Plants

Editorial

3 pages, 207 KiB

Open AccessEditorial

Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications

by Olga A. Aleynova and Konstantin V. Kiselev

Plants 2023, 12(4), 714; https://doi.org/10.3390/plants12040714 - 6 Feb 2023

Cited by 10 | Viewed by 2383

Abstract

Endophytes are microorganisms that live asymptomatically inside plant tissues [...] Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

Research

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12 pages, 2734 KiB

Open AccessArticle

The Diversity of Fungi Involved in Damage to Japanese Quince

by Inta Jakobija, Biruta Bankina, Alise Klūga, Ance Roga, Edmunds Skinderskis and Dāvids Fridmanis

Plants 2022, 11(19), 2572; https://doi.org/10.3390/plants11192572 - 29 Sep 2022

Cited by 2 | Viewed by 1920

Abstract

In recent years, Japanese quince (Chaenomeles japonica) plantations in Latvia have increased. Interest in breeding Japanese quince is also known in other European countries and Russia. The occurrence and harmfulness of fungal diseases have become increasingly significant. However, there is a [...] Read more.

In recent years, Japanese quince (Chaenomeles japonica) plantations in Latvia have increased. Interest in breeding Japanese quince is also known in other European countries and Russia. The occurrence and harmfulness of fungal diseases have become increasingly significant. However, there is a lack of overall information in the literature about the diversity of fungi afflicting C. japonica. In our study, we aimed to determine the diversity of fungi associated with C. japonica in Latvia, with the possibility of identifying the fungi that are most characteristically associated with certain parts of the plant. Our research was conducted from 2017 to 2019 in eight Japanese quince plantations in Latvia. Samples of plant parts with disease symptoms were collected. Pure cultures of fungi were obtained and identified using ITS region sequencing. We determined the relative density of identified genera of fungi, which were grouped using hierarchical cluster analysis depending on the plant part from which they were found. Various disease-like symptoms were observed and described. A total of 538 isolates of fungi were obtained that belong to 36 genera and represent different ecological niches. Fusarium, Alternaria, Botrytis, and Sarocladium were the genera most frequently found during our study. The number of identified cases of fungal genera differed depending on the part of the plant from which the fungi were obtained. However, it is not possible to relate a specific genus of fungus to only one certain part of a plant. Further research is needed to clarify the pathogenicity of detected fungi and the composition of species in the detected genera of fungi. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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17 pages, 1010 KiB

Open AccessArticle

High Temporal Variability in Late Blight Pathogen Diversity, Virulence, and Fungicide Resistance in Potato Breeding Fields: Results from a Long-Term Monitoring Study

by Eve Runno-Paurson, Helina Nassar, Terje Tähtjärv, Viacheslav Eremeev, Merili Hansen and Ülo Niinemets

Plants 2022, 11(18), 2426; https://doi.org/10.3390/plants11182426 - 16 Sep 2022

Cited by 9 | Viewed by 2427

Abstract

Long-term site-specific studies describing changes in the phenotypic variability of Phytophthora infestans populations allow quantitative predictions of pathogen spread and possible outbreaks of epidemics, and provide key input for regional resistance breeding programs. Late blight samples were collected from potato (Solanum tuberosum [...] Read more.

Long-term site-specific studies describing changes in the phenotypic variability of Phytophthora infestans populations allow quantitative predictions of pathogen spread and possible outbreaks of epidemics, and provide key input for regional resistance breeding programs. Late blight samples were collected from potato (Solanum tuberosum) breeding fields in Estonia during a twelve-year study period between 2001 and 2014. In total, 207 isolates were assessed for mating type and 235 isolates for metalaxyl resistance and 251 isolates for virulence factors. The frequency of mating types strongly fluctuated across the years, whereas the later period of 2010–2014 was dominated by the A2 mating. Despite fluctuations, both mating types were recorded in the same fields in most years, indicating sustained sexual reproduction of P. infestans with oospore production. Metalaxyl-resistant and intermediately resistant strains dominated in the first years of study, but with the progression of the study, metalaxyl-sensitive isolates became dominant, reaching up to 88%. Racial diversity, characterized by normalized Shannon diversity index decreased in time, varying from 1.00 in 2003 to 0.43 in 2013. The frequency of several virulence factors changed in a time-dependent manner, with R2 increasing and R6, R8, and R9 decreasing in time. Potato cultivar resistance background did not influence the frequency of P. infestans mating type, response to metalaxyl, and racial diversity. However, the diversity index decreased in time among isolates collected from resistant and susceptible cultivars, and remained at a high level in moderately resistant cultivars. These data demonstrate major time-dependent changes in racial diversity, fungicide resistance, and virulence factors in P. infestans, consistent with alterations in the control strategies and popularity of potato cultivars with different resistance. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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18 pages, 2785 KiB

Open AccessArticle

Crop Rotation with Marigold Promotes Soil Bacterial Structure to Assist in Mitigating Clubroot Incidence in Chinese Cabbage

by Jinhao Zhang, Waqar Ahmed, Xinghai Zhou, Bo Yao, Zulei He, Yue Qiu, Fangjun Wei, Yilu He, Lanfang Wei and Guanghai Ji

Plants 2022, 11(17), 2295; https://doi.org/10.3390/plants11172295 - 2 Sep 2022

Cited by 9 | Viewed by 2564

Abstract

Clubroot caused by Plasmodiophora brassicae is an economically important soilborne disease of Chinese cabbage worldwide. Integrated biological control through crop rotation is considered a good disease management approach to suppress the incidence of soilborne diseases. In this study, we evaluated the effect of [...] Read more.

Clubroot caused by Plasmodiophora brassicae is an economically important soilborne disease of Chinese cabbage worldwide. Integrated biological control through crop rotation is considered a good disease management approach to suppress the incidence of soilborne diseases. In this study, we evaluated the effect of a marigold plant (root exudates, crude extract, and powder) on the germination and death of resting spores of P. brassicae in vitro assays. Additionally, we also performed 16S high throughput sequencing, to investigate the impact of marigold–Chinese cabbage crop rotation on soil bacterial community composition, to manage this devastating pathogen. This study revealed that the marigold root exudates, crude extract, and powder significantly promoted the germination and death of P. brassicae resting spores. Under field conditions, marigold–Chinese cabbage crop rotation with an empty period of at least 15 days enhanced the germination of P. brassicae resting spores, shifted the rhizosphere bacterial community composition, and suppressed the incidence of clubroot by up to 63.35%. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia were the most dominant phyla and were present at high relative levels in the rhizosphere soil of Chinese cabbage. We concluded that crop rotation of Chinese cabbage with marigold can significantly reduce the incidence of clubroot disease in the next crop. To our knowledge, this is the first comprehensive study on the prevention and control of clubroot disease in Chinese cabbage through crop rotation with marigold. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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12 pages, 1993 KiB

Open AccessArticle

Evaluating the Rhizosphere and Endophytic Microbiomes of a Bamboo Plant in Response to the Long-Term Application of Heavy Organic Amendment

by Xiaoping Zhang, Zhiyuan Huang, Zheke Zhong, Qiaoling Li, Fangyuan Bian, Guibin Gao, Chuanbao Yang and Xing Wen

Plants 2022, 11(16), 2129; https://doi.org/10.3390/plants11162129 - 16 Aug 2022

Cited by 4 | Viewed by 1905

Abstract

Root-associated bacteria play a major role in plant health and productivity. However, how organic amendment influences root-associated bacteria is uncertain in Lei bamboo (Phyllostachys praecox) plantations. Here, we compared the rhizosphere and endophytic microbiomes in two Lei bamboo plantations with (IMS) [...] Read more.

Root-associated bacteria play a major role in plant health and productivity. However, how organic amendment influences root-associated bacteria is uncertain in Lei bamboo (Phyllostachys praecox) plantations. Here, we compared the rhizosphere and endophytic microbiomes in two Lei bamboo plantations with (IMS) and without (TMS) the application of organic amendment for 16 years. The results showed IMS significantly increased (p < 0.05) the relative abundance of Proteobacteria and significantly decreased (p < 0.05) the relative abundance of Acidobacteria, Bacteroidetes, and Verrucomicrobiota. The root endophytic Proteobacteria and Acidobacteria were significantly higher in abundance (p < 0.05) in the IMS than in the TMS, while Actinobacteria and Firmicutes were significantly lower in abundance. Five taxa were assigned to Proteobacteria and Acidobacteria, which were identified as keystones in the rhizosphere soil microbiome, while two species taxonomically affiliated with Proteobacteria were identified as keystones in the root endophytic microbiota, indicating this phylum can be an indicator for a root-associated microbiome in response to IMS. The soil pH, soil total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP), available potassium (AK), and TOC:TP ratio were significantly correlated (p < 0.05) with the bacterial community composition of both rhizosphere soils and root endophytes. TMS increased the microbial network complexity of root endophytes but decreased the microbial network complexity of rhizosphere soil. Our results suggest IMS shapes the rhizosphere and endophytic bacterial community compositions and their interactions differently, which should be paid attention to when designing management practices for the sustainable development of forest ecosystems. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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18 pages, 3204 KiB

Open AccessArticle

Exploring Relationships among Grapevine Chemical and Physiological Parameters and Leaf and Berry Mycobiome Composition

by Anna Molnár, József Geml, Adrienn Geiger, Carla Mota Leal, Glodia Kgobe, Adrienn Mária Tóth, Szabolcs Villangó, Lili Mézes, Márk Czeglédi, György Lőrincz and Zsolt Zsófi

Plants 2022, 11(15), 1924; https://doi.org/10.3390/plants11151924 - 25 Jul 2022

Cited by 3 | Viewed by 2765

Abstract

Improving our knowledge on biotic and abiotic factors that influence the composition of the grapevine mycobiome is of great agricultural significance, due to potential effects on plant health, productivity, and wine characteristics. Here, we assessed the influence of scion cultivar on the diversity [...] Read more.

Improving our knowledge on biotic and abiotic factors that influence the composition of the grapevine mycobiome is of great agricultural significance, due to potential effects on plant health, productivity, and wine characteristics. Here, we assessed the influence of scion cultivar on the diversity and composition of fungal communities in the berries and leaves of three different cultivars. We generated DNA metabarcoding data, and statistically compared the richness, relative abundance, and composition of several functional groups of fungi among cultivars, which are partly explained by measured differences in chemical composition of leaves and berries and physiological traits of leaves. Fungal communities in leaves and berries show contrasting patterns among cultivars. The richness and relative abundance of fungal functional groups statistically differ among berry and leaf samples, but less so among cultivars. Community composition of the dominant functional groups of fungi, i.e., plant pathogens in leaves and saprotrophs in berries, differs significantly among cultivars. We also detect cultivar-level differences in the macro- and microelement content of the leaves, and in acidity and sugar concentration of berries. Our findings suggest that there appears to be a relatively diverse set of fungi that make up the grapevine mycobiome at the sampled terroir that spans several cultivars, and that both berry and leaf mycobiomes are likely influenced by the chemical characteristics of berries and leaves, e.g., pH and the availability of nutrients and simple carbohydrates. Finally, the correlation between fungal community composition and physiological variables in leaves is noteworthy, and merits further research to explore causality. Our findings offer novel insights into the microbial dynamics of grapevine considering plant chemistry and physiology, with implications for viticulture. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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17 pages, 5076 KiB

Open AccessArticle

Endophytic Fungal and Bacterial Microbiota Shift in Rice and Barnyardgrass Grown under Co-Culture Condition

by Shuyan Li, Qiling Yan, Jieyu Wang and Qiong Peng

Plants 2022, 11(12), 1592; https://doi.org/10.3390/plants11121592 - 16 Jun 2022

Cited by 3 | Viewed by 2170

Abstract

Although barnyardgrass (Echinochloa crus-galli L.) is more competitive than rice (Oryza sativa L.) in the aboveground part, little is known about whether barnyardgrass is still competitive in recruiting endophytes and the root microbiota composition variation of rice under the barnyardgrass stress. [...] Read more.

Although barnyardgrass (Echinochloa crus-galli L.) is more competitive than rice (Oryza sativa L.) in the aboveground part, little is known about whether barnyardgrass is still competitive in recruiting endophytes and the root microbiota composition variation of rice under the barnyardgrass stress. Here, by detailed temporal characterization of root-associated microbiomes of rice plants during co-planted barnyardgrass stress and a comparison with the microbiomes of unplanted soil, we found that the bacterial community diversity of rice was dramatically higher while the fungal community richness was significantly lower than that of barnyardgrass at BBCH 45 and 57. More importantly, rice recruited more endophytic bacteria at BBCH 45 and 57, and more endophytic fungi at BBCH 17, 24, 37 to aginst the biotic stress from barnyardgrass. Principal coordinates analysis (PCoA) showed that rice and barnyardgrass had different community compositions of endophytic bacteria and fungi in roots. The PICRUSt predictive analysis indicated that majority of metabolic pathways of bacteria were overrepresented in barnyardgrass. However, eleven pathways were significantly presented in rice. In addition, rice and barnyardgrass harbored different fungal trophic modes using FUNGuild analysis. A negative correlation between bacteria and fungi in rice and barnyardgrass roots was found via network analysis. Actinobacteria was the vital bacteria in rice, while Proteobacteria dominated in barnyardgrass, and Ascomycota was the vital fungi in each species. These findings provided data and a theoretical basis for the in-depth understanding of the competition of barnyardgrass and endophytes and have implications relevant to weed prevention and control strategies using root microbiota. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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13 pages, 1450 KiB

Open AccessArticle

Changes in Diversity and Community Composition of Root Endophytic Fungi Associated with Aristolochia chilensis along an Aridity Gradient in the Atacama Desert

by María José Guevara-Araya, Víctor M. Escobedo, Valeria Palma-Onetto and Marcia González-Teuber

Plants 2022, 11(11), 1511; https://doi.org/10.3390/plants11111511 - 5 Jun 2022

Cited by 6 | Viewed by 2241

Abstract

Despite the widespread occurrence of fungal endophytes (FE) in plants inhabiting arid ecosystems, the environmental and soil factors that modulate changes in FE diversity and community composition along an aridity gradient have been little explored. We studied three locations along the coast of [...] Read more.

Despite the widespread occurrence of fungal endophytes (FE) in plants inhabiting arid ecosystems, the environmental and soil factors that modulate changes in FE diversity and community composition along an aridity gradient have been little explored. We studied three locations along the coast of the Atacama Desert in Chile, in which the plant Aristolochia chilensis naturally grows, and that differ in their aridity gradient from hyper-arid to semi-arid. We evaluated if root-associated FE diversity (frequency, richness and diversity indexes) and community composition vary as a function of aridity. Additionally, we assessed whether edaphic factors co-varying with aridity (soil water potential, soil moisture, pH and nutrients) may structure FE communities. We expected that FE diversity would gradually increase towards the aridity gradient declines, and that those locations that had the most contrasting environments would show more dissimilar FE communities. We found that richness indexes were inversely related to aridity, although this pattern was only partially observed for FE frequency and diversity. FE community composition was dissimilar among contrasting locations, and soil water availability significantly influenced FE community composition across the gradient. The results indicate that FE diversity and community composition associated with A. chilensis relate to differences in the aridity level across the gradient. Overall, our findings reveal the importance of climate-related factors in shaping changes in diversity, structure and distribution of FE in desert ecosystems. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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19 pages, 3815 KiB

Open AccessArticle

The Biodiversity of Grapevine Bacterial Endophytes of Vitis amurensis Rupr.

by Olga A. Aleynova, Nikolay N. Nityagovsky, Alexandra S. Dubrovina and Konstantin V. Kiselev

Plants 2022, 11(9), 1128; https://doi.org/10.3390/plants11091128 - 21 Apr 2022

Cited by 11 | Viewed by 2588

Abstract

In this paper, the composition profiles of bacterial endophytes in wild-growing Amur grape Vitis amurensis Rupr. grown in the south of the Russian Far East were analyzed using both a cultivation-dependent (sowing bacteria) and a cultivation-independent (next generation sequencing, NGS) approach. Both methods [...] Read more.

In this paper, the composition profiles of bacterial endophytes in wild-growing Amur grape Vitis amurensis Rupr. grown in the south of the Russian Far East were analyzed using both a cultivation-dependent (sowing bacteria) and a cultivation-independent (next generation sequencing, NGS) approach. Both methods revealed the prevalent endophytes in V. amurensis were represented by Gammaproteobacteria—40.3–75.8%, Alphaproteobacteria—8.6–18.7%, Actinobacteria—9.2–15.4%, and Bacilli—6.1–6.6%. NGS also showed a large proportion of Bacteroidia (12.2%) and a small proportion of other classes (less than 5.7%). In general, NGS revealed a greater variety of classes and genera in the endophytic bacterial community due to a high number of reads (574,207) in comparison with the number of colonies (933) obtained after the cultivation-dependent method. A comparative analysis performed in this study showed that both wild grape V. amurensis from Russia and domesticated cultivars of V. vinifera from Germany and California (USA) exhibit the same basic composition of endophytic bacteria, while the percentages of major taxa and minor taxa showed some differences depending on the plant organ, grape individuals, environmental conditions, and sampling time. Furthermore, the obtained data revealed that lower temperatures and increased precipitation favored the number and diversity of endophytic bacteria in the wild Amur grape. Thus, this study firstly described and analyzed the biodiversity of endophytic bacteria in wild grapevine V. amurensis. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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14 pages, 1918 KiB

Open AccessEditor’s ChoiceArticle

Grape Cultivar Features Differentiate the Grape Rhizosphere Microbiota

by Lijun Bao, Bo Sun, Yingxue Wei, Nan Xu, Shiwei Zhang, Likun Gu and Zhihui Bai

Plants 2022, 11(9), 1111; https://doi.org/10.3390/plants11091111 - 20 Apr 2022

Cited by 13 | Viewed by 3763

Abstract

Rhizosphere microflora are key determinants that contribute to plant growth and productivity, which are involved in improving the uptake of nutrients, regulation of plants’ metabolisms and activation of plants’ responses against both biotic and abiotic stresses. However, the structure and diversity of the [...] Read more.

Rhizosphere microflora are key determinants that contribute to plant growth and productivity, which are involved in improving the uptake of nutrients, regulation of plants’ metabolisms and activation of plants’ responses against both biotic and abiotic stresses. However, the structure and diversity of the grape rhizosphere microbiota remains poorly described. To gain a detailed understanding of the assembly of rhizosphere microbiota, we investigated the rhizosphere microbiota of nine grape varieties in northern China by high-throughput sequencing. We found that the richness and diversity of bacterial and fungal community networking in the root compartments were significantly influenced by the grape variety. The bacterial linear discriminant analysis showed that Pseudomonas and Rhizobium, which were considered as potential plant-growth-promoting bacteria, were more enriched in Pinot noir, and Nitrosospira was enriched in Gem. The fungal linear discriminant analysis showed that Fusarium was more enriched in Longan, Sporormiella was more enriched in Merlot, Gibberella and Pseudallescheria were more enriched in Gem and Mortierella was more abundant in Cabernet Sauvignon. The 16S rRNA functional prediction indicated that no significance differentiates among the grape varieties. Understanding the rhizosphere soil microbial diversity characteristics of different grape varieties could provide the basis for exploring microbial associations and maintaining the health of grapes. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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19 pages, 3260 KiB

Open AccessEditor’s ChoiceArticle

Improved Medicago sativa Nodulation under Stress Assisted by Variovorax sp. Endophytes

by Noris J. Flores-Duarte, Julia Pérez-Pérez, Salvadora Navarro-Torre, Enrique Mateos-Naranjo, Susana Redondo-Gómez, Eloísa Pajuelo and Ignacio D. Rodríguez-Llorente

Plants 2022, 11(8), 1091; https://doi.org/10.3390/plants11081091 - 17 Apr 2022

Cited by 21 | Viewed by 2914

Abstract

Legumes are the recommended crops to fight against soil degradation and loss of fertility because of their known positive impacts on soils. Our interest is focused on the identification of plant-growth-promoting endophytes inhabiting nodules able to enhance legume growth in poor and/or degraded [...] Read more.

Legumes are the recommended crops to fight against soil degradation and loss of fertility because of their known positive impacts on soils. Our interest is focused on the identification of plant-growth-promoting endophytes inhabiting nodules able to enhance legume growth in poor and/or degraded soils. The ability of Variovorax paradoxus S110^T and Variovorax gossypii JM-310^T to promote alfalfa growth in nutrient-poor and metal-contaminated estuarine soils was studied. Both strains behaved as nodule endophytes and improved in vitro seed germination and plant growth, as well as nodulation in co-inoculation with Ensifer medicae MA11. Variovorax ameliorated the physiological status of the plant, increased nodulation, chlorophyll and nitrogen content, and the response to stress and metal accumulation in the roots of alfalfa growing in degraded soils with moderate to high levels of contamination. The presence of plant-growth-promoting traits in Variovorax, particularly ACC deaminase activity, could be under the observed in planta effects. Although the couple V. gossypii-MA11 reported a great benefit to plant growth and nodulation, the best result was observed in plants inoculated with the combination of the three bacteria. These results suggest that Variovorax strains could be used as biofertilizers to improve the adaptation of legumes to degraded soils in soil-recovery programs. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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18 pages, 3196 KiB

Open AccessArticle

Genome Mining and Gene Expression Reveal Maytansine Biosynthetic Genes from Endophytic Communities Living inside Gymnosporia heterophylla (Eckl. and Zeyh.) Loes. and the Relationship with the Plant Biosynthetic Gene, Friedelin Synthase

by Thanet Pitakbut, Michael Spiteller and Oliver Kayser

Plants 2022, 11(3), 321; https://doi.org/10.3390/plants11030321 - 25 Jan 2022

Cited by 6 | Viewed by 3170

Abstract

Even though maytansine was first discovered from Celastraceae plants, it was later proven to be an endophytic bacterial metabolite. However, a pure bacterial culture cannot synthesize maytansine. Therefore, an exclusive interaction between plant and endophytes is required for maytansine production. Unfortunately, our understanding [...] Read more.

Even though maytansine was first discovered from Celastraceae plants, it was later proven to be an endophytic bacterial metabolite. However, a pure bacterial culture cannot synthesize maytansine. Therefore, an exclusive interaction between plant and endophytes is required for maytansine production. Unfortunately, our understanding of plant–endophyte interaction is minimal, and critical questions remain. For example: how do endophytes synthesize maytansine inside their plant host, and what is the impact of maytansine production in plant secondary metabolites? Our study aimed to address these questions. We selected Gymnosporia heterophylla as our model and used amino-hydroxybenzoic acid (AHBA) synthase and halogenase genes as biomarkers, as these two genes respond to biosynthesize maytansine. As a result, we found a consortium of seven endophytes involved in maytansine production in G. heterophylla, based on genome mining and gene expression experiments. Subsequently, we evaluated the friedelin synthase (FRS) gene’s expression level in response to biosynthesized 20-hydroxymaytenin in the plant. We found that the FRS expression level was elevated and linked with the expression of the maytansine biosynthetic genes. Thus, we achieved our goals and provided new evidence on endophyte–endophyte and plant–endophyte interactions, focusing on maytansine production and its impact on plant metabolite biosynthesis in G. heterophylla. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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14 pages, 1857 KiB

Open AccessArticle

Identification of Volatile Organic Compounds Emitted by Two Beneficial Endophytic Pseudomonas Strains from Olive Roots

by Nuria Montes-Osuna, Tomislav Cernava, Carmen Gómez-Lama Cabanás, Gabriele Berg and Jesús Mercado-Blanco

Plants 2022, 11(3), 318; https://doi.org/10.3390/plants11030318 - 25 Jan 2022

Cited by 20 | Viewed by 4331

Abstract

The production of volatile organic compounds (VOCs) represents a promising strategy of plant-beneficial bacteria to control soil-borne phytopathogens. Pseudomonas sp. PICF6 and Pseudomonas simiae PICF7 are two indigenous inhabitants of olive roots displaying effective biological control against Verticillium dahliae. Additionally, strain PICF7 is [...] Read more.

The production of volatile organic compounds (VOCs) represents a promising strategy of plant-beneficial bacteria to control soil-borne phytopathogens. Pseudomonas sp. PICF6 and Pseudomonas simiae PICF7 are two indigenous inhabitants of olive roots displaying effective biological control against Verticillium dahliae. Additionally, strain PICF7 is able to promote the growth of barley and Arabidopsis thaliana, VOCs being involved in the growth of the latter species. In this study, the antagonistic capacity of these endophytic bacteria against relevant phytopathogens (Verticillium spp., Rhizoctonia solani, Sclerotinia sclerotiorum and Fusarium oxysporum f.sp. lycopersici) was assessed. Under in vitro conditions, PICF6 and PICF7 were only able to antagonize representative isolates of V. dahliae and V. longisporum. Remarkably, both strains produced an impressive portfolio of up to twenty VOCs, that included compounds with reported antifungal (e.g., 1-undecene, (methyldisulfanyl) methane and 1-decene) or plant growth promoting (e.g., tridecane, 1-decene) activities. Moreover, their volatilomes differed strongly in the absence and presence of V. dahliae. For example, when co incubated with the defoliating pathotype of V. dahliae, the antifungal compound 4-methyl-2,6-bis(2-methyl-2-propanyl)phenol was produced. Results suggest that volatiles emitted by these endophytes may differ in their modes of action, and that potential benefits for the host needs further investigation in planta. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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11 pages, 13008 KiB

Open AccessArticle

Antagonistic Activity of Fungal Strains against Fusarium Crown Rot

by Xingli Zhao, Dianyun Hou, Jiaqi Xu, Kaixuan Wang and Zhenjie Hu

Plants 2022, 11(3), 255; https://doi.org/10.3390/plants11030255 - 19 Jan 2022

Cited by 11 | Viewed by 4398

Abstract

The crown rot of wheat is a destructive soil-borne pathogen that severely reduces the yield and quality of wheat. This study aimed to screen and identify the antagonistic strains against Fusarium pseudograminearum (Fp), which is the dominant pathogen associated with the [...] Read more.

The crown rot of wheat is a destructive soil-borne pathogen that severely reduces the yield and quality of wheat. This study aimed to screen and identify the antagonistic strains against Fusarium pseudograminearum (Fp), which is the dominant pathogen associated with the crown rot of wheat in China, and evaluate their biosynthetic potential. The antagonistic strains were screened via a dual-culture antagonism assay, and then identified by combining the morphological characteristics and internal transcribed spacer gene sequencing. The polyketide synthases (PKS-I and PKS-II) and non-ribosomal peptide synthetase (NRPS) genes in the antagonistic strains were detected via specific amplification of chromosomal DNA. Eleven out of 157 fungal strains, including six strains with matrix competition and five strains with antibiosis, were obtained. The eleven antagonistic strains belonged to the following four genera: Alternaria, Botryosphaeria, Phoma and Talaromyces. The inhibition rate of six strains with matrix competition was greater than 50%, with B. dothidea S2-22 demonstrating the highest at 80.3%. The width of the inhibition zone of T. trachyspermus R-17 among the five strains with antibiosis was the widest at 11 mm. Among the eleven antagonistic strains, three strains of A. alternata and the strain P. moricola only contained the PKS-II gene, the strain A. tenuissima contained PKS-I and PKS-II genes, three strains of B. dothidea contained PKS-II and NRPS genes, while three strains of T. trachyspermus did not contain any genes. These results demonstrated potential strains for the biocontrol of the crown rot of wheat. In particular, T. trachyspermus R-17 can be investigated further as a promising agent, and the active substances secreted by antagonistic strains may be synthesized by other pathways. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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13 pages, 4370 KiB

Open AccessArticle

Microbial Diversity Characteristics of Areca Palm Rhizosphere Soil at Different Growth Stages

by Siyuan Ma, Yubin Lin, Yongqiang Qin, Xiaoping Diao and Peng Li

Plants 2021, 10(12), 2706; https://doi.org/10.3390/plants10122706 - 9 Dec 2021

Cited by 6 | Viewed by 3505

Abstract

The rhizosphere microflora are key determinants that contribute to plant health and productivity, which can support plant nutrition and resistance to biotic and abiotic stressors. However, limited research is conducted on the areca palm rhizosphere microbiota. To further study the effect of the [...] Read more.

The rhizosphere microflora are key determinants that contribute to plant health and productivity, which can support plant nutrition and resistance to biotic and abiotic stressors. However, limited research is conducted on the areca palm rhizosphere microbiota. To further study the effect of the areca palm’s developmental stages on the rhizosphere microbiota, the rhizosphere microbiota of areca palm (Areca catechu) grown in its main producing area were examined in Wanning, Hainan province, at different vegetation stages by an Illumina Miseq sequence analysis of the 16S ribosomal ribonucleic acid and internal transcribed spacer genes. Significant shifts of the taxonomic composition of the bacteria and fungi were observed in the four stages. Burkholderia-Caballeronia-Paraburkholderia were the most dominant group in stage T1 and T2; the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium were decreased significantly from T1 to T2; and the genera Acidothermus and Bacillus were the most dominant in stage T3 and T4, respectively. Meanwhile, Neocosmospora, Saitozyma, Penicillium, and Trichoderma were the most dominant genera in the stage T1, T2, T3, and T4, respectively. Among the core microbiota, the dominant bacterial genera were Burkholderia-Caballeronia-Paraburkholderia and Bacillus, and the dominant fungal genera were Saitozyma and Trichoderma. In addition, we identified five bacterial genera and five fungal genera that reached significant levels during development. Finally, we constructed the OTU (top 30) interaction network of bacteria and fungi, revealed its interaction characteristics, and found that the bacterial OTUs exhibited more extensive interactions than the fungal OTUs. Understanding the rhizosphere soil microbial diversity characteristics of the areca palm could provide the basis for exploring microbial association and maintaining the areca palm’s health. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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12 pages, 2215 KiB

Open AccessArticle

Nematicidal Activity of the Endophyte Serratia ureilytica against Nacobbus aberrans in Chili Plants (Capsicum annuum L.) and Identification of Genes Related to Biological Control

by Arnoldo Wong-Villarreal, Erick Williams Méndez-Santiago, Olga Gómez-Rodríguez, Liliana Aguilar-Marcelino, Daniel Cerqueda García, José Q. García-Maldonado, Victor M. Hernández-Velázquez, Gustavo Yañez-Ocampo, Saúl Espinosa-Zaragoza, Sandra I. Ramírez-González and Diana Sanzón-Gómez

Plants 2021, 10(12), 2655; https://doi.org/10.3390/plants10122655 - 3 Dec 2021

Cited by 5 | Viewed by 2690

Abstract

The genus Serratia is widely distributed in soil, water, plants, animals, invertebrates, and humans. Some species of this genus have antifungal, antibacterial, and nematicidal activity. In this work, the nematicidal activity of the endophytic strain of Serratia sp. in chili, Capsicum annuum L., [...] Read more.

The genus Serratia is widely distributed in soil, water, plants, animals, invertebrates, and humans. Some species of this genus have antifungal, antibacterial, and nematicidal activity. In this work, the nematicidal activity of the endophytic strain of Serratia sp. in chili, Capsicum annuum L., is reported, where at a bacterial concentration of 4 × 10⁹ cel/mL, the penetration of nematodes into the roots significantly decreased by 91 and 55% at 7 and 21 days after inoculation. This bacterial concentration also significantly decreased the number of galls, eggs, egg masses and reproduction factor produced by Nacobbus aberrans in Chili plants, with respect to the control where this bacterial strain was not applied. In the analysis of the genome of the strain, based on average nucleotide identity (ANI), the isolate could be affiliated to the species Serratia ureilytica. The size of the genome is 5.4 Mb, with a 59.3% content of GC. Genes related to the synthesis of chitinases, siderophores, proteases C, serralisins, hemolysin, and serrawettin W2 that have been reported for biocontrol of nematodes were identified in the genome. It is the first report of Serratia ureilytica with nematicidal activity. Based on these results of nematicidal activity, this strain can be evaluated in the field as an alternative in the biocontrol of Nacobbus aberrans in chili cultivation. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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20 pages, 2852 KiB

Open AccessArticle

Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant–Bacteria Interactions

by Tongda Li, Ross Mann, Jatinder Kaur, German Spangenberg and Timothy Sawbridge

Plants 2021, 10(9), 1802; https://doi.org/10.3390/plants10091802 - 30 Aug 2021

Cited by 13 | Viewed by 3948

Abstract

Plant growth-promoting bacteria can improve host plant traits including nutrient uptake and metabolism and tolerance to biotic and abiotic stresses. Understanding the molecular basis of plant–bacteria interactions using dual RNA-seq analyses provides key knowledge of both host and bacteria simultaneously, leading to future [...] Read more.

Plant growth-promoting bacteria can improve host plant traits including nutrient uptake and metabolism and tolerance to biotic and abiotic stresses. Understanding the molecular basis of plant–bacteria interactions using dual RNA-seq analyses provides key knowledge of both host and bacteria simultaneously, leading to future enhancements of beneficial interactions. In this study, dual RNA-seq analyses were performed to provide insights into the early-stage interactions between barley seedlings and three novel bacterial strains (two Paenibacillus sp. strains and one Erwinia gerundensis strain) isolated from the perennial ryegrass seed microbiome. Differentially expressed bacterial and barley genes/transcripts involved in plant–bacteria interactions were identified, with varying species- and strain-specific responses. Overall, transcriptome profiles suggested that all three strains improved stress response, signal transduction, and nutrient uptake and metabolism of barley seedlings. Results also suggested potential improvements in seedling root growth via repressing ethylene biosynthesis in roots. Bacterial secondary metabolite gene clusters producing compounds that are potentially associated with interactions with the barley endophytic microbiome and associated with stress tolerance of plants under nutrient limiting conditions were also identified. The results of this study provided the molecular basis of plant growth-promoting activities of three novel bacterial strains in barley, laid a solid foundation for the future development of these three bacterial strains as biofertilisers, and identified key differences between bacterial strains of the same species in their responses to plants. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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13 pages, 2099 KiB

Open AccessArticle

The Influence of the Grapevine Bacterial and Fungal Endophytes on Biomass Accumulation and Stilbene Production by the In Vitro Cultivated Cells of Vitis amurensis Rupr.

by Olga A. Aleynova, Andrey R. Suprun, Nikolay N. Nityagovsky, Alexandra S. Dubrovina and Konstantin V. Kiselev

Plants 2021, 10(7), 1276; https://doi.org/10.3390/plants10071276 - 23 Jun 2021

Cited by 22 | Viewed by 3135

Abstract

Plant endophytes are known to alter the profile of secondary metabolites in plant hosts. In this study, we identified the main bacterial and fungal representatives of the wild grape Vitis amurensis Rupr. microbiome and investigated a cocultivation effect of the 14 endophytes and [...] Read more.

Plant endophytes are known to alter the profile of secondary metabolites in plant hosts. In this study, we identified the main bacterial and fungal representatives of the wild grape Vitis amurensis Rupr. microbiome and investigated a cocultivation effect of the 14 endophytes and the V. amurensis cell suspension on biomass accumulation and stilbene biosynthesis. The cocultivation of the V. amurensis cell culture with the bacteria Agrobacterium sp., Bacillus sp., and Curtobacterium sp. for 2 weeks did not significantly affect the accumulation of cell culture fresh biomass. However, it was significantly inhibited by the bacteria Erwinia sp., Pantoea sp., Pseudomonas sp., and Xanthomonas sp. and fungi Alternaria sp., Biscogniauxia sp., Cladosporium sp., Didymella sp. 2, and Fusarium sp. Cocultivation of the grapevine cell suspension with the fungi Didymella sp. 1 and Trichoderma sp. resulted in cell death. The addition of endophytic bacteria increased the total stilbene content by 2.2–5.3 times, while the addition of endophytic fungi was more effective in inducing stilbene accumulation by 2.6–16.3 times. The highest content of stilbenes in the grapevine cells cocultured with endophytic fungi was 13.63 and 13.76 mg/g of the cell dry weight (DW) after cultivation with Biscogniauxia sp. and Didymella sp. 2, respectively. The highest content of stilbenes in the grapevine cells cocultured with endophytic bacteria was 4.49 mg/g DW after cultivation with Xanthomonas sp. The increase in stilbene production was due to a significant activation of phenylalanine ammonia lyase (PAL) and stilbene synthase (STS) gene expression. We also analyzed the sensitivity of the selected endophytes to eight antibiotics, fluconazole, and trans-resveratrol. The endophytic bacteria were sensitive to gentamicin and kanamycin, while all selected fungal strains were resistant to fluconazole with the exception of Cladosporium sp. All endophytes were tolerant of trans-resveratrol. This study showed that grape endophytes stimulate the production of stilbenes in grape cell suspension, which could further contribute to the generation of a new stimulator of stilbene biosynthesis in grapevine or grape cell cultures. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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Review

Jump to: Editorial, Research

12 pages, 270 KiB

Open AccessEditor’s ChoiceReview

The Endosphere Microbiome of Ginseng

by Paul H. Goodwin

Plants 2022, 11(3), 415; https://doi.org/10.3390/plants11030415 - 2 Feb 2022

Cited by 17 | Viewed by 3351

Abstract

The endosphere of ginseng contains a variety of fungal, bacterial, archaeal and viral endophytes. Bacterial endophytes are primarily members of the Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, and fungal endophytes are primarily members of the Ascomycota, Zygomycota and Basidiomycota. Although archaea and viruses have [...] Read more.

The endosphere of ginseng contains a variety of fungal, bacterial, archaeal and viral endophytes. Bacterial endophytes are primarily members of the Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, and fungal endophytes are primarily members of the Ascomycota, Zygomycota and Basidiomycota. Although archaea and viruses have been detected in symptomless ginseng plants, little is known about them. Many but not all studies have shown roots having the highest abundance and diversity of bacterial and fungal endophytes, with some endophytes showing specificity to above or belowground tissues. Abundance often increases with root age, although diversity can decrease, possibly related to increases in potential latent fungal pathogen infections. The descriptions of many endophytes that can metabolize ginsenosides indicate an adaptation of the microbes to the unique combination of secondary metabolites found in ginseng tissues. Most research on the benefits provided by bacterial and fungal endophytes has concentrated on improved plant nutrition, growth promotion and increased disease resistance, but little on their ability to increase abiotic stress resistance. Some other areas where more research is needed is field trials with endophyte-treated plants grown in various environments, genomic/metagenomic analysis of endophytes, and the effects of endophytes on induced disease resistance and abiotic stress tolerance. Full article

(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Molecular Aspects, Biological Functions, Community Composition, and Practical Applications)

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