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16 pages, 1378 KiB

Open AccessArticle

Genome Analysis of Endobacterium cerealis, a Novel Genus and Species Isolated from Zea mays Roots in North Spain

by Esther Menéndez, Jose David Flores-Félix, Martha Helena Ramírez-Bahena, Jose M. Igual, Paula García-Fraile, Alvaro Peix and Encarna Velázquez

Microorganisms 2020, 8(6), 939; https://doi.org/10.3390/microorganisms8060939 - 22 Jun 2020

Cited by 9 | Viewed by 4295

Abstract

In the present work, we analyse the genomic and phenotypic characteristics of a strain named RZME27^T isolated from roots of a Zea mays plant grown in Spain. The phylogenetic analyses of 16S rRNA gene and whole genome sequences showed that the strain [...] Read more.

In the present work, we analyse the genomic and phenotypic characteristics of a strain named RZME27^T isolated from roots of a Zea mays plant grown in Spain. The phylogenetic analyses of 16S rRNA gene and whole genome sequences showed that the strain RZME27^T clustered with the type strains of Neorhizobium galegae and Pseudorhizobium pelagicum from the family Rhizobiaceae. This family encompasses several genera establishing symbiosis with legumes, but the genes involved in nodulation and nitrogen fixation are absent in its genome. Nevertheless, genes related to plant colonization, such as those involved in motility, chemotaxis, quorum sensing, exopolysaccharide biosynthesis and hydrolytic enzymes production were found. The comparative pangenomic analyses showed that 78 protein clusters present in the strain RZME27^T were not found in the type strains of its closest relatives N. galegae and P. pelagicum. The calculated average nucleotide identity (ANI) values between the strain RZME27^T and the type strains of N. galegae and P. pelagicum were 75.61% and 75.1%, respectively, similar or lower than those found for other genera from family Rhizobiaceae. Several phenotypic differences were also found, highlighting the absence of the fatty acid C_19:0 cyclo ω8c and propionate assimilation. These results support the definition of a novel genus and species named Endobacterium cerealis gen. nov. sp. nov. whose type strain is RZME27^T. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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20 pages, 3742 KiB

Open AccessArticle

Gene Expression Profile of Mexican Lime (Citrus aurantifolia) Trees in Response to Huanglongbing Disease caused by Candidatus Liberibacter asiaticus

by Ángela Paulina Arce-Leal, Rocío Bautista, Edgar Antonio Rodríguez-Negrete, Miguel Ángel Manzanilla-Ramírez, José Joaquín Velázquez-Monreal, María Elena Santos-Cervantes, Jesús Méndez-Lozano, Carmen R. Beuzón, Eduardo R. Bejarano, Araceli G. Castillo, M. Gonzalo Claros and Norma Elena Leyva-López

Microorganisms 2020, 8(4), 528; https://doi.org/10.3390/microorganisms8040528 - 7 Apr 2020

Cited by 28 | Viewed by 4772

Abstract

Nowadays, Huanglongbing (HLB) disease, associated with Candidatus Liberibacter asiaticus (CLas), seriously affects citriculture worldwide, and no cure is currently available. Transcriptomic analysis of host–pathogen interaction is the first step to understand the molecular landscape of a disease. Previous works have reported the transcriptome [...] Read more.

Nowadays, Huanglongbing (HLB) disease, associated with Candidatus Liberibacter asiaticus (CLas), seriously affects citriculture worldwide, and no cure is currently available. Transcriptomic analysis of host–pathogen interaction is the first step to understand the molecular landscape of a disease. Previous works have reported the transcriptome profiling in response to HLB in different susceptible citrus species; however, similar studies in tolerant citrus species, including Mexican lime, are limited. In this work, we have obtained an RNA-seq-based differential expression profile of Mexican lime plants challenged against CLas infection, at both asymptomatic and symptomatic stages. Typical HLB-responsive differentially expressed genes (DEGs) are involved in photosynthesis, secondary metabolism, and phytohormone homeostasis. Enrichment of DEGs associated with biotic response showed that genes related to cell wall, secondary metabolism, transcription factors, signaling, and redox reactions could play a role in the tolerance of Mexican lime against CLas infection. Interestingly, despite some concordance observed between transcriptional responses of different tolerant citrus species, a subset of DEGs appeared to be species-specific. Our data highlights the importance of studying the host response during HLB disease using as model tolerant citrus species, in order to design new and opportune diagnostic and management methods. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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18 pages, 4896 KiB

Open AccessArticle

Diversity, Phylogeny and Plant Growth Promotion Traits of Nodule Associated Bacteria Isolated from Lotus parviflorus

by Ricardo Soares, Jesús Trejo, Maria J. Lorite, Etelvina Figueira, Juan Sanjuán and Isabel Videira e Castro

Microorganisms 2020, 8(4), 499; https://doi.org/10.3390/microorganisms8040499 - 31 Mar 2020

Cited by 24 | Viewed by 5415

Abstract

Lotus spp. are widely used as a forage to improve pastures, and inoculation with elite rhizobial strains is a common practice in many countries. However, only a few Lotus species have been studied in the context of plant-rhizobia interactions. In this study, forty [...] Read more.

Lotus spp. are widely used as a forage to improve pastures, and inoculation with elite rhizobial strains is a common practice in many countries. However, only a few Lotus species have been studied in the context of plant-rhizobia interactions. In this study, forty highly diverse bacterial strains were isolated from root nodules of wild Lotus parviflorus plants growing in two field locations in Portugal. However, only 10% of these isolates could nodulate one or more legume hosts tested, whereas 90% were thought to be opportunistic nodule associated bacteria. Phylogenetic studies place the nodulating isolates within the Bradyrhizobium genus, which is closely related to B. canariense and other Bradyrhizobium sp. strains isolated from genistoid legumes and Ornithopus spp. Symbiotic nodC and nifH gene phylogenies were fully consistent with the taxonomic assignment and host range. The non-nodulating bacteria isolated were alpha- (Rhizobium/Agrobacterium), beta- (Massilia) and gamma-proteobacteria (Pseudomonas, Lysobacter, Luteibacter, Stenotrophomonas and Rahnella), as well as some bacteroidetes from genera Sphingobacterium and Mucilaginibacter. Some of these nodule-associated bacteria expressed plant growth promotion (PGP) traits, such as production of lytic enzymes, antagonistic activity against phytopathogens, phosphate solubilization, or siderophore production. This argues for a potential beneficial role of these L. parviflorus nodule-associated bacteria. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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16 pages, 2289 KiB

Open AccessArticle

The Effect of Biochars and Endophytic Bacteria on Growth and Root Rot Disease Incidence of Fusarium Infested Narrow-Leafed Lupin (Lupinus angustifolius L.)

by Dilfuza Egamberdieva, Vyacheslav Shurigin, Burak Alaylar, Hua Ma, Marina E. H. Müller, Stephan Wirth, Moritz Reckling and Sonoko Dorothea Bellingrath-Kimura

Microorganisms 2020, 8(4), 496; https://doi.org/10.3390/microorganisms8040496 - 31 Mar 2020

Cited by 35 | Viewed by 6319

Abstract

The effects of biochar on plant growth vary depending on the applied biochar type, study site environmental conditions, microbial species, and plant–microbial interactions. The objectives of the present study were therefore to assess 1) the response of growth parameters of lupin and root [...] Read more.

The effects of biochar on plant growth vary depending on the applied biochar type, study site environmental conditions, microbial species, and plant–microbial interactions. The objectives of the present study were therefore to assess 1) the response of growth parameters of lupin and root disease incidence to the application of three biochar types in a loamy sandy soil, and 2) the role of endophytic bacteria in biological control of root rot disease incidence in lupin after the amendment of soil with different biochar types. As biochar types we tested (i) hydrochar (HTC) from maize silage, (ii) pyrolysis char from maize (MBC), and (iii) pyrolysis char from wood (WBC) at three different concentrations (1%, 2%, and 3% of char as soil amendments). There were no significant effects in lupin shoot and root growth in soils amended with WBC at any of the concentrations. MBC did not affect plant growth except for root dry weight at 2% MBC. HTC char at 2% concentration, significantly increased the root dry weight of lupin by 54–75%, and shoot dry weight by 21–25%. Lupin plants grown in soil amended with 2% and 3% WBC and MBC chars showed 40–50% and 10–20% disease symptoms, respectively. Plants grown in soil without biochar and with HTC char were healthy, and no disease incidence occurred. Pseudomonas putida L2 and Stenotrophomonas pavanii L8 isolates demonstrated a disease reduction compared to un-inoculated plants under MBC and WBC amended soil that was infested with Fusarium solani. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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22 pages, 3917 KiB

Open AccessArticle

Pseudomonas PS01 Isolated from Maize Rhizosphere Alters Root System Architecture and Promotes Plant Growth

by Thanh Nguyen Chu, Le Van Bui and Minh Thi Thanh Hoang

Microorganisms 2020, 8(4), 471; https://doi.org/10.3390/microorganisms8040471 - 26 Mar 2020

Cited by 37 | Viewed by 4891

Abstract

The objectives of this study were to evaluate the plant growth promoting effects on Arabidopsis by Pseudomonas sp. strains associated with rhizosphere of crop plants grown in Mekong Delta, Vietnam. Out of all the screened isolates, Pseudomonas PS01 isolated from maize rhizosphere showed [...] Read more.

The objectives of this study were to evaluate the plant growth promoting effects on Arabidopsis by Pseudomonas sp. strains associated with rhizosphere of crop plants grown in Mekong Delta, Vietnam. Out of all the screened isolates, Pseudomonas PS01 isolated from maize rhizosphere showed the most prominent plant growth promoting effects on Arabidopsis and maize (Zea mays). We also found that PS01 altered root system architecture (RSA). The full genome of PS01 was resolved using high-throughput sequencing. Phylogenetic analysis identified PS01 as a member of the Pseudomonas putida subclade, which is closely related to Pseudomonas taiwanensis. PS01 genome size is 5.3 Mb, assembled in 71 scaffolds comprising of 4820 putative coding sequence. PS01 encodes genes for the indole-3-acetic acid (IAA), acetoin and 2,3-butanediol biosynthesis pathways. PS01 promoted the growth of Arabidopsis and altered the root system architecture by inhibiting primary root elongation and promoting lateral root and root hair formation. By employing gene expression analysis, genetic screening and pharmacological approaches, we suggested that the plant-growth promoting effects of PS01 and the alteration of RSA might be independent of bacterial auxin and could be caused by a combination of different diffusible compounds and volatile organic compounds (VOCs). Taken together, our results suggest that PS01 is a potential candidate to be used as bio-fertilizer agent for enhancing plant growth. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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17 pages, 3241 KiB

Open AccessArticle

Litterbox—A gnotobiotic Zeolite-Clay System to Investigate Arabidopsis–Microbe Interactions

by Moritz Miebach, Rudolf O. Schlechter, John Clemens, Paula E. Jameson and Mitja N.P. Remus-Emsermann

Microorganisms 2020, 8(4), 464; https://doi.org/10.3390/microorganisms8040464 - 25 Mar 2020

Cited by 10 | Viewed by 4894

Abstract

Plants are colonised by millions of microorganisms representing thousands of species with varying effects on plant growth and health. The microbial communities found on plants are compositionally consistent and their overall positive effect on the plant is well known. However, the effects of [...] Read more.

Plants are colonised by millions of microorganisms representing thousands of species with varying effects on plant growth and health. The microbial communities found on plants are compositionally consistent and their overall positive effect on the plant is well known. However, the effects of individual microbiota members on plant hosts and vice versa, as well as the underlying mechanisms, remain largely unknown. Here, we describe “Litterbox”, a highly controlled system to investigate plant–microbe interactions. Plants were grown gnotobiotically, otherwise sterile, on zeolite-clay, a soil replacement that retains enough moisture to avoid subsequent watering. Litterbox-grown plants resemble greenhouse-grown plants more closely than agar-grown plants and exhibit lower leaf epiphyte densities (10⁶ cfu/g), reflecting natural conditions. A polydimethylsiloxane (PDMS) sheet was used to cover the zeolite, significantly lowering the bacterial load in the zeolite and rhizosphere. This reduced the likelihood of potential systemic responses in leaves induced by microbial rhizosphere colonisation. We present results of example experiments studying the transcriptional responses of leaves to defined microbiota members and the spatial distribution of bacteria on leaves. We anticipate that this versatile and affordable plant growth system will promote microbiota research and help in elucidating plant-microbe interactions and their underlying mechanisms. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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19 pages, 11196 KiB

Open AccessArticle

Unlocking the Microbiome Communities of Banana (Musa spp.) under Disease Stressed (Fusarium wilt) and Non-Stressed Conditions

by Manoj Kaushal, Rony Swennen and George Mahuku

Microorganisms 2020, 8(3), 443; https://doi.org/10.3390/microorganisms8030443 - 20 Mar 2020

Cited by 38 | Viewed by 10390

Abstract

We assessed the diversity, structure, and assemblage of bacterial and fungal communities associated with banana plants with and without Fusarium oxysporum f. sp. cubense (Foc) symptoms. A total of 117,814 bacterial and 17,317 fungal operational taxonomy units (OTUs) were identified in the rhizosphere, [...] Read more.

We assessed the diversity, structure, and assemblage of bacterial and fungal communities associated with banana plants with and without Fusarium oxysporum f. sp. cubense (Foc) symptoms. A total of 117,814 bacterial and 17,317 fungal operational taxonomy units (OTUs) were identified in the rhizosphere, roots, and corm of the host plant. Results revealed that bacterial and fungal microbiota present in roots and corm primarily emanated from the rhizosphere. The composition of bacterial communities in the rhizosphere, roots, and corm were different, with more diversity observed in the rhizosphere and less in the corm. However, distinct sample types i.e., without (asymptomatic) and with (symptomatic) Fusarium symptoms were the major drivers of the fungal community composition. Considering the high relative abundance among samples, we identified core microbiomes with bacterial and fungal OTUs classified into 20 families and colonizing distinct plant components of banana. Our core microbiome assigned 129 bacterial and 37 fungal genera to known taxa. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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15 pages, 1574 KiB

Open AccessArticle

Plant Growth Promotion Abilities of Phylogenetically Diverse Mesorhizobium Strains: Effect in the Root Colonization and Development of Tomato Seedlings

by Esther Menéndez, Juan Pérez-Yépez, Mercedes Hernández, Ana Rodríguez-Pérez, Encarna Velázquez and Milagros León-Barrios

Microorganisms 2020, 8(3), 412; https://doi.org/10.3390/microorganisms8030412 - 14 Mar 2020

Cited by 30 | Viewed by 3926

Abstract

Mesorhizobium contains species widely known as nitrogen-fixing bacteria with legumes, but their ability to promote the growth of non-legumes has been poorly studied. Here, we analyzed the production of indole acetic acid (IAA), siderophores and the solubilization of phosphate and potassium in a [...] Read more.

Mesorhizobium contains species widely known as nitrogen-fixing bacteria with legumes, but their ability to promote the growth of non-legumes has been poorly studied. Here, we analyzed the production of indole acetic acid (IAA), siderophores and the solubilization of phosphate and potassium in a collection of 24 strains belonging to different Mesorhizobium species. All these strains produce IAA, 46% solubilized potassium, 33% solubilize phosphate and 17% produce siderophores. The highest production of IAA was found in the strains Mesorhizobium ciceri CCANP14 and Mesorhizobium tamadayense CCANP122, which were also able to solubilize potassium. Moreover, the strain CCANP14 showed the maximum phosphate solubilization index, and the strain CCANP122 was able to produce siderophores. These two strains were able to produce cellulases and cellulose and to originate biofilms in abiotic surfaces and tomato root surface. Tomato seedlings responded positively to the inoculation with these two strains, showing significantly higher plant growth traits than uninoculated seedlings. This is the first report about the potential of different Mesorhizobium species to promote the growth of a vegetable. Considering their use as safe for humans, animals and plants, they are an environmentally friendly alternative to chemical fertilizers for non-legume crops in the framework of sustainable agriculture. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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15 pages, 3029 KiB

Open AccessArticle

Development of PCR-Based Detection System for Soft Rot Pectobacteriaceae Pathogens Using Molecular Signatures

by Md Niamul Kabir, Ali Taheri and C. Korsi Dumenyo

Microorganisms 2020, 8(3), 358; https://doi.org/10.3390/microorganisms8030358 - 2 Mar 2020

Cited by 12 | Viewed by 5121

Abstract

Pectobacterium and Dickeya species, usually referred to as soft rot Enterobacteriaceae, are phytopathogenic genera of bacteria that cause soft rot and blackleg diseases and are responsible for significant yield losses in many crops across the globe. Diagnosis of soft rot disease is difficult [...] Read more.

Pectobacterium and Dickeya species, usually referred to as soft rot Enterobacteriaceae, are phytopathogenic genera of bacteria that cause soft rot and blackleg diseases and are responsible for significant yield losses in many crops across the globe. Diagnosis of soft rot disease is difficult through visual disease symptoms. Pathogen detection and identification methods based on cultural and morphological identification are time-consuming and not always reliable. A polymerase chain reaction (PCR)-based detection method with the species-specific primers is fast and reliable for detecting soft rot pathogens. We have developed a specific and sensitive detection system for some species of soft rot Pectobacteriaceae pathogens in the Pectobacterium and Dickeya genera based on the use of species-specific primers to amplify unique genomic segments. The specificities of primers were verified by PCR analysis of genomic DNA from 14 strains of Pectobacterium, 8 strains of Dickeya, and 6 strains of non-soft rot bacteria. This PCR assay provides a quick, simple, powerful, and reliable method for detection of soft rot bacteria. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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20 pages, 2532 KiB

Open AccessArticle

Metabolomics Analysis Reveals the Alkali Tolerance Mechanism in Puccinellia tenuiflora Plants Inoculated with Arbuscular Mycorrhizal Fungi

by Chunxue Yang, Wenna Zhao, Yingnan Wang, Liang Zhang, Shouchen Huang and Jixiang Lin

Microorganisms 2020, 8(3), 327; https://doi.org/10.3390/microorganisms8030327 - 26 Feb 2020

Cited by 36 | Viewed by 4000

Abstract

Soil alkalization is a major environmental threat that affects plant distribution and yield in northeastern China. Puccinellia tenuiflora is an alkali-tolerant grass species that is used for salt-alkali grassland restoration. However, little is known about the molecular mechanisms by which arbuscular mycorrhizal fungi [...] Read more.

Soil alkalization is a major environmental threat that affects plant distribution and yield in northeastern China. Puccinellia tenuiflora is an alkali-tolerant grass species that is used for salt-alkali grassland restoration. However, little is known about the molecular mechanisms by which arbuscular mycorrhizal fungi (AMF) enhance P. tenuiflora responses to alkali stress. Here, metabolite profiling in P. tenuiflora seedlings with or without arbuscular mycorrhizal fungi (AMF) under alkali stress was conducted using liquid chromatography combined with time-of-flight mass spectrometry (LC/TOF-MS). The results showed that AMF colonization increased seedling biomass under alkali stress. In addition, principal component analysis (PCA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) demonstrated that non-AM and AM seedlings showed different responses under alkali stress. A heat map analysis showed that the levels of 88 metabolites were significantly changed in non-AM seedlings, but those of only 31 metabolites were significantly changed in AM seedlings. Moreover, the levels of a total of 62 metabolites were significantly changed in P. tenuiflora seedlings after AMF inoculation. The results suggested that AMF inoculation significantly increased amino acid, organic acid, flavonoid and sterol contents to improve osmotic adjustment and maintain cell membrane stability under alkali stress. P. tenuiflora seedlings after AMF inoculation produced more plant hormones (salicylic acid and abscisic acid) than the non-AM seedlings, probably to enhance the antioxidant system and facilitate ion balance under stress conditions. In conclusion, these findings provide new insights into the metabolic mechanisms of P. tenuiflora seedlings with arbuscular mycorrhizal fungi under alkali conditions and clarify the role of AM in the molecular regulation of this species under alkali stress. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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15 pages, 2338 KiB

Open AccessArticle

A Potent Burkholderia Endophyte against Boxwood Blight Caused by Calonectria pseudonaviculata

by Ping Kong and Chuanxue Hong

Microorganisms 2020, 8(2), 310; https://doi.org/10.3390/microorganisms8020310 - 24 Feb 2020

Cited by 27 | Viewed by 3621

Abstract

Calonectria pseudonaviculata (Cps) poses an increasing threat to boxwood, a major nursery crop and iconic landscape plant worldwide. Here, we report on a potent biocontrol agent that produces small sage green (SSG) colonies on potato dextrose agar. SSG is a bacterial [...] Read more.

Calonectria pseudonaviculata (Cps) poses an increasing threat to boxwood, a major nursery crop and iconic landscape plant worldwide. Here, we report on a potent biocontrol agent that produces small sage green (SSG) colonies on potato dextrose agar. SSG is a bacterial strain recovered from Justin Brouwers boxwood leaves with unusual response to Cps inoculation. Water-soaked symptoms developed on leaves 2 days after inoculation then disappeared a few days later. This endophyte affected several major steps of the boxwood blight disease cycle. SSG at 10⁷ cfu/mL lysed all conidia in mixed broth culture. SSG at 10⁸ cfu/mL reduced blight incidence by >98% when applied one day before or 3 h after boxwood were inoculated with Cps. Its control efficacy decreased with decreasing bacterial concentration to 10³ cfu/mL and increasing lead time up to 20 days. When applied on diseased leaf litter under boxwood plants, SSG reduced Cps sporulation and consequently mitigated blight incidence by 90%. SSG was identified as a new member of the Burkholderia cepacia complex with distinct characters from known clinical strains. With these protective, curative, and sanitizing properties, this Burkholderia endophyte offers great promise for sustainable blight management at production and in the landscape. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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16 pages, 2684 KiB

Open AccessArticle

Bacterial Community Structure of Pinus Thunbergii Naturally Infected by the Nematode Bursaphelenchus Xylophilus

by Yang Ma, Zhao-Lei Qu, Bing Liu, Jia-Jin Tan, Fred O. Asiegbu and Hui Sun

Microorganisms 2020, 8(2), 307; https://doi.org/10.3390/microorganisms8020307 - 23 Feb 2020

Cited by 22 | Viewed by 3614

Abstract

Pine wilt disease (PWD) caused by the nematode Bursaphelenchus xylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function [...] Read more.

Pine wilt disease (PWD) caused by the nematode Bursaphelenchus xylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function in the needles, roots, and soil of diseased pine were studied under field conditions using Illumina MiSeq coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved states (PICRUSt) software. The results showed that the community and functional structure of healthy and diseased trees differed only in the roots and needles, respectively (p < 0.05). The needles, roots, and soil formed unique bacterial community and functional structures. The abundant phyla across all samples were Proteobacteria (41.9% of total sequence), Actinobacteria (29.0%), Acidobacteria (12.2%), Bacteroidetes (4.8%), and Planctomycetes (2.1%). The bacterial community in the healthy roots was dominated by Acidobacteria, Planctomycetes, and Rhizobiales, whereas in the diseased roots, Proteobacteria, Firmicutes, and Burkholderiales were dominant. Functionally, groups involved in the cell process and genetic information processing had a higher abundance in the diseased needles, which contributed to the difference in functional structure. The results indicate that PWD can only affect the host bacteria community structure and function in certain anatomical regions of the host tree. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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12 pages, 1629 KiB

Open AccessArticle

The Root Nodule Microbiome of Cultivated and Wild Halophytic Legumes Showed Similar Diversity but Distinct Community Structure in Yellow River Delta Saline Soils

by Yanfen Zheng, Jing Liang, Dong-Lin Zhao, Chen Meng, Zong-Chang Xu, Zhi-Hong Xie and Cheng-Sheng Zhang

Microorganisms 2020, 8(2), 207; https://doi.org/10.3390/microorganisms8020207 - 3 Feb 2020

Cited by 31 | Viewed by 5309

Abstract

Symbiotic associations between leguminous plants and their nodule microbiome play a key role in sustainable agriculture by facilitating the fixation of atmospheric nitrogen and enhancing plant stress resistance. This study aimed to decipher the root nodule microbiome of two halophytic legumes, Sesbania cannabina [...] Read more.

Symbiotic associations between leguminous plants and their nodule microbiome play a key role in sustainable agriculture by facilitating the fixation of atmospheric nitrogen and enhancing plant stress resistance. This study aimed to decipher the root nodule microbiome of two halophytic legumes, Sesbania cannabina and Glycine soja, which grow in saline soils of the Yellow River Delta, China, using PacBio’s circular consensus sequencing for full-length bacterial 16S rRNA gene to obtain finer taxonomic information. The cultivated legume Glycine max was used for comparison. We identified 18 bacterial genera and 55 species in nodule samples, which mainly classified to Proteobacteria, and rhizobial genus Ensifer was the predominant group. The three legumes showed similarity in operational taxonomic unit (OTU) diversity but distinction in OTU richness, indicating that they harbor similar bacterial species with different relative contents. The results of principal coordinates analysis and ANOSIM tests indicated that G. soja and G. max have similar nodule bacterial communities, and these communities differ from that of S. cannabina. Wild legumes S. cannabina and G. soja both harbored a higher number of rhizobia, while G. max possessed more non-rhizobial bacteria. These differences could be associated with their adaptability to saline–alkali stress and revealed clues on the nodule endophytes with relative importance of culturable rhizobial symbionts. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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15 pages, 2571 KiB

Open AccessArticle

Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota

by Zhiqiang Cheng, Shaonan Lei, Ye Li, Wei Huang, Rongqin Ma, Juan Xiong, Ting Zhang, Lingyue Jin, Hafeez ul Haq, Xiaohong Xu and Baoyu Tian

Microorganisms 2020, 8(2), 170; https://doi.org/10.3390/microorganisms8020170 - 25 Jan 2020

Cited by 43 | Viewed by 5838

Abstract

Microorganisms that colonize the plant rhizosphere can contribute to plant health, growth and productivity. Although the importance of the rhizosphere microbiome is known, we know little about the underlying mechanisms that drive microbiome assembly and composition. In this study, the variation, assembly and [...] Read more.

Microorganisms that colonize the plant rhizosphere can contribute to plant health, growth and productivity. Although the importance of the rhizosphere microbiome is known, we know little about the underlying mechanisms that drive microbiome assembly and composition. In this study, the variation, assembly and composition of rhizobacterial communities in 11 tomato cultivars, combined with one cultivar in seven different sources of soil and growing substrate, were systematically investigated. The tomato rhizosphere microbiota was dominated by bacteria from the phyla Proteobacteria, Bacteroidetes, and Acidobacteria, mainly comprising Rhizobiales, Xanthomonadales, Burkholderiales, Nitrosomonadales, Myxococcales, Sphingobacteriales, Cytophagales and Acidobacteria subgroups. The bacterial community in the rhizosphere microbiota of the samples in the cultivar experiment mostly overlapped with that of tomato cultivar MG, which was grown in five natural field soils, DM, JX, HQ, QS and XC. The results supported the hypothesis that tomato harbors largely conserved communities and compositions of rhizosphere microbiota that remains consistent in different cultivars of tomato and even in tomato cultivar grown in five natural field soils. However, significant differences in OTU richness (p < 0.0001) and bacterial diversity (p = 0.0014 < 0.01) were observed among the 7 different sources of soil and growing substrate. Two artificial commercial nutrient soils, HF and CF, resulted in a distinct tomato rhizosphere microbiota in terms of assembly and core community compared with that observed in natural field soils. PERMANOVA of beta diversity based on the combined data from the cultivar and soil experiments demonstrated that soil (growing substrate) and plant genotype (cultivar) had significant impacts on the rhizosphere microbial communities of tomato plants (soil, F = 22.29, R² = 0.7399, p < 0.001; cultivar, F = 2.04, R² = 0.3223, p = 0.008). Of these two factors, soil explained a larger proportion of the compositional variance in the tomato rhizosphere microbiota. The results demonstrated that the assembly process of rhizosphere bacterial communities was collectively influenced by soil, including the available bacterial sources and biochemical properties of the rhizosphere soils, and plant genotype. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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27 pages, 4283 KiB

Open AccessArticle

Effects of Foliar Treatment with a Trichoderma Plant Biostimulant Consortium on Passiflora caerulea L. Yield and Quality

by Tatiana Eugenia Şesan, Anca Olguța Oancea, Laura Mihaela Ştefan, Vasile Sorin Mănoiu, Marius Ghiurea, Iuliana Răut, Diana Constantinescu-Aruxandei, Agnes Toma, Simona Savin, Adriana Florina Bira, Cristian Mihai Pomohaci and Florin Oancea

Microorganisms 2020, 8(1), 123; https://doi.org/10.3390/microorganisms8010123 - 16 Jan 2020

Cited by 38 | Viewed by 10113

Abstract

The influence of spore concentration on the ability of a Trichoderma consortium to colonize the Passiflora caerulea phyllosphere was evaluated by determining the effects of foliar treatments with two spore concentrations, in two repeated treatments, on the morphological, physiological, and ultrastructural characteristics, and [...] Read more.

The influence of spore concentration on the ability of a Trichoderma consortium to colonize the Passiflora caerulea phyllosphere was evaluated by determining the effects of foliar treatments with two spore concentrations, in two repeated treatments, on the morphological, physiological, and ultrastructural characteristics, and on the yield and quality of P. caerulea. The studied crop quality features were related to its nutraceutical use: the accumulation of polyphenols and flavonoids, antioxidant activity, and effects on mouse fibroblast L929 cells. The Trichoderma consortium consisted of two strains, T. asperellum T36b and T. harzianum Td50b, and the concentrations used were 10⁶ colony forming units (cfu)/mL and 10⁸ cfu/mL. As a reference treatment, a commercial product that was based on herbs and algal extracts was used. As compared to the negative control, the treatment with the Trichoderma consortium at 10⁸ cfu/mL concentration determines the accumulation of higher level of polyphenols and flavonoids and increased antioxidant activity. This enhancement of P. caerulea quality characteristics after treatment with the higher concentration of Trichoderma consortium was associated with larger leaves, increased number and size of chloroplasts, improved plant physiology characteristics, and an increased yield. The treatment with high concentration of Trichoderma consortium spores promotes phyllosphere colonization and benefits both crop yield and quality. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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21 pages, 2914 KiB

Open AccessArticle

Identification of Differentially Expressed Proteins in Sugarcane in Response to Infection by Xanthomonas albilineans Using iTRAQ Quantitative Proteomics

by Jian-Yu Meng, Mbuya Sylvain Ntambo, Philippe C. Rott, Hua-Ying Fu, Mei-Ting Huang, Hui-Li Zhang and San-Ji Gao

Microorganisms 2020, 8(1), 76; https://doi.org/10.3390/microorganisms8010076 - 3 Jan 2020

Cited by 18 | Viewed by 3594

Abstract

Sugarcane can suffer severe yield losses when affected by leaf scald, a disease caused by Xanthomonas albilineans. This bacterial pathogen colonizes the vascular system of sugarcane, which can result in reduced plant growth and plant death. In order to better understand the [...] Read more.

Sugarcane can suffer severe yield losses when affected by leaf scald, a disease caused by Xanthomonas albilineans. This bacterial pathogen colonizes the vascular system of sugarcane, which can result in reduced plant growth and plant death. In order to better understand the molecular mechanisms involved in the resistance of sugarcane to leaf scald, a comparative proteomic study was performed with two sugarcane cultivars inoculated with X. albilineans: one resistant (LCP 85-384) and one susceptible (ROC20) to leaf scald. The iTRAQ (isobaric tags for relative and absolute quantification) approach at 0 and 48 h post-inoculation (hpi) was used to identify and annotate differentially expressed proteins (DEPs). A total of 4295 proteins were associated with 1099 gene ontology (GO) terms by GO analysis. Among those, 285 were DEPs during X. albilineans infection in cultivars LCP 85-384 and ROC20. One hundred seventy-two DEPs were identified in resistant cultivar LCP 85-384, and 113 of these proteins were upregulated and 59 were downregulated. One hundred ninety-two DEPs were found in susceptible cultivar ROC20 and half of these (92) were upregulated, whereas the other half corresponded to downregulated proteins. The significantly upregulated DEPs in LCP 85-384 were involved in metabolic pathways, the biosynthesis of secondary metabolites, and the phenylpropanoid biosynthesis pathway. Additionally, the expression of seven candidate genes related to photosynthesis and glycolytic pathways, plant innate immune system, glycosylation process, plant cytochrome P450, and non-specific lipid transfer protein was verified based on transcription levels in sugarcane during infection by X. albilineans. Our findings shed new light on the differential expression of proteins in sugarcane cultivars in response to infection by X. albilineans. The identification of these genes provides important information for sugarcane variety improvement programs using molecular breeding strategies. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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12 pages, 2208 KiB

Open AccessArticle

Enhancing the 1-Aminocyclopropane-1-Carboxylate Metabolic Rate of Pseudomonas sp. UW4 Intensifies Chemotactic Rhizocompetence

by Xiyang Gao, Tao Li, Wenliang Liu, Yan Zhang, Di Shang, Yuqian Gao, Yuancheng Qi and Liyou Qiu

Microorganisms 2020, 8(1), 71; https://doi.org/10.3390/microorganisms8010071 - 2 Jan 2020

Cited by 18 | Viewed by 3168

Abstract

1-aminocyclopropane-1-carboxylic acid (ACC) is a strong metabolism-dependent chemoattractant for the plant beneficial rhizobacterium Pseudomonas sp. UW4. It is unknown whether enhancing the metabolic rate of ACC can intensify the chemotaxis activity towards ACC and rhizocompetence. In this study, we selected four promoters to [...] Read more.

1-aminocyclopropane-1-carboxylic acid (ACC) is a strong metabolism-dependent chemoattractant for the plant beneficial rhizobacterium Pseudomonas sp. UW4. It is unknown whether enhancing the metabolic rate of ACC can intensify the chemotaxis activity towards ACC and rhizocompetence. In this study, we selected four promoters to transcribe the UW4 ACC deaminase (AcdS) gene in the UW4 ΔAcdS mutant. PA is the UW4 AcdS gene promoter, PB20, PB10 and PB1 are synthetic promoters. The order of the AcdS gene expression level and AcdS activity of the four strains harboring the promoters were PB20 > PA > PB10 > PB1. Interestingly, the AcdS activity of the four strains and their parent strain UW4 was significantly positively correlated with their chemotactic activity towards ACC, rhizosphere colonization, roots elongation and dry weight promotion. The results released that enhancing the AcdS activity of PGPRenable them to achieve strong chemotactic responses to ACC, rhizocompetence and plant growth promotion. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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23 pages, 1572 KiB

Open AccessArticle

Deciphering the Symbiotic Significance of Quorum Sensing Systems of Sinorhizobium fredii HH103

by Sebastián Acosta-Jurado, Cynthia Alías-Villegas, Andrés Almozara, M. Rosario Espuny, José-María Vinardell and Francisco Pérez-Montaño

Microorganisms 2020, 8(1), 68; https://doi.org/10.3390/microorganisms8010068 - 2 Jan 2020

Cited by 9 | Viewed by 3152

Abstract

Quorum sensing (QS) is a bacterial cell-to-cell signaling mechanism that collectively regulates and synchronizes behaviors by means of small diffusible chemical molecules. In rhizobia, QS systems usually relies on the synthesis and detection of N-acyl-homoserine lactones (AHLs). In the model bacterium Sinorhizobium [...] Read more.

Quorum sensing (QS) is a bacterial cell-to-cell signaling mechanism that collectively regulates and synchronizes behaviors by means of small diffusible chemical molecules. In rhizobia, QS systems usually relies on the synthesis and detection of N-acyl-homoserine lactones (AHLs). In the model bacterium Sinorhizobium meliloti functions regulated by the QS systems TraI-TraR and SinI-SinR(-ExpR) include plasmid transfer, production of surface polysaccharides, motility, growth rate and nodulation. These systems are also present in other bacteria of the Sinorhizobium genus, with variations at the species and strain level. In Sinorhizobium fredii NGR234 phenotypes regulated by QS are plasmid transfer, growth rate, sedimentation, motility, biofilm formation, EPS production and copy number of the symbiotic plasmid (pSym). The analysis of the S. fredii HH103 genomes reveal also the presence of both QS systems. In this manuscript we characterized the QS systems of S. fredii HH103, determining that both TraI and SinI AHL-synthases proteins are responsible of the production of short- and long-chain AHLs, respectively, at very low and not physiological concentrations. Interestingly, the main HH103 luxR-type genes, expR and traR, are split into two ORFs, suggesting that in S. fredii HH103 the corresponding carboxy-terminal proteins, which contain the DNA-binding motives, may control target genes in an AHL-independent manner. The presence of a split traR gene is common in other S. fredii strains. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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16 pages, 1800 KiB

Open AccessArticle

Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota

by Matteo Chialva, Stefano Ghignone, Mara Novero, Wael N. Hozzein, Luisa Lanfranco and Paola Bonfante

Microorganisms 2020, 8(1), 38; https://doi.org/10.3390/microorganisms8010038 - 24 Dec 2019

Cited by 14 | Viewed by 4966

Abstract

Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early “omics” experiments focused mainly on the species composition of microbial [...] Read more.

Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early “omics” experiments focused mainly on the species composition of microbial communities, new “meta-omics” approaches such as meta-transcriptomics provide hints about the functions of the microbes when interacting with their plant host. Here, we used an RNA-seq dataset previously generated for tomato (Solanum lycopersicum) plants growing on different native soils to test the hypothesis that host-targeted transcriptomics can detect the taxonomic and functional diversity of root microbiota. Even though the sequencing throughput for the microbial populations was limited, we were able to reconstruct the microbial communities and obtain an overview of their functional diversity. Comparisons of the host transcriptome and the meta-transcriptome suggested that the composition and the metabolic activities of the microbiota shape plant responses at the molecular level. Despite the limitations, mining available next-generation sequencing datasets can provide unexpected results and potential benefits for microbiota research. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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19 pages, 2359 KiB

Open AccessArticle

Global Gene Responses of Resistant and Susceptible Sugarcane Cultivars to Acidovorax avenae subsp. avenae Identified Using Comparative Transcriptome Analysis

by Na Chu, Jing-Ru Zhou, Hua-Ying Fu, Mei-Ting Huang, Hui-Li Zhang and San-Ji Gao

Microorganisms 2020, 8(1), 10; https://doi.org/10.3390/microorganisms8010010 - 19 Dec 2019

Cited by 20 | Viewed by 3375

Abstract

Red stripe disease in sugarcane caused by Acidovorax avenae subsp. avenae (Aaa) is related to serious global losses in yield. However, the underlying molecular mechanisms associated with responses of sugarcane plants to infection by this pathogen remain largely unknown. Here, we [...] Read more.

Red stripe disease in sugarcane caused by Acidovorax avenae subsp. avenae (Aaa) is related to serious global losses in yield. However, the underlying molecular mechanisms associated with responses of sugarcane plants to infection by this pathogen remain largely unknown. Here, we used Illumina RNA-sequencing (RNA-seq) to perform large-scale transcriptome sequencing of two sugarcane cultivars to contrast gene expression patterns of plants between Aaa and mock inoculations, and identify key genes and pathways involved in sugarcane defense responses to Aaa infection. At 0–72 hours post-inoculation (hpi) of the red stripe disease-resistant cultivar ROC22, a total of 18,689 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples. Of these, 8498 and 10,196 genes were up- and downregulated, respectively. In MT11-610, which is susceptible to red stripe disease, 15,782 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples and 8807 and 6984 genes were up- and downregulated, respectively. The genes that were differentially expressed following Aaa inoculation were mainly involved in photosynthesis and carbon metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and plant–pathogen interaction pathways. Further, qRT-PCR and RNA-seq used for additional validation of 12 differentially expressed genes (DEGs) showed that eight genes in particular were highly expressed in ROC22. These eight genes participated in the biosynthesis of lignin and coumarin, as well as signal transduction by salicylic acid, jasmonic acid, ethylene, and mitogen-activated protein kinase (MAPK), suggesting that they play essential roles in sugarcane resistance to Aaa. Collectively, our results characterized the sugarcane transcriptome during early infection with Aaa, thereby providing insights into the molecular mechanisms responsible for bacterial tolerance. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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16 pages, 3899 KiB

Open AccessArticle

Biochar Suppresses Bacterial Wilt of Tomato by Improving Soil Chemical Properties and Shifting Soil Microbial Community

by Yang Gao, Yang Lu, Weipeng Lin, Jihui Tian and Kunzheng Cai

Microorganisms 2019, 7(12), 676; https://doi.org/10.3390/microorganisms7120676 - 10 Dec 2019

Cited by 39 | Viewed by 4987

Abstract

The role of biochar amendments in enhancing plant disease resistance has been well documented, but its mechanism is not yet fully understood. In the present study, 2% biochar made from wheat straw was added to the soil of tomato infected by Ralstonia solanacearum [...] Read more.

The role of biochar amendments in enhancing plant disease resistance has been well documented, but its mechanism is not yet fully understood. In the present study, 2% biochar made from wheat straw was added to the soil of tomato infected by Ralstonia solanacearum to explore the interrelation among biochar, tomato bacterial wilt resistance, soil chemical properties, and soil microbial community and to decipher the disease suppression mechanisms from a soil microbial perspective. Biochar application significantly reduced the disease severity of bacterial wilt, increased soil total organic carbon, total nitrogen, C:N ratio, organic matter, available P, available K, pH, and electrical conductivity. Biochar treatment also increased soil acid phosphatase activity under the non-R.-solanacearum-inoculated condition. High-throughput sequencing of 16S rRNA revealed substantial differences in rhizosphere bacterial community structures between biochar-amended and nonamended treatments. Biochar did not influence soil microbial richness and diversity but significantly increased the relative abundance of Bacteroidetes and Proteobacteria in soil at the phylum level under R. solanacearum inoculation. Furthermore, biochar amendment harbored a higher abundance of Chitinophaga, Flavitalea, Adhaeribacter, Pontibacter, Pedobacter, and Ohtaekwangia at the genus level of Bacteroides and Pseudomonas at the genus level of Proteobacteria under R. solanacearum inoculation. Our findings suggest that a biochar-shifted soil bacterial community structure can favorably contribute to the resistance of tomato plants against bacterial wilt. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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22 pages, 1584 KiB

Open AccessArticle

Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew

by Luca Nerva, Chiara Pagliarani, Massimo Pugliese, Matteo Monchiero, Solène Gonthier, Maria Lodovica Gullino, Giorgio Gambino and Walter Chitarra

Microorganisms 2019, 7(12), 662; https://doi.org/10.3390/microorganisms7120662 - 7 Dec 2019

Cited by 21 | Viewed by 4108

Abstract

The reduction of antimicrobial treatments and mainly the application of environmentally friendly compounds, such as resistance elicitors, is an impelling challenge to undertake more sustainable agriculture. We performed this research to study the effectiveness of non-conventional compounds in reducing leaf fungal attack and [...] Read more.

The reduction of antimicrobial treatments and mainly the application of environmentally friendly compounds, such as resistance elicitors, is an impelling challenge to undertake more sustainable agriculture. We performed this research to study the effectiveness of non-conventional compounds in reducing leaf fungal attack and to investigate whether they influence the grape phyllosphere. Pathogenicity tests were conducted on potted Vitis vinifera “Nebbiolo” and “Moscato” cultivars infected with the powdery mildew agent (Erysiphe necator) and treated with three elicitors. Differences in the foliar microbial community were then evaluated by community-level physiological profiling by using Biolog^TM EcoPlates, high throughput sequencing of the Internal Transcribed Spacer (ITS) region, and RNA sequencing for the viral community. In both cultivars, all products were effective as they significantly reduced pathogen development. EcoPlate analysis and ITS sequencing showed that the microbial communities were not influenced by the alternative compound application, confirming their specific activity as plant defense elicitors. Nevertheless, “Moscato” plants were less susceptible to the disease and presented different phyllosphere composition, resulting in a richer viral community, when compared with the “Nebbiolo” plants. The observed effect on microbial communities pointed to the existence of distinct genotype-specific defense mechanisms independently of the elicitor application. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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21 pages, 2659 KiB

Open AccessArticle

Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities

by Ratna Prabha, Dhananjaya P. Singh, Shailendra Gupta, Vijai Kumar Gupta, Hesham A. El-Enshasy and Mukesh K. Verma

Microorganisms 2019, 7(12), 608; https://doi.org/10.3390/microorganisms7120608 - 23 Nov 2019

Cited by 21 | Viewed by 6267

Abstract

Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum [...] Read more.

Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum scrobiculatum L.(kodo millet) rhizopshere revealed taxonomic communities with functional capabilities linked to support growth and development of the plants under nutrient-deprived, semi-arid and dry biotic conditions. Among 65 taxonomically diverse phyla identified in the rhizobiome, Actinobacteria were the most abundant followed by the Proteobacteria. Functions identified for different genes/proteins led to revelations that multifunctional rhizobiome performs several metabolic functions including carbon fixation, nitrogen, phosphorus, sulfur, iron and aromatic compound metabolism, stress response, secondary metabolite synthesis and virulence, disease, and defense. Abundance of genes linked with N, P, S, Fe and aromatic compound metabolism and phytohormone synthesis—along with other prominent functions—clearly justifies growth, development, and survival of the plants under nutrient deprived dry environment conditions. The dominance of actinobacteria, the known antibiotic producing communities shows that the kodo rhizobiome possesses metabolic capabilities to defend themselves against biotic stresses. The study opens avenues to revisit multi-functionalities of the crop rhizosphere for establishing link between taxonomic abundance and targeted functions that help plant growth and development in stressed and nutrient deprived soil conditions. It further helps in understanding the role of rhizosphere microbiome in adaptation and survival of plants in harsh abiotic conditions. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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17 pages, 3290 KiB

Open AccessArticle

The Type III Accessory Protein HrpE of Xanthomonas oryzae pv. oryzae Surpasses the Secretion Role, and Enhances Plant Resistance and Photosynthesis

by Taha Majid Mahmood Sheikh, Liyuan Zhang, Muhammad Zubair, Alvina Hanif, Ping Li, Ayaz Farzand, Haider Ali, Muhammad Saqib Bilal, Yiqun Hu, Xiaochen Chen, Congfeng Song, Hansong Dong and Meixiang Zhang

Microorganisms 2019, 7(11), 572; https://doi.org/10.3390/microorganisms7110572 - 18 Nov 2019

Cited by 7 | Viewed by 4505

Abstract

Many species of plant-pathogenic gram-negative bacteria deploy the type III (T3) secretion system to secrete virulence components, which are mostly characteristic of protein effectors targeting the cytosol of the plant cell following secretion. Xanthomonas oryzae pv. oryzae (Xoo), a rice pathogen [...] Read more.

Many species of plant-pathogenic gram-negative bacteria deploy the type III (T3) secretion system to secrete virulence components, which are mostly characteristic of protein effectors targeting the cytosol of the plant cell following secretion. Xanthomonas oryzae pv. oryzae (Xoo), a rice pathogen causing bacterial blight disease, uses the T3 accessory protein HrpE to assemble the pilus pathway, which in turn secretes transcription activator-like (TAL) effectors. The hrpE gene can execute extensive physiological and pathological functions beyond effector secretion. As evidenced in this study, when the hrpE gene was deleted from the Xoo genome, the bacteria incur seriouimpairments in multiplication, motility, and virulence. The virulence nullification is attributed to reduced secretion and translocation of PthXo1, which is a TAL effector that determines the bacterial virulence in the susceptible rice varieties. When the HrpE protein produced by prokaryotic expression is applied to plants, the recombinant protein is highly effective at inducing the defense response. Moreover, leaf photosynthesis efficiency is enhanced in HrpE-treated plants. These results provide experimental avenues to modulate the plant defense and growth tradeoff by manipulating a bacterial T3 accessory protein. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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17 pages, 2281 KiB

Open AccessArticle

Distinct Microbial Community of Phyllosphere Associated with Five Tropical Plants on Yongxing Island, South China Sea

by Lijun Bao, Wenyang Cai, Xiaofen Zhang, Jinhong Liu, Hao Chen, Yuansong Wei, Xiuxiu Jia and Zhihui Bai

Microorganisms 2019, 7(11), 525; https://doi.org/10.3390/microorganisms7110525 - 4 Nov 2019

Cited by 17 | Viewed by 5110

Abstract

The surfaces of a leaf are unique and wide habitats for a microbial community. These microorganisms play a key role in plant growth and adaptation to adverse conditions, such as producing growth factors to promote plant growth and inhibiting pathogens to protect host [...] Read more.

The surfaces of a leaf are unique and wide habitats for a microbial community. These microorganisms play a key role in plant growth and adaptation to adverse conditions, such as producing growth factors to promote plant growth and inhibiting pathogens to protect host plants. The composition of microbial communities very greatly amongst different plant species, yet there is little data on the composition of the microbiome of the host plants on the coral island in the South China Sea. In this study, we investigated the abundances and members of a major microbial community (fungi, bacteria, and diazotrophs) on the leaves of five dominant plant species (Ipomoea pes-caprae, Wedelia chinensis, Scaevola sericea, Cocos nucifera, and Sesuvium portulacastrum) on the island using real-time quantitative polymerase chain reaction (PCR) and high-throughput amplicon sequencing. Quantitative PCR results showed that fungi and bacteria were ubiquitous and variable among different host plants. Scaevola sericea showed the lowest absolute abundance and highest diversity of fungi and bacteria, while Cocos nucifera had the lowest abundance and the highest diversity of diazotrophs compare to the other four plants. There was a small proportion of shared microorganisms among the five different plants, while unique fungi, bacteria and diazotrophs were significantly enriched for different host plant species in this study (p < 0.05). Some of the most abundant organisms found in the communities of these different host plants are involved in important biogeochemical cycles that can benefit their host, including carbon and nitrogen cycles. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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19 pages, 2234 KiB

Open AccessArticle

Bacterial Consortium for Improved Maize (Zea mays L.) Production

by Oluwaseyi Samuel Olanrewaju and Olubukola Oluranti Babalola

Microorganisms 2019, 7(11), 519; https://doi.org/10.3390/microorganisms7110519 - 1 Nov 2019

Cited by 52 | Viewed by 6463

Abstract

The ever-increasing human population is a major concern for food security. Maize is the third largest most important food crop. The major problems of cultivation arise from urbanization and land pollution. This reduces the amount of land available for agriculture. The use of [...] Read more.

The ever-increasing human population is a major concern for food security. Maize is the third largest most important food crop. The major problems of cultivation arise from urbanization and land pollution. This reduces the amount of land available for agriculture. The use of chemicals in agriculture is not environmentally friendly. Thus, plant growth-promoting bacteria (PGPB) have been proposed as alternatives. This study aims to test the growth-promoting effect of maize inoculated with six indigenous PGPB isolates. These isolates were assayed for various biochemical and plant growth-promoting activities. They were also assayed for biocontrol activities. Based on the results, six isolates viz A1, A18, A29, NWU4, NWU14, and NWU198 were used to inoculate maize seeds. The inoculated seeds were tried out on the field. A randomized block design was used. PGPB used were in single, consortia of two, and three organisms. The length of the leaves, roots, and stem, plant height, numbers of leaves, and weight of 100 seeds were taken at the fourth and eighth weeks after planting. Microbial consortia increased growth parameters compared to single inoculant treatments. Thus, they can be of advantage in the eradication of low yield. They can also serve as reliable alternatives to chemical fertilizers. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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18 pages, 1642 KiB

Open AccessArticle

Responses of Rhizosphere Fungal Communities to the Sewage Sludge Application into the Soil

by Katarína Ondreičková, Marcela Gubišová, Michaela Piliarová, Miroslav Horník, Pavel Matušinský, Jozef Gubiš, Lenka Klčová, Martina Hudcovicová and Ján Kraic

Microorganisms 2019, 7(11), 505; https://doi.org/10.3390/microorganisms7110505 - 29 Oct 2019

Cited by 15 | Viewed by 3236

Abstract

Due to the increasing sewage sludge production in the world and problems with its disposal, an application of sludge to the soil appears to be a suitable solution considering its fertilizer properties and ability to improve the soil physical conditions. On the other [...] Read more.

Due to the increasing sewage sludge production in the world and problems with its disposal, an application of sludge to the soil appears to be a suitable solution considering its fertilizer properties and ability to improve the soil physical conditions. On the other hand, the sludge may also contain undesirable and toxic substances. Since soil microorganisms are sensitive to environmental changes, they can be used as indicators of soil quality. In this study, we used sewage sludge (SS) from two municipal wastewater treatment plants (SS-A and SS-B) in the dose of 5 t/ha and 15 t/ha in order to determine possible changes in the fungal community diversity, especially arbuscular mycorrhizal fungi (AMF), in the rhizosphere of Arundo donax L. Rhizosphere samples were collected in summer and autumn for two consecutive years and the fungal diversity was examined using terminal restriction fragment length polymorphism and 18S rDNA sequencing. Fungal alpha diversity was more affected by SS-A than SS-B probably due to the higher heavy metal content. However, based on principal component analysis and ANOSIM, significant changes in overall fungal diversity were not observed. Simultaneously, 18S rDNA sequencing showed that more various fungal taxa were detected in the sample with sewage sludge than in the control. Glomus sp. as a representative of AMF was the most represented. Moreover, Funneliformis in both samples and Rhizophagus in control with Septoglomus in the sludge sample were other representatives of AMF. Our results indicate that the short-term sewage sludge application into the soil does not cause a shift in the fungal community composition. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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18 pages, 2255 KiB

Open AccessArticle

Phylogenetic Analyses of Xanthomonads Causing Bacterial Leaf Spot of Tomato and Pepper: Xanthomonas euvesicatoria Revealed Homologous Populations Despite Distant Geographical Distribution

by Upasana Dhakal, Shefali Dobhal, Anne M. Alvarez and Mohammad Arif

Microorganisms 2019, 7(10), 462; https://doi.org/10.3390/microorganisms7100462 - 16 Oct 2019

Cited by 9 | Viewed by 4025

Abstract

Bacterial leaf spot of tomato and pepper (BLS), an economically important bacterial disease caused by four species of Xanthomonas (X. euvesicatoria (Xe), X. vesicatoria (Xv), X. gardneri (Xg), and X. perforans (Xp)), is a [...] Read more.

Bacterial leaf spot of tomato and pepper (BLS), an economically important bacterial disease caused by four species of Xanthomonas (X. euvesicatoria (Xe), X. vesicatoria (Xv), X. gardneri (Xg), and X. perforans (Xp)), is a global problem and can cause over 50% crop loss under unfavorable conditions. Among the four species, Xe and Xv are prevalent worldwide. Characterization of the pathogens is crucial for disease management and regulatory purposes. In this study, we performed a multilocus sequence analysis (MLSA) with six genes (hrcN, dnaA gyrB, gapA, pdg, and hmbs) on BLS strains. Other Xanthomonas species were included to determine phylogenetic relationships within and among the tested strains. Four BLS species comprising 76 strains from different serological groups and diverse geographical locations were resolved into three major clades. BLS xanthomonads formed distinct clusters in the phylogenetic analyses. Three other xanthomonads, including X. albilineans, X. sacchari, and X. translucens pv. undolusa revealed less than 85%, 88%, and 89% average nucleotide identity (ANI), respectively, with the other species of Xanthomonas included in this study. Both antibody and MLSA data showed that Xv was clearly separated from Xe and that the latter strains were remarkably clonal, even though they originated from distant geographical locations. The Xe strains formed two separate phylogenetic groups; Xe group A1 consisted only of tomato strains, whereas Xe group A2 included strains from pepper and tomato. In contrast, the Xv group showed greater heterogeneity. Some Xv strains from South America were closely related to strains from California, while others grouped closer to a strain from Indiana and more distantly to a strain from Hawaii. Using this information molecular tests can now be devised to track distribution of clonal populations that may be introduced into new geographic areas through seeds and other infected plant materials. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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12 pages, 2415 KiB

Open AccessArticle

One Small RNA of Fusarium graminearum Targets and Silences CEBiP Gene in Common Wheat

by Jiao Jian and Xu Liang

Microorganisms 2019, 7(10), 425; https://doi.org/10.3390/microorganisms7100425 - 9 Oct 2019

Cited by 25 | Viewed by 3980

Abstract

The pathogenic fungus Fusarium graminearum (F. graminearum), causing Fusarium head blight (FHB) or scab, is one of the most important cereal killers worldwide, exerting great economic and agronomic losses on global grain production. To repress pathogen invasion, plants have evolved a [...] Read more.

The pathogenic fungus Fusarium graminearum (F. graminearum), causing Fusarium head blight (FHB) or scab, is one of the most important cereal killers worldwide, exerting great economic and agronomic losses on global grain production. To repress pathogen invasion, plants have evolved a sophisticated innate immunity system for pathogen recognition and defense activation. Simultaneously, pathogens continue to evolve more effective means of invasion to conquer plant resistance systems. In the process of co-evolution of plants and pathogens, several small RNAs (sRNAs) have been proved in regulating plant immune response and plant-microbial interaction. In this study, we report that a F. graminearum sRNA (Fg-sRNA1) can suppress wheat defense response by targeting and silencing a resistance-related gene, which codes a Chitin Elicitor Binding Protein (TaCEBiP). Transcriptional level evidence indicates that Fg-sRNA1 can target TaCEBiP mRNA and trigger silencing of TaCEBiP in vivo, and in Nicotiana benthamiana (N. benthamiana) plants, Western blotting experiments and YFP Fluorescence observation proofs show that Fg-sRNA1 can suppress the accumulation of protein coding by TaCEBiP gene in vitro. F. graminearum PH-1 strain displays a weakening ability to invasion when Barley stripe mosaic virus (BSMV) vector induces effective silencing Fg-sRNA1 in PH-1 infected wheat plants. Taken together, our results suggest that a small RNA from F. graminearum can target and silence the wheat TaCEBiP gene to enhance invasion of F. graminearum. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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19 pages, 952 KiB

Open AccessArticle

Genome Insights into the Novel Species Microvirga brassicacearum, a Rapeseed Endophyte with Biotechnological Potential

by Alejandro Jiménez-Gómez, Zaki Saati-Santamaría, José M. Igual, Raúl Rivas, Pedro F. Mateos and Paula García-Fraile

Microorganisms 2019, 7(9), 354; https://doi.org/10.3390/microorganisms7090354 - 14 Sep 2019

Cited by 28 | Viewed by 5150

Abstract

Plants harbor a diversity of microorganisms constituting the plant microbiome. Many bioinoculants for agricultural crops have been isolated from plants. Nevertheless, plants are an underexplored niche for the isolation of microorganisms with other biotechnological applications. As a part of a collection of canola [...] Read more.

Plants harbor a diversity of microorganisms constituting the plant microbiome. Many bioinoculants for agricultural crops have been isolated from plants. Nevertheless, plants are an underexplored niche for the isolation of microorganisms with other biotechnological applications. As a part of a collection of canola endophytes, we isolated strain CDVBN77^T. Its genome sequence shows not only plant growth-promoting (PGP) mechanisms, but also genetic machinery to produce secondary metabolites, with potential applications in the pharmaceutical industry, and to synthesize hydrolytic enzymes, with potential applications in biomass degradation industries. Phylogenetic analysis of the 16S rRNA gene of strain CDVBN77^T shows that it belongs to the genus Microvirga, its closest related species being M. aerophila DSM 21344^T (97.64% similarity) and M. flavescens c27j1^T (97.50% similarity). It contains ubiquinone 10 as the predominant quinone, C19:0 cycloω8c and summed feature 8 as the major fatty acids, and phosphatidylcholine and phosphatidylethanolamine as the most abundant polar lipids. Its genomic DNA G+C content is 62.3 (mol %). Based on phylogenetic, chemotaxonomic, and phenotypic analyses, we suggest the classification of strain CDVBN77^T within a new species of the genus Microvirga and propose the name Microvirga brassicacearum sp. nov. (type strain CDVBN77^T = CECT 9905^T = LMG 31419^T). Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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17 pages, 3836 KiB

Open AccessArticle

Identification and Functional Analysis of NLP-Encoding Genes from the Postharvest Pathogen Penicillium expansum

by Elena Levin, Ginat Raphael, Jing Ma, Ana-Rosa Ballester, Oleg Feygenberg, John Norelli, Radi Aly, Luis Gonzalez-Candelas, Michael Wisniewski and Samir Droby

Microorganisms 2019, 7(6), 175; https://doi.org/10.3390/microorganisms7060175 - 15 Jun 2019

Cited by 25 | Viewed by 4825

Abstract

Penicillium expansum is a major postharvest pathogen that infects different fruits, mainly through injuries inflicted during harvest or subsequent handling after harvest. Several effectors were suggested to mediate pathogenicity of P. expansum in fruit tissue. Among these effectors Nep1-like proteins (NLPs), produced by [...] Read more.

Penicillium expansum is a major postharvest pathogen that infects different fruits, mainly through injuries inflicted during harvest or subsequent handling after harvest. Several effectors were suggested to mediate pathogenicity of P. expansum in fruit tissue. Among these effectors Nep1-like proteins (NLPs), produced by various microorganisms with different lifestyles, are known for their ability to induce necrosis in dicot plants and were shown to be involved in virulence of several plant-related pathogens. This study was aimed at the identification and functional characterization of two NLP genes found in the genome of P. expansum. The genes were designated Penlp1 and Penlp2 and were found to code type1 and type3 NLP respectively. Necrosis-inducing activity of the two proteins was demonstrated by transient expression in Nicotiana benthamiana leaves. While Penlp1 expression was induced during apple infection and in liquid culture, the highest level of Penlp2 expression was found in ungerminated spores. Deletion of Penlp1, but not Penlp2, resulted in reduced virulence on apples manifested by reduced rate of lesion development (disease severity). Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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13 pages, 3693 KiB

Open AccessArticle

The Gene Encoding NAD-Dependent Epimerase/Dehydratase, wcaG, Affects Cell Surface Properties, Virulence, and Extracellular Enzyme Production in the Soft Rot Phytopathogen, Pectobacterium carotovorum

by Rabiul Islam, Shyretha Brown, Ali Taheri and C. Korsi Dumenyo

Microorganisms 2019, 7(6), 172; https://doi.org/10.3390/microorganisms7060172 - 13 Jun 2019

Cited by 18 | Viewed by 5002

Abstract

Pectobacterium carotovorum is a gram-negative bacterium that, together with other soft rot Enterobacteriaceae causes soft rot disease in vegetables, fruits, and ornamental plants through the action of exoproteins including plant cell wall-degrading enzymes (PCWDEs). Although pathogenicity in these bacteria is complex, virulence levels [...] Read more.

Pectobacterium carotovorum is a gram-negative bacterium that, together with other soft rot Enterobacteriaceae causes soft rot disease in vegetables, fruits, and ornamental plants through the action of exoproteins including plant cell wall-degrading enzymes (PCWDEs). Although pathogenicity in these bacteria is complex, virulence levels are proportional to the levels of plant cell wall-degrading exoenzymes (PCWDEs) secreted. Two low enzyme-producing transposon Tn5 mutants were isolated, and compared to their parent KD100, the mutants were less virulent on celery petioles and carrot disks. The inactivated gene responsible for the reduced virulence phenotype in both mutants was identified as wcaG. The gene, wcaG (previously denoted fcl) encodes NAD-dependent epimerase/dehydratase, a homologue of GDP-fucose synthetase of Escherichia coli. In Escherichia coli, GDP-fucose synthetase is involved in the biosynthesis of the exopolysaccharide, colanic acid (CA). The wcaG mutants of P. carotovorum formed an enhanced level of biofilm in comparison to their parent. In the hydrophobicity test the mutants showed more hydrophobicity than the parent in hexane and hexadecane as solvents. Complementation of the mutants with extrachromosomal copies of the wild type gene restored these functions to parental levels. These data indicate that NAD-dependent epimerase/dehydratase plays a vital rule in cell surface properties, exoenzyme production, and virulence in P. carotovorum. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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Review

Jump to: Research, Other

18 pages, 972 KiB

Open AccessReview

Citrus Postharvest Green Mold: Recent Advances in Fungal Pathogenicity and Fruit Resistance

by Yulin Cheng, Yunlong Lin, Haohao Cao and Zhengguo Li

Microorganisms 2020, 8(3), 449; https://doi.org/10.3390/microorganisms8030449 - 23 Mar 2020

Cited by 60 | Viewed by 7066

Abstract

As the major postharvest disease of citrus fruit, postharvest green mold is caused by the necrotrophic fungus Penicillium digitatum (Pd), which leads to huge economic losses worldwide. Fungicides are still the main method currently used to control postharvest green mold in [...] Read more.

As the major postharvest disease of citrus fruit, postharvest green mold is caused by the necrotrophic fungus Penicillium digitatum (Pd), which leads to huge economic losses worldwide. Fungicides are still the main method currently used to control postharvest green mold in citrus fruit storage. Investigating molecular mechanisms of plant–pathogen interactions, including pathogenicity and plant resistance, is crucial for developing novel and safer strategies for effectively controlling plant diseases. Despite fruit–pathogen interactions remaining relatively unexplored compared with well-studied leaf–pathogen interactions, progress has occurred in the citrus fruit–Pd interaction in recent years, mainly due to their genome sequencing and establishment or optimization of their genetic transformation systems. Recent advances in Pd pathogenicity on citrus fruit and fruit resistance against Pd infection are summarized in this review. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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23 pages, 1279 KiB

Open AccessReview

Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria

by Marta Robledo, Natalia I. García-Tomsig and José I. Jiménez-Zurdo

Microorganisms 2020, 8(3), 384; https://doi.org/10.3390/microorganisms8030384 - 10 Mar 2020

Cited by 13 | Viewed by 4587

Abstract

Small non-coding RNAs (sRNAs) are ubiquitous components of bacterial adaptive regulatory networks underlying stress responses and chronic intracellular infection of eukaryotic hosts. Thus, sRNA-mediated regulation of gene expression is expected to play a major role in the establishment of mutualistic root nodule endosymbiosis [...] Read more.

Small non-coding RNAs (sRNAs) are ubiquitous components of bacterial adaptive regulatory networks underlying stress responses and chronic intracellular infection of eukaryotic hosts. Thus, sRNA-mediated regulation of gene expression is expected to play a major role in the establishment of mutualistic root nodule endosymbiosis between nitrogen-fixing rhizobia and legume plants. However, knowledge about this level of genetic regulation in this group of plant-interacting bacteria is still rather scarce. Here, we review insights into the rhizobial non-coding transcriptome and sRNA-mediated post-transcriptional regulation of symbiotic relevant traits such as nutrient uptake, cell cycle, quorum sensing, or nodule development. We provide details about the transcriptional control and protein-assisted activity mechanisms of the functionally characterized sRNAs involved in these processes. Finally, we discuss the forthcoming research on riboregulation in legume symbionts. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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17 pages, 2748 KiB

Open AccessReview

Impact of Cover Crops on the Soil Microbiome of Tree Crops

by Antonio Castellano-Hinojosa and Sarah L. Strauss

Microorganisms 2020, 8(3), 328; https://doi.org/10.3390/microorganisms8030328 - 26 Feb 2020

Cited by 47 | Viewed by 9096

Abstract

Increased concerns associated with interactions between herbicides, inorganic fertilizers, soil nutrient availability, and plant phytotoxicity in perennial tree crop production systems have renewed interest in the use of cover crops in the inter-row middles or between trees as an alternative sustainable management strategy [...] Read more.

Increased concerns associated with interactions between herbicides, inorganic fertilizers, soil nutrient availability, and plant phytotoxicity in perennial tree crop production systems have renewed interest in the use of cover crops in the inter-row middles or between trees as an alternative sustainable management strategy for these systems. Although interactions between the soil microbiome and cover crops have been examined for annual cropping systems, there are critical differences in management and growth in perennial cropping systems that can influence the soil microbiome and, therefore, the response to cover crops. Here, we discuss the importance of cover crops in tree cropping systems using multispecies cover crop mixtures and minimum tillage and no-tillage to not only enhance the soil microbiome but also carbon, nitrogen, and phosphorus cycling compared to monocropping, conventional tillage, and inorganic fertilization. We also identify potentially important taxa and research gaps that need to be addressed to facilitate assessments of the relationships between cover crops, soil microbes, and the health of tree crops. Additional evaluations of the interactions between the soil microbiome, cover crops, nutrient cycling, and tree performance will allow for more effective and sustainable management of perennial cropping systems. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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32 pages, 4059 KiB

Open AccessReview

Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era

by Rahul Mahadev Shelake, Dibyajyoti Pramanik and Jae-Yean Kim

Microorganisms 2019, 7(8), 269; https://doi.org/10.3390/microorganisms7080269 - 17 Aug 2019

Cited by 88 | Viewed by 20451

Abstract

Plants and microbes are co-evolved and interact with each other in nature. Plant-associated microbes, often referred to as plant microbiota, are an integral part of plant life. Depending on the health effects on hosts, plant–microbe (PM) interactions are either beneficial or harmful. The [...] Read more.

Plants and microbes are co-evolved and interact with each other in nature. Plant-associated microbes, often referred to as plant microbiota, are an integral part of plant life. Depending on the health effects on hosts, plant–microbe (PM) interactions are either beneficial or harmful. The role of microbiota in plant growth promotion (PGP) and protection against various stresses is well known. Recently, our knowledge of community composition of plant microbiome and significant driving factors have significantly improved. So, the use of plant microbiome is a reliable approach for a next green revolution and to meet the global food demand in sustainable and eco-friendly agriculture. An application of the multifaceted PM interactions needs the use of novel tools to know critical genetic and molecular aspects. Recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) tools are of great interest to explore PM interactions. A systematic understanding of the PM interactions will enable the application of GE tools to enhance the capacity of microbes or plants for agronomic trait improvement. This review focuses on applying GE techniques in plants or associated microbiota for discovering the fundamentals of the PM interactions, disease resistance, PGP activity, and future implications in agriculture. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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