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Plant Microbiome Responses to Environmental Changes
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Plant Microbiome Responses to Environmental Changes

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Environmental Sciences".

Deadline for manuscript submissions: closed (20 January 2023) | Viewed by 14500

Special Issue Editors

Dr. Lidia Błaszczyk

E-Mail Website
Guest Editor
Department of Plant Microbiomics, Institute of Plant Genetics Polish Academy of Sciences, 60-479 Poznań, Poland
Interests: crops; microbiome; plant pathogenic and beneficial fungi; mycoparasitic fungi; endophytes; plant – symbiont - pathogen interactions, plant and fungi proteome; transcriptome; metabolome; molecular identification; phylogenetic analysis
Special Issues, Collections and Topics in MDPI journals
Dr. Sylwia Salamon

E-Mail Website
Guest Editor
Department of Plant Microbiomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland
Interests: plant-fungal interactions; molecular biology; Epigenetics; DNA methylation; miRNA; amiRNA; lncRNA; Wheat; endophytes

Special Issue Information

Dear Colleagues,

We are inviting submissions to the Special Issue on Plant Microbiome Responses to Environmental Changes.

Plants are not individual entities but attractive holobionts inhabited by numerous microorganisms. The role of these residents varies from beneficial endophytes, through neutral commensals to harmful pathogens. The function, as well as the community structure of the plant inhabitant, may be changeable and is shaped by climatic conditions and agricultural management. It has been shown that the plant microbiome plays a vital role in host growth and fitness, as well as may alleviate the abiotic and biotic stresses effects.

Due to the importance of plant-associated fungi and bacteria in host adaptation, there is a need to understand how the microbiome responds to environmental changes and thus shape the plant's response to changing environmental conditions. Deciphering the plant–microbial relationship is critical to designing new crop management strategies to improve plant health and growth.

Dr. Lidia Błaszczyk
Dr. Sylwia Salamon
Guest Editors

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Keywords

  • fungi
  • bacteria
  • drought
  • heat
  • cold
  • crop
  • climatic changes
  • pollutions
  • endosphere
  • rhizosphere
  • phyllosphere

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Published Papers (3 papers)

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Research

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21 pages, 7327 KiB  
Article
ATP-Binding Cassette (ABC) Transporters in Fusarium Specific Mycoparasite Sphaerodes mycoparasitica during Biotrophic Mycoparasitism
by Seon Hwa Kim and Vladimir Vujanovic
Appl. Sci. 2022, 12(15), 7641; https://doi.org/10.3390/app12157641 - 29 Jul 2022
Cited by 2 | Viewed by 2221
Abstract
Recent transcriptomic profiling has revealed importance membrane transporters such as ATP-binding cassette (ABC) transporters in fungal necrotrophic mycoparasites. In this study, RNA-Seq allowed rapid detection of ABC transcripts involved in biotrophic mycoparasitism of Sphaerodes mycoparasitica against the phytopathogenic and mycotoxigenic Fusarium graminearum [...] Read more.
Recent transcriptomic profiling has revealed importance membrane transporters such as ATP-binding cassette (ABC) transporters in fungal necrotrophic mycoparasites. In this study, RNA-Seq allowed rapid detection of ABC transcripts involved in biotrophic mycoparasitism of Sphaerodes mycoparasitica against the phytopathogenic and mycotoxigenic Fusarium graminearum host, the causal agent of Fusarium head blight (FHB). Transcriptomic analyses of highly expressed S. mycoparasitica genes, and their phylogenetic relationships with other eukaryotic fungi, portrayed the ABC transporters’ evolutionary paths towards biotrophic mycoparasitism. Prior to the in silico phylogenetic analyses, transmission electron microscopy (TEM) was used to confirm the formation of appressorium/haustorium infection structures in S. mycoparasitica during early (1.5 d and 3.5 d) stages of mycoparasitism. Transcripts encoding biotrophy-associated secreted proteins did uncover the enrolment of ABC transporter genes in this specific biocontrol mode of action, while tandem ABC and BUB2 (non-ABC) transcripts seemed to be proper for appressorium development. The next-generation HiSeq transcriptomic profiling of the mycoparasitic hypha samples, revealed 81 transcripts annotated to ABC transporters consisting of a variety of ABC-B (14%), ABC-C (22%), and ABC-G (23%), and to ABC-A, ABC-F, aliphatic sulfonates importer (TC 3.A.1.17.2), BtuF, ribose importer (TC 3.A.1.2.1), and unknown families. The most abundant transcripts belonged to the multidrug resistance exporter (TC 3.A.1.201) subfamily of the ABC-B family, the conjugate transporter (TC 3.A.1.208) subfamily of the ABC-C family, and the pleiotropic drug resistance (PDR) (TC 3.A.1.205) subfamily of the ABC-G family. These findings highlight the significance of ABC transporter genes that control cellular detoxification against toxic substances (e.g., chemical pesticides and mycotoxins) in sustaining a virulence of S. mycoparasitica for effective biotrophic mycoparasitism on the F. graminearum host. The findings of this study provide clues to better understand the biotrophic mycoparasitism of S. mycoparasitica interacting with the Fusarium host, which implies that the ABC transporter group of key proteins is involved in the mycoparasite’s virulence and multidrug resistance to toxic substances including cellular detoxification. Full article
(This article belongs to the Special Issue Plant Microbiome Responses to Environmental Changes)
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10 pages, 10583 KiB  
Article
Optimization of Protocol for Construction of Fungal ITS Amplicon Library for High-Throughput Illumina Sequencing to Study the Mycobiome of Aspen Leaves
by Abu Bakar Siddique, Benedicte Riber Albrectsen, Hulya Ilbi and Abu Bakar Siddique
Appl. Sci. 2022, 12(3), 1136; https://doi.org/10.3390/app12031136 - 21 Jan 2022
Cited by 6 | Viewed by 5810
Abstract
High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number [...] Read more.
High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS. Full article
(This article belongs to the Special Issue Plant Microbiome Responses to Environmental Changes)
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Review

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23 pages, 3005 KiB  
Review
Evolution of Fusarium Head Blight Management in Wheat: Scientific Perspectives on Biological Control Agents and Crop Genotypes Protocooperation
by Antonia J. Powell and Vladimir Vujanovic
Appl. Sci. 2021, 11(19), 8960; https://doi.org/10.3390/app11198960 - 26 Sep 2021
Cited by 19 | Viewed by 5326
Abstract
Over the past century, the economically devastating Fusarium Head Blight (FHB) disease has persistently ravished small grain cereal crops worldwide. Annually, losses globally are in the billions of United States dollars (USD), with common bread wheat and durum wheat accounting for a major [...] Read more.
Over the past century, the economically devastating Fusarium Head Blight (FHB) disease has persistently ravished small grain cereal crops worldwide. Annually, losses globally are in the billions of United States dollars (USD), with common bread wheat and durum wheat accounting for a major portion of these losses. Since the unforgettable FHB epidemics of the 1990s and early 2000s in North America, different management strategies have been employed to treat this disease. However, even with some of the best practices including chemical fungicides and innovative breeding technological advances that have given rise to a spectrum of moderately resistant cultivars, FHB still remains an obstinate problem in cereal farms globally. This is in part due to several constraints such as the Fusarium complex of species and the struggle to develop and employ methods that can effectively combat more than one pathogenic line or species simultaneously. This review highlights the last 100 years of major FHB epidemics in the US and Canada, as well as the evolution of different management strategies, and recent progress in resistance and cultivar development. It also takes a look at protocooperation between specific biocontrol agents and cereal genotypes as a promising tool for combatting FHB. Full article
(This article belongs to the Special Issue Plant Microbiome Responses to Environmental Changes)
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