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

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 52809

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Prof. Dr. Philippe Jeandet

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Research Unit “Induced Resistance and Plant Bioprotection”, RIBP-USC INRAe 1488, University of Reims Champagne-Ardenne, 51100 Reims, France
Interests: phytoalexins; chemistry of natural products; secondary metabolites; plant defences
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Prof. Dr. Essaid Ait Barka

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Research Unit Induced Resistance and Plant Bioprotection, University of Reims, EA 4707 USC INRAe 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France
Interests: plant-microbe interaction; stress physiology plants responses to biotic and abiotic stress; crop protection; biological control
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Prof. Dr. Rachid Lahlali

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Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Km 10, BP S/40, Meknès 50001, Morocco
Interests: plant–microbe interaction; crop protection; biological control; horticultural crops
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plants offer an exceptional ecosystem for microorganisms, including members of phyla as diverse as viruses, bacteria, oomycetes, fungi, and eukaryotic protozoans, which intimately interact with plant cells and tissues with different levels of dependence ranging from mutualism to pathogenicity.

Some of these microorganisms cause harm by employing diverse strategies to attack plants and impair plant growth and reproduction, others improve the plant growth through different physiological activities that may have profound effects on the growth and/or health of plants. On the other hand, beneficial microorganisms are able to improve the plant fitness through different physiological activities that may have a profound effect on their growth and/or health. They are also able to compete with pathogens for nutrients and niches or exert antagonism through antimicrobial compounds. These beneficial microbes are also able to interfere with pathogen signals or trigger the plant host immunity.

Why do some microbes attack only certain plants? Is it because those plants are genetically less well-armed to repel pathogen attacks, or because the pathogens have the required arsenals to invade plant tissues? Why are some microbes pathogenic, and others not? How are beneficial microorganisms able to modulate the plant’s signaling to trigger the plant immunity?

These are some questions that will be targeted in this Issue. We encourage the contribution of high-quality and review articles related to different aspects of plant–microbe interactions.

Prof Dr. Philippe Jeandet
Prof. Dr. Essaid Ait Barka
Prof. Dr. Rachid Lahlali
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

beneficial microorganisms
pathogens
plant immunity
plant–microbe interaction
virulence factors

Published Papers (11 papers)

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Editorial

Jump to: Research, Review

6 pages, 211 KiB

Open AccessEditorial

The Hidden World within Plants

by Philippe Jeandet, Rachid Lahlali and Essaid Ait Barka

Microorganisms 2022, 10(10), 1951; https://doi.org/10.3390/microorganisms10101951 - 30 Sep 2022

Cited by 1 | Viewed by 1118

Abstract

Plants offer an ecosystem for microorganisms from diverse phylogenetic domains and phyla as well as viruses and viroids [...] Full article

(This article belongs to the Special Issue The Hidden World within Plants)

Research

Jump to: Editorial, Review

13 pages, 1164 KiB

Open AccessArticle

Diversity and Identification of Plant-Parasitic Nematodes in Wheat-Growing Ecosystems

by Ayça İrem Keçici, Refik Bozbuğa, Atilla Öcal, Ebubekir Yüksel, Göksel Özer, Şenol Yildiz, Rachid Lahlali, Brigitte Slaats, Abdelfattah A. Dababat and Mustafa İmren

Microorganisms 2022, 10(8), 1534; https://doi.org/10.3390/microorganisms10081534 - 29 Jul 2022

Cited by 6 | Viewed by 2117

Abstract

Several nematode species can be found in different densities in almost any soil ecosystem, and their diversity in those ecosystems depends on numerous reasons, such as climatic conditions and host presence. Cereals are one of the main hosts of plant-parasitic nematodes (PPN), chiefly root-lesion nematodes (RLN, Pratylenchus spp.) and cereal cyst nematodes (CCN, Heterodera spp.). These nematodes are known as major parasites of the cereal crops; however, agricultural areas accommodate various nematodes showing biological variation. The diversity of parasitic nematodes on cereals in the Sakarya provinces of Türkiye, where cereals are intensively grown and located in the middle of two climatic zones, has not been well studied. Therefore, in this study, we aimed to determine the diversity, identification, and molecular phylogeny of PPNs in wheat-growing ecosystems in the Hendek, Pamukova, Geyve, Akyazı, and Central districts of Sakarya. The diversity of PPNs was calculated using the Shannon diversity index. Thirteen PPN genera were detected in 92% of soil samples. Heterodera filipjevi was identified in 24% of the soil samples using morphological, morphometrical, and molecular tools. In the morphological and molecular analyses, intraspecific polymorphism was observed in H. filipjevi populations. The result indicated that the high infestation rate of H. filipjevi was recorded from Geyve and Pamukova, followed by Hendek and Akyazı; however, a low infestation rate was detected in the Central district. The moderate value of the Shannon index of migratory nematode species was obtained in wheat fields as 2.31, whereas the value of evenness was 0.93, implying moderate diversity and high evenness of nematodes. This study is the first comprehensive report on H. filipjevi from wheat cropping areas in the Sakarya province. Intensified cereal cropping systems with/without non-cereal rotations increased the risk of plant-parasitic nematodes, especially RLNs and H. filipjevi infection of wheat production areas in the province. Full article

(This article belongs to the Special Issue The Hidden World within Plants)

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16 pages, 3955 KiB

Open AccessArticle

Cyanobacterial Root Associations of Leafless Epiphytic Orchids

by Elena A. Tsavkelova, Irina D. Glukhareva, Elena A. Volynchikova, Maria A. Egorova, Maria R. Leontieva, Dina V. Malakhova, Galina L. Kolomeitseva and Alexander I. Netrusov

Microorganisms 2022, 10(5), 1006; https://doi.org/10.3390/microorganisms10051006 - 11 May 2022

Cited by 7 | Viewed by 2801

Abstract

The leafless orchids are rare epiphytic plants with extremely reduced leaves, and their aerial roots adopted for photosynthesis. The beneficial plant–microbial interactions contribute significantly to host nutrition, fitness, and growth. However, there are no data available on the bacterial associations, inhabiting leafless orchids. Here, we describe the diversity of cyanobacteria, which colonize the roots of greenhouse Microcoelia moreauae and Chiloschista parishii. The biodiversity and structure of the cyanobacterial community were analyzed using a complex approach, comprising traditional cultivable techniques, denaturing gradient gel electrophoresis (DGGE), and phylogenetic analysis, as well as the light and scanning electron microscopy (SEM). A wide diversity of associated bacteria colonize the root surface, forming massive biofilms on the aerial roots. The dominant populations of filamentous nitrogen-fixing cyanobacteria belonged to the orders Oscillatoriales, Synechococcales, and Nostocales. The composition of the cyanobacterial community varied, depending on the nitrogen supply. Two major groups prevailed under nitrogen-limiting conditions, belonging to Leptolyngbya sp. and Komarekiella sp. The latter was characterized by DGGE profiling and sequencing, as well as by its distinctive features of morphological plasticity. The leading role of these phototrophophic and diazotrophic cyanobacteria is discussed in terms of the epiphytic lifestyle of the leafless orchids. Full article

(This article belongs to the Special Issue The Hidden World within Plants)

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14 pages, 994 KiB

Open AccessArticle

Fungal Communities in the Native New Zealand Medicinal Plant Pseudowintera colorata (Horopito) Are Determined by Plant Organ Type and Host Maturity with Key Members Promoting Plant Growth

by Neeraj Purushotham, Eirian Jones, Jana Monk and Hayley Ridgway

Microorganisms 2021, 9(12), 2576; https://doi.org/10.3390/microorganisms9122576 - 13 Dec 2021

Cited by 4 | Viewed by 2644

Abstract

The plant Pseudowintera colorata is well known for its antimicrobial and medicinal properties and is endemic to New Zealand. Using PCR-Denaturing gradient gel electrophoresis (DGGE), we investigated the factors influencing the composition of endophytic fungal communities in P. colorata from ten distinct sites across New Zealand. Our results showed that plant organs of P. colorata influenced the diversity and richness of endophytic fungi (PERMANOVA, p < 0.05). In addition, plant maturity and its interactions revealed that endophytic fungal communities formed discrete clusters in leaves, stems, and roots of mature and immature P. colorata plants (PERMANOVA; p = 0.002, p = 0.001 and p = 0.039, respectively). For identifying isolates with biocontrol potential, dual culture tests were set up against four different phytopathogenic fungi. Isolates with high activity (zone of inhibition > 10 mm) were sequenced and identified as Trichoderma harzianum, Pezicula neosporulosa, Fusariumtricinctum, Metarhizium sp., and Chaetomium sp. Applying selected endophytic fungi (n = 7) as soil drenchers significantly increased the growth of P. colorata seedlings and produced more internodes. Seedling shoots treated with Trichoderma sp. PRY2BA21 were 2.2 × longer (8.36 cm) than the untreated controls (3.72 cm). Our results elucidate the main plant factors influencing fungal community composition and demonstrate a role for endophytic fungi in P. colorata growth and further demonstrate that medicinal plants are a rich source of endophytes with potential as biocontrol agents. Full article

(This article belongs to the Special Issue The Hidden World within Plants)

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13 pages, 832 KiB

Open AccessArticle

The Influence of Artificial Fusarium Infection on Oat Grain Quality

by Michaela Havrlentová, Svetlana Šliková, Veronika Gregusová, Bernadett Kovácsová, Andrea Lančaričová, Peter Nemeček, Jana Hendrichová and Peter Hozlár

Microorganisms 2021, 9(10), 2108; https://doi.org/10.3390/microorganisms9102108 - 07 Oct 2021

Cited by 11 | Viewed by 1960

Abstract

Adverse environmental conditions, such as various biotic and abiotic stresses, are the primary reason for decreased crop productivity. Oat, as one of the world’s major crops, is an important cereal in human nutrition. The aim of this work was to analyze the effect of inoculation with two species of the genus Fusarium on the selected qualitative parameters of oat grain intended for the food industry. Artificial inoculation caused a statistically significant decrease in the content of starch, oleic, linoleic, and α-linolenic acids in oat grains compared to the control. Moreover, artificial inoculation had no statistically significant effect on the content of β-D-glucans, total dietary fiber, total lipids, palmitic, stearic, and cis-vaccenic acids. An increase in the content of polyunsaturated fatty acids in oat grains was observed after inoculation. The most important indicator of Fusarium infection was the presence of the mycotoxin deoxynivalenol in the grain. The content of β-D-glucans, as a possible protective barrier in the cell wall, did not have a statistically significant effect on the inoculation manifestation in the grain. Full article

(This article belongs to the Special Issue The Hidden World within Plants)

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18 pages, 4103 KiB

Open AccessArticle

Phytopythium vexans Associated with Apple and Pear Decline in the Saïss Plain of Morocco

by Salma Jabiri, Chaimaa Bahra, Dustin MacLean, Nabil Radouane, Essaid Ait Barka, Mohamed Bendriss Amraoui and Rachid Lahlali

Microorganisms 2021, 9(9), 1916; https://doi.org/10.3390/microorganisms9091916 - 09 Sep 2021

Cited by 9 | Viewed by 3641

Abstract

An extensive survey conducted in the Saïss plain of Morocco during the 2017–2018 growing season revealed that 35 out of 50 apple and pear orchards were infested with a pathogen that causes the decline disease. Morphological and phylogenetic tree analyses using the cox II gene allowed us to identify the pathogen as Phytopythium vexans. Interestingly, no Phytophthora and Pythium species were isolated. The occurrence and prevalence of the disease varied between locations; the most infested locations were Meknes (100%), Imouzzer (83%), and Sefrou (80%). To fulfill Koch’s postulate, a greenhouse pathogenicity test was performed on the stem and collar of one-year-old healthy seedlings of apple rootstock M115. Symptoms similar to those observed in the field were reproduced in less than 4 months post-inoculation with root rot disease severity ranging from 70 to 100%. The survey results evidenced that apple rootstocks, soil type, and irrigation procedure may contribute significantly to the occurrence of the disease. The disease was most prevalent in drip water irrigation and sandy-clay soil on wild apple rootstock. Accordingly, a rational drip advanced watering system and good sanitation practices could eliminate water stagnation and help prevent the onset of this disease. It was concluded that Pp. vexans occurrence may be strongly influenced by irrigation mode and type of soil. Therefore, the obtained findings of this study could help to better understand the recurrence of this disease and to develop a reliable integrated strategy for its management. Full article

(This article belongs to the Special Issue The Hidden World within Plants)

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18 pages, 7309 KiB

Open AccessArticle

A Plant Endophytic Bacterium, Burkholderia seminalis Strain 869T2, Promotes Plant Growth in Arabidopsis, Pak Choi, Chinese Amaranth, Lettuces, and Other Vegetables

by Hau-Hsuan Hwang, Pei-Ru Chien, Fan-Chen Huang, Shih-Hsun Hung, Chih-Horng Kuo, Wen-Ling Deng, En-Pei Isabel Chiang and Chieh-Chen Huang

Microorganisms 2021, 9(8), 1703; https://doi.org/10.3390/microorganisms9081703 - 10 Aug 2021

Cited by 19 | Viewed by 4414

Abstract

Plant endophytic bacteria live inside host plants, can be isolated from surface-sterilized plant tissues, and are non-pathogenic. These bacteria can assist host plants in obtaining more nutrients and can improve plant growth via multiple mechanisms. Certain Gram-negative Burkholderia species, including rhizobacteria, bioremediators, and biocontrol strains, have been recognized for their plant-growth-promoting abilities, while other isolates have been identified as opportunistic plant or human pathogens. In this study, we observed the auxin production, siderophore synthesis, and phosphate solubilization abilities of B. seminalis strain 869T2. Our results demonstrated that strain 869T2 promoted growth in Arabidopsis, ching chiang pak choi, pak choi, loose-leaf lettuce, romaine lettuce, red leaf lettuce, and Chinese amaranth. Leafy vegetables inoculated with strain 869T2 were larger, heavier, and had more and larger leaves and longer and heavier roots than mock-inoculated plants. Furthermore, inoculations of strain 869T2 into hot pepper caused increased flower and fruit production, and a higher percentage of fruits turned red. Inoculation of strain 869T2 into okra plants resulted in earlier flowering and increased fruit weight. In conclusion, the plant endophytic bacterium Burkholderia seminalis 869T2 exerted positive effects on growth and production in several plant species. Full article

(This article belongs to the Special Issue The Hidden World within Plants)

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12 pages, 2095 KiB

Open AccessArticle

Examining the Effects of the Nitrogen Environment on Growth and N₂-Fixation of Endophytic Herbaspirillum seropedicae in Maize Seedlings by Applying ¹¹C Radiotracing

by Spenser Waller, Stacy L. Wilder, Michael J. Schueller, Alexandra B. Housh, Stephanie Scott, Mary Benoit, Avery Powell, Garren Powell and Richard A. Ferrieri

Microorganisms 2021, 9(8), 1582; https://doi.org/10.3390/microorganisms9081582 - 25 Jul 2021

Cited by 4 | Viewed by 1781

Abstract

Herbaspirillum seropedicae, as an endophyte and prolific root colonizer of numerous cereal crops, occupies an important ecological niche in agriculture because of its ability to promote plant growth and potentially improve crop yield. More importantly, there exists the untapped potential to harness its ability, as a diazotroph, to fix atmospheric N₂ as an alternative nitrogen resource to synthetic fertilizers. While mechanisms for plant growth promotion remain controversial, especially in cereal crops, one irrefutable fact is these microorganisms rely heavily on plant-borne carbon as their main energy source in support of their own growth and biological functions. Biological nitrogen fixation (BNF), a microbial function that is reliant on nitrogenase enzyme activity, is extremely sensitive to the localized nitrogen environment of the microorganism. However, whether internal root colonization can serve to shield the microorganisms and de-sensitize nitrogenase activity to changes in the soil nitrogen status remains unanswered. We used RAM10, a GFP-reporting strain of H. seropedicae, and administered radioactive ¹¹CO₂ tracer to intact 3-week-old maize leaves and followed ¹¹C-photosynthates to sites within intact roots where actively fluorescing microbial colonies assimilated the tracer. We examined the influence of administering either 1 mM or 10 mM nitrate during plant growth on microbial demands for plant-borne ¹¹C. Nitrogenase activity was also examined under the same growth conditions using the acetylene reduction assay. We found that plant growth under low nitrate resulted in higher nitrogenase activity as well as higher microbial demands for plant-borne carbon than plant growth under high nitrate. However, carbon availability was significantly diminished under low nitrate growth due to reduced host CO₂ fixation and reduced allocation of carbon resources to the roots. This response of the host caused significant inhibition of microbial growth. In summary, internal root colonization did little to shield these endophytic microorganisms from the nitrogen environment. Full article

(This article belongs to the Special Issue The Hidden World within Plants)

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18 pages, 3076 KiB

Open AccessArticle

Beneficial Microorganisms to Control the Gray Mold of Grapevine: From Screening to Mechanisms

by Zakaria Amarouchi, Qassim Esmaeel, Lisa Sanchez, Cédric Jacquard, Majida Hafidi, Nathalie Vaillant-Gaveau and Essaid Ait Barka

Microorganisms 2021, 9(7), 1386; https://doi.org/10.3390/microorganisms9071386 - 25 Jun 2021

Cited by 6 | Viewed by 2908

Abstract

In many vineyards around the world, Botrytis cinerea (B. cinerea) causes one of the most serious diseases of aerial grapevine (Vitis vinifera L.) organs. The control of the disease relies mainly on the use of chemical products whose use is increasingly challenged. To develop new sustainable methods to better resist B. cinerea, beneficial bacteria were isolated from vineyard soil. Once screened based on their antimicrobial effect through an in vivo test, two bacterial strains, S3 and S6, were able to restrict the development of the pathogen and significantly reduced the Botrytis-related necrosis. The photosynthesis analysis showed that the antagonistic strains also prevent grapevines from considerable irreversible PSII photo-inhibition four days after infection with B. cinerea. The 16S rRNA gene sequences of S3 exhibited 100% similarity to Bacillus velezensis, whereas S6 had 98.5% similarity to Enterobacter cloacae. On the other hand, the in silico analysis of the whole genome of isolated strains has revealed the presence of “biocontrol-related” genes supporting their plant growth and biocontrol activities. The study concludes that those bacteria could be potentially useful as a suitable biocontrol agent in harvested grapevine. Full article

(This article belongs to the Special Issue The Hidden World within Plants)

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Review

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33 pages, 2776 KiB

Open AccessReview

Biological Control of Plant Pathogens: A Global Perspective

by Rachid Lahlali, Said Ezrari, Nabil Radouane, Jihane Kenfaoui, Qassim Esmaeel, Hajar El Hamss, Zineb Belabess and Essaid Ait Barka

Microorganisms 2022, 10(3), 596; https://doi.org/10.3390/microorganisms10030596 - 09 Mar 2022

Cited by 222 | Viewed by 24230

Abstract

The increase in the world population has generated an important need for both quality and quantity agricultural products, which has led to a significant surge in the use of chemical pesticides to fight crop diseases. Consumers, however, have become very concerned in recent years over the side effects of chemical fungicides on human health and the environment. As a result, research into alternative solutions to protect crops has been imposed and attracted wide attention from researchers worldwide. Among these alternatives, biological controls through beneficial microorganisms have gained considerable importance, whilst several biological control agents (BCAs) have been screened, among them Bacillus, Pantoea, Streptomyces, Trichoderma, Clonostachys, Pseudomonas, Burkholderia, and certain yeasts. At present, biopesticide products have been developed and marketed either to fight leaf diseases, root diseases, or fruit storage diseases. However, no positive correlation has been observed between the number of screened BCAs and available marketed products. Therefore, this review emphasizes the development of biofungicides products from screening to marketing and the problems that hinder their development. Finally, particular attention was given to the gaps observed in this sector and factors that hamper its development, particularly in terms of efficacy and legislation procedures. Full article

(This article belongs to the Special Issue The Hidden World within Plants)

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24 pages, 6404 KiB

Open AccessReview

Citrus Stubborn Disease: Current Insights on an Enigmatic Problem Prevailing in Citrus Orchards

by Tourya Sagouti, Zineb Belabess, Naima Rhallabi, Essaid Ait Barka, Abdessalem Tahiri and Rachid Lahlali

Microorganisms 2022, 10(1), 183; https://doi.org/10.3390/microorganisms10010183 - 14 Jan 2022

Cited by 3 | Viewed by 3181

Abstract

Citrus stubborn was initially observed in California in 1915 and was later proven as a graft-transmissible disease in 1942. In the field, diseased citrus trees have compressed and stunted appearances, and yield poor-quality fruits with little market value. The disease is caused by Spiroplasma citri, a phloem-restricted pathogenic mollicute, which belongs to the Spiroplasmataceae family (Mollicutes). S. citri has the largest genome of any Mollicutes investigated, with a genome size of roughly 1780 Kbp. It is a helical, motile mollicute that lacks a cell wall and peptidoglycan. Several quick and sensitive molecular-based and immuno-enzymatic pathogen detection technologies are available. Infected weeds are the primary source of transmission to citrus, with only a minor percentage of transmission from infected citrus to citrus. Several phloem-feeding leafhopper species (Cicadellidae, Hemiptera) support the natural spread of S. citri in a persistent, propagative manner. S. citri-free buds are used in new orchard plantings and bud certification, and indexing initiatives have been launched. Further, a quarantine system for newly introduced types has been implemented to limit citrus stubborn disease (CSD). The present state of knowledge about CSD around the world is summarized in this overview, where recent advances in S. citri detection, characterization, control and eradication were highlighted to prevent or limit disease spread through the adoption of best practices. Full article

(This article belongs to the Special Issue The Hidden World within Plants)

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