated. In this study, a field experiment was conducted with single, double and triple inoculants to clarify their divergent impacts on plant growth, Cd uptake and accumulation at different growth stages of Brassica juncea L. by three different PGPB strains (Cupriavidus SaCR1, Burkholdria SaMR10 and Sphingomonas SaMR12). The results show that SaCR1 + SaMR10 + SaMR12 combined inoculants were more effective for growth promotion at the bud stage, flowering stage, and mature stage. Single/combined PGPB agents of SaMR12 and SaMR10 were more efficient for Cd uptake promotion. In addition, SaMR10 + SaMR12 combined the inoculants greatly facilitated Cd uptake and accumulation in shoots, and enhanced the straw Cd extraction rates by 156%. Therefore, it is concluded that the application of PGPB inoculants elevated Cd phytoextraction efficiency, and the combined inoculants were more conductive than single inoculants. These results enriched the existing understanding of PGPB agents and provided technical support for the further exploration of PGPB interacting mechanisms strains on plant growth and Cd phytoextraction, which helped establish an efficient plant–microbe combined phytoremediation system and augment the phytoextraction efficiency in Cd-contaminated farmlands. [ABSTRACT FROM AUTHOR]

Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants. [ABSTRACT FROM AUTHOR]

Ensuring food and nutritional security, it is crucial to use chemicals in agriculture to boost yields and protect the crops against biotic and abiotic perturbations. Conversely, excessive use of chemicals has led to many deleterious effects on the environment like pollution of soil, water, and air; loss of soil fertility; and development of pest resistance, and is now posing serious threats to biodiversity. Therefore, farming systems need to be upgraded towards the use of biological agents to retain agricultural and environmental sustainability. Plants exhibit a huge and varied niche for endophytic microorganisms inside the planta, resulting in a closer association between them. Endophytic microorganisms play pivotal roles in plant physiological and morphological characteristics, including growth promotion, survival, and fitness. Their mechanism of action includes both direct and indirect, such as mineral phosphate solubilization, fixating nitrogen, synthesis of auxins, production of siderophore, and various phytohormones. Medicinal and aromatic plants (MAPs) hold a crucial position worldwide for their valued essential oils and several phytopharmaceutically important bioactive compounds since ancient times; conversely, owing to the high demand for natural products, commercial cultivation of MAPs is on the upswing. Furthermore, the vulnerability to various pests and diseases enforces noteworthy production restraints that affect both crop yield and quality. Efforts have been made towards enhancing yields of plant crude drugs by improving crop varieties, cell cultures, transgenic plants, etc., but these are highly cost-demanding and time-consuming measures. Thus, it is essential to evolve efficient, eco-friendly, cost-effective simpler approaches for improvement in the yield and health of the plants. Harnessing endophytic microorganisms as biostimulants can be an effective and alternative step. This review summarizes the concept of endophytes, their multidimensional interaction inside the host plant, and the salient benefits associated with endophytic microorganisms in MAPs.

Plant roots are colonized by a multitude of microbial taxa that dynamically influence plant health. Plant-microbe interactions at the root-soil interface occur at the micro-scale and are affected by variation in root phenotypes. Different root phenotypes can have distinct impacts on physical and chemical gradients at the root-soil interface, leading to heterogeneous microhabitats for microbial colonization. Microbes that influence plant physiology will establish across these heterogeneous microhabitats, and, therefore, exploiting variation in root phenotypes can allow for targeted manipulation of plant-associated microbes. In this mini-review, we discuss how changes in root anatomy and architecture can influence resource availability and the spatial configuration of microbial microhabitats. We then propose research priorities that integrate root phenotypes and microbial microhabitats for advancing the manipulation of root-associated microbiomes. We foresee the yet-unexplored potential to harness diverse root phenotypes as a new level of precision in microbiome management in plant-root systems.

Major crops such as corn, wheat, and rice can benefit from interactions with various plant growth-promoting bacteria (PGPB). Naturally, several studies have investigated the primary mechanisms by which these PGPB promote plant growth. These mechanisms involve biological nitrogen fixation, phytohormone synthesis, protection against biotic and abiotic stresses, etc. Decades of genetic and biochemical studies in the legume-rhizobia symbiosis and arbuscular mycorrhizal symbiosis have identified a few key plant and microbial signals regulating these symbioses. Furthermore, genetic studies in legumes have identified the host genetic pathways controlling these symbioses. But, the same depth of information does not exist for the interactions between host plants and PGPB. For instance, our knowledge of the host genes and the pathways involved in these interactions is very poor. However, some transcriptomic studies have investigated the regulation of gene expression in host plants during these interactions in recent years. In this review, we discuss some of the major findings from these studies and discuss what lies ahead. Identifying the genetic pathway(s) regulating these plant-PGPB interactions will be important as we explore ways to improve crop production sustainably.

Change in global climate has started to show its effect in the form of extremes of temperatures and water scarcity which is bound to impact adversely the global food security in near future. In the current review we discuss the impact of drought on plants and highlight the ability of endophytes, microbes that inhabit the plants asymptomatically, to confer stress tolerance to their host. For this we first describe the symbiotic association between plant and the endophytes and then focus on the molecular and physiological strategies/mechanisms adopted by these endophytes to confer stress tolerance. These include root alteration, osmotic adjustment, ROS scavenging, detoxification, production of phytohormones, and promoting plant growth under adverse conditions. The review further elaborates on how omics-based techniques have advanced our understanding of molecular basis of endophyte mediated drought tolerance of host plant. Detailed analysis of whole genome sequences of endophytes followed by comparative genomics facilitates in identification of genes involved in endophyte-host interaction while functional genomics further unveils the microbial targets that can be exploited for enhancing the stress tolerance of the host. Thus, an amalgamation of endophytes with other sustainable agricultural practices seems to be an appeasing approach to produce climate-resilient crops.

ABSTRACT Ralstonia solanacearum, the causative agent of bacterial wilt disease, has been a major threat to tobacco production globally. Several control methods have failed. Thus, it is imperative to find effective management for this disease. The biocontrol agent Bacillus amyloliquefaciens WS-10 displayed a significant control effect due to biofilm formation, and secretion of hydrolytic enzymes and exopolysaccharides. In addition, strain WS-10 can produce antimicrobial compounds, which was confirmed by the presence of genes encoding antimicrobial lipopeptides (fengycin, iturin, surfactin, and bacillomycinD) and polyketides (difficidin, bacilysin, bacillibactin, and bacillaene). Strain WS-10 successfully colonized tobacco plant roots and rhizosphere soil and suppressed the incidence of bacterial wilt disease up to 72.02% by reducing the R. solanacearum population dynamic in rhizosphere soil. Plant-microbe interaction was considered a key driver of disease outcome. To further explore the impact of strain WS-10 on rhizosphere microbial communities, V3-V4 and ITS1 variable regions of 16S and ITS rRNA were amplified, respectively. Results revealed that strain WS-10 influences the rhizosphere microbial communities and dramatically changed the diversity and composition of rhizosphere microbial communities. Interestingly, the relative abundance of genus Ralstonia significantly decreased when treated with strain WS-10. A complex microbial co-occurrence network was present in a diseased state, and the introduction of strain WS-10 significantly changed the structure of rhizosphere microbiota. This study suggests that strain WS-10 can be used as a novel biocontrol agent to attain sustainability in disease management due to its intense antibacterial activity, efficient colonization in the host plant, and ability to transform the microbial community structure toward a healthy state. IMPORTANCE The plant rhizosphere acts as the first line of defense against the invasion of pathogens. The perturbation in the rhizosphere microbiome is directly related to plant health and disease development. The introduction of beneficial microorganisms in the soil shifted the rhizosphere microbiome, induced resistance in plants, and suppressed the incidence of soilborne disease. Bacillus sp. is widely used as a biocontrol agent against soilborne diseases due to its ability to produce broad-spectrum antimicrobial compounds and colonization with the host plant. In our study, we found that the application of native Bacillus amyloliquefaciens WS-10 significantly suppressed the incidence of tobacco bacterial wilt disease by shifting the rhizosphere microbiome and reducing the interaction between rhizosphere microorganisms and bacterial wilt pathogen.

In the United Arab Emirates (UAE), sudden decline syndrome (SDS) is one of the major fungal diseases caused by Fusarium solani affecting date palm plantations. To minimize the impact of the causal agent of SDS on date palm, native actinobacterial strains isolated from rhizosphere soils of healthy date palm plants were characterized according to their antifungal activities against F. solani DSM 106836 (Fs). Based on their in vitro abilities, two promising biocontrol agents (BCAs), namely Streptomyces tendae UAE1 (St) andStreptomyces violaceoruber UAE1 (Sv), were selected for the production of antifungal compounds and cell wall degrading enzymes (CWDEs), albeit their variations in synthesizing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD). Although both isolates showed antagonism when applied 7 days before the pathogen in the greenhouse experiments, the ACCD-producing Sv was relatively superior in its efficacy against SDS over the non-ACCD-producing St. This was evident from the symptoms of SDS in diseased date palm seedlings which were greatly reduced by Sv compared to St. On a scale of 5.0, the estimated disease severity indices in Fs-diseased seedlings were significantly (P < 0.05) reduced from 4.8 to 1.5 and 0.5 by St and Sv, respectively. Thus, the number of conidia of Fs recovered from plants pre-treated with both BCAs was comparable, but significantly (P < 0.05) reduced compared to plants without any BCA treatment. In addition, a significant (P < 0.05) decrease in ACC levels of both the root and shoot tissues was detected inSv + Fs seedlings to almost similar levels of healthy seedlings. However, in planta ACC levels highly increased in seedlings grown in soils infested with the pathogen alone or amended with St prior to F. solani infestation (St + Fs). This suggests a major role of ACCD production in relieving the stress of date palm seedlings infected with F. solani, thus supporting the integrated preventive disease management programs against this pathogen. This is the first report of effective rhizosphere actinobacterial BCAs to provide protection against SDS on date palm, and to help increase agricultural productivity in a more sustainable manner in the UAE and the other arid regions.

The Amazonian rainforest is a hyper-diverse ecosystem in the number of species and the myriad of intertaxon relationships that are mostly understudied. In order to characterize a dominant and economically important Amazonian species, the Brazil nut tree (Bertholletia excelsa Bonpl.), at the genome level, wegenerated high-coverage long-read sequencing data from the leaves of a single individual. The genome assembly revealed an unexpected discovery: two circular contigs that could be assigned to the chromosome and a plasmid of a Pantoea stewartii strain. Comparative genomics revealed that this strain belongs to the indologenes subspecies and displays high synteny with other strains isolated from diseased leaves of the neotropical palm Bactris gasipaes Kunth. Investigation of pathogenicity-related genes revealed the absence of the entire type III secretion system gene cluster in the plasmid, which was otherwise highly similar to a plasmid from an isolate known to cause disease in Dracaena sanderiana Mast. In contrast, several genes associated with plant-growth promoting traits were detected, including genes involved in indole-3-acetic acid (IAA) production, phosphate solubilization, and biosynthesis of siderophores. In summary, we report the genome of an uncultivated P. stewartii subsp. indologenes strain associated with the Brazil nut tree and potentially a plant growth-promoting bacteria.

Combined inoculation of legumes with rhizobia and plant growth-promoting rhizobacteria or endophytes is a known technique for increasing the efficiency of nitrogen-fixing symbiosis and plant productivity. The aim of this work was to expand knowledge about the synergistic effects between commercial rhizobia of pasture legumes and root nodule bacteria of relict legume species. Pot experiments were performed on common vetch (Vicia sativa L.) and red clover (Trifolium pratense L.) co-inoculated with the participation of the corresponding commercial rhizobial strains (R. leguminosarum bv. viciae RCAM0626 and R. leguminosarum bv. trifolii RCAM1365) and seven strains isolated from nodules of relict legumes inhabiting the Baikal Lake region and the Altai Republic: Oxytropis popoviana, Astragalus chorinensis, O. tragacanthoides and Vicia costata. The inoculation of plants with combinations of strains (commercial strain plus the isolate from relict legume) had a different effect on symbiosis depending on the plant species: the increase in the number of nodules was mainly observed on vetch, whereas increased acetylene reduction activity was evident on clover. It was shown that the relict isolates differ significantly in the set of genes related to different genetic systems that affect plant–microbe interactions. At the same time, they had additional genes that are involved in the formation of symbiosis and determine its effectiveness, but are absent in the used commercial strains: symbiotic genes fix, nif, nod, noe and nol, as well as genes associated with the hormonal status of the plant and the processes of symbiogenesis (acdRS, genes for gibberellins and auxins biosynthesis, genes of T3SS, T4SS and T6SS secretion systems). It can be expected that the accumulation of knowledge about microbial synergy on the example of the joint use of commercial and relict rhizobia will allow in the future the development of methods for the targeted selection of co-microsymbionts to increase the efficiency of agricultural legume–rhizobia systems.