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Macro and Microorganism Interactions

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Systems Microbiology".

Deadline for manuscript submissions: closed (30 June 2019) | Viewed by 51759

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Prof. Dr. Luciana Giovannetti

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Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine 18, 50144 Firenze, Italy
Interests: molecular microbiology; soil microbial ecology; metagenomics
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Carlo Viti

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Guest Editor

Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine 18, 50144 Firenze, Italy
Interests: microbial ecology; metagenomics; phenomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The knowledge of symbiotic, parasitic, and commensal interactions between macro and microorganisms is fundamental to explain their coexistence, ecology, and productivity. These interactions constitute an extraordinarily complex web that includes trophic structures and molecular communications. The net of interactions between macro and microorganisms is very tight and shows its own metabolic and regulatory processes. Therefore, some authors have introduced the terms “holobiont” and “superorganism”. Nowadays, the use of traditional approaches and omics technologies allows the improvement of our knowledge about many aspects of this emerging and exciting field of research. Therefore, we decided to launch a Special Issue on macro and microorganism interactions, to which you are kindly invited to contribute with either an original paper or a review article. These are the topics that will be considered for the Special Issue:

a) Plant–microorganism interactions;

b) Algae–microorganism interactions;

c) Animal–microorganism interactions.

Prof. Luciana Giovannetti
Prof. Carlo Viti
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

plant–microorganism interactions
algae–microorganism interactions
animal–microorganism interactions
symbiotic
parasitic
commensal

Published Papers (11 papers)

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Editorial

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3 pages, 171 KiB

Open AccessEditorial

Editorial for the Special Issue: Macro and Microorganism Interactions

by Luciana Giovannetti and Carlo Viti

Microorganisms 2020, 8(11), 1751; https://doi.org/10.3390/microorganisms8111751 - 7 Nov 2020

Viewed by 1592

Abstract

The knowledge of symbiotic, parasitic, and commensal interactions between macro and microorganisms is fundamental to explaining their coexistence, ecology, and productivity [...] Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

Research

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17 pages, 9958 KiB

Open AccessArticle

A MATE Transporter is Involved in Pathogenicity and IAA Homeostasis in the Hyperplastic Plant Pathogen Pseudomonas savastanoi pv. nerii

by Stefania Tegli, Lorenzo Bini, Silvia Calamai, Matteo Cerboneschi and Carola Biancalani

Microorganisms 2020, 8(2), 156; https://doi.org/10.3390/microorganisms8020156 - 22 Jan 2020

Cited by 8 | Viewed by 3395

Abstract

During the last years, many evidences have been accumulating about the phytohormone indole-3-acetic acid (IAA) as a multifaceted compound in the microbial world, with IAA playing a role as a bacterial intra and intercellular signaling molecule or as an effector during pathogenic or beneficial plant–bacteria interactions. However, pretty much nothing is known on the mechanisms that bacteria use to modulate IAA homeostasis, in particular on IAA active transport systems. Here, by an approach combining in silico three-dimensional (3D) structural modeling and docking, mutagenesis, quantitative gene expression analysis, and HPLC FLD auxin quantitative detection, for the first time a bacterial multidrug and toxic compound extrusion (MATE) transporter was demonstrated to be involved in the efflux of IAA, as well as of its conjugate IAA–Lysine, in the plant pathogenic hyperplastic bacterium Pseudomonas savastanoi pv. nerii strain Psn23. Furthermore, according to the role proved to be played by Psn23 MatE in the development of plant disease, and to the presence of Psn23 MatE homologs in all the genomospecies of the P. syringae complex, this membrane transporter could likely represent a promising target for the design of novel and selective anti-infective molecules for plant disease control. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

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16 pages, 2461 KiB

Open AccessArticle

Peroxynitrite Generation and Increased Heterotrophic Capacity Are Linked to the Disruption of the Coral–Dinoflagellate Symbiosis in a Scleractinian and Hydrocoral Species

by Laura Fernandes de Barros Marangoni, Miguel Mies, Arthur Z. Güth, Thomás N. S. Banha, Alex Inague, Juliana da Silva Fonseca, Camila Dalmolin, Samuel Coelho Faria, Christine Ferrier-Pagès and Adalto Bianchini

Microorganisms 2019, 7(10), 426; https://doi.org/10.3390/microorganisms7100426 - 9 Oct 2019

Cited by 21 | Viewed by 3271

Abstract

Ocean warming is one of the greatest global threats to coral reef ecosystems; it leads to the disruption of the coral–dinoflagellate symbiosis (bleaching) and to nutrient starvation, because corals mostly rely on autotrophy (i.e., the supply of photosynthates from the dinoflagellate symbionts) for their energy requirements. Although coral bleaching has been well studied, the early warning signs of bleaching, as well as the capacity of corals to shift from autotrophy to heterotrophy, are still under investigation. In this study, we evaluated the bleaching occurrence of the scleractinian coral Mussismillia harttii and the hydrocoral Millepora alcicornis during a natural thermal stress event, under the 2015–2016 El Niño influence in three reef sites of the South Atlantic. We focused on the link between peroxynitrite (ONOO⁻) generation and coral bleaching, as ONOO⁻ has been very poorly investigated in corals and never during a natural bleaching event. We also investigated the natural trophic plasticity of the two corals through the use of new lipid biomarkers. The results obtained first demonstrate that ONOO⁻ is linked to the onset and intensity of bleaching in both scleractinian corals and hydrocorals. Indeed, ONOO⁻ concentrations were correlated with bleaching intensity, with the highest levels preceding the highest bleaching intensity. The time lag between bleaching and ONOO⁻ peak was, however, species-specific. In addition, we observed that elevated temperatures forced heterotrophy in scleractinian corals, as Mu. harttii presented high heterotrophic activity 15 to 30 days prior bleaching occurrence. On the contrary, a lower heterotrophic activity was monitored for the hydrocoral Mi. alicornis, which also experienced higher bleaching levels compared to Mu. hartii. Overall, we showed that the levels of ONOO⁻ in coral tissue, combined to the heterotrophic capacity, are two good proxies explaining the intensity of coral bleaching. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

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16 pages, 1066 KiB

Open AccessArticle

Maize Inoculation with Microbial Consortia: Contrasting Effects on Rhizosphere Activities, Nutrient Acquisition and Early Growth in Different Soils

by Klára Bradáčová, Maximilian Sittinger, Katharina Tietz, Benjamin Neuhäuser, Ellen Kandeler, Nils Berger, Uwe Ludewig and Günter Neumann

Microorganisms 2019, 7(9), 329; https://doi.org/10.3390/microorganisms7090329 - 7 Sep 2019

Cited by 21 | Viewed by 4373

Abstract

The benefit of plant growth-promoting microorganisms (PGPMs) as plant inoculants is influenced by a wide range of environmental factors. Therefore, microbial consortia products (MCPs) based on multiple PGPM strains with complementary functions, have been proposed as superior, particularly under challenging environmental conditions and for restoration of beneficial microbial communities in disturbed soil environments. To test this hypothesis, the performance of a commercial MCP inoculant based on 22 PGPM strains was investigated in greenhouse experiments with maize on three soils with contrasting pH, organic matter content and microbial activity, under different P and N fertilization regimes. Interestingly, the MCP inoculant stimulated root and shoot growth and improved the acquisition of macronutrients only on a freshly collected field soil with high organic matter content, exclusively in combination with stabilized ammonium fertilization. This was associated with transiently increased expression of AuxIAA5 in the root tissue, a gene responsive to exogenous auxin supply, suggesting root growth promotion by microbial auxin production as a major mode of action of the MCP inoculant. High microbial activity was indicated by intense expression of soil enzyme activities involved in C, N and P cycling in the rhizosphere (cellulase, leucine peptidase, alkaline and acid phosphatases) but without MCP effects. By contrast, the MCP inoculation did not affect maize biomass production or nutrient acquisition on soils with very little C_org and low microbial activity, although moderate stimulation of rhizosphere enzymes involved in N and P cycling was recorded. There was also no indication for MCP-induced solubilization of Ca-phosphates on a calcareous sub-soil fertilized with rock-phosphate. The results demonstrate that the combination of multiple PGPM strains with complementary properties as MCP inoculants does not necessarily translate into plant benefits in challenging environments. Thus, a better understanding of the conditions determining successful MCP application is mandatory. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

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16 pages, 4334 KiB

Open AccessArticle

Plant Tissue Localization and Morphological Conversion of Azospirillum brasilense upon Initial Interaction with Allium cepa L.

by Leidong Hong, Yoshitake Orikasa, Hisayo Sakamoto and Takuji Ohwada

Microorganisms 2019, 7(9), 275; https://doi.org/10.3390/microorganisms7090275 - 21 Aug 2019

Cited by 8 | Viewed by 4561

Abstract

The genus Azospirillum is recognized as plant growth-promoting bacteria that exert beneficial effects on the host plant and is morphologically converted into cyst-like cells (i.e., c-form) in association with poly-β-hydroxybutyrate (PHB) accumulation in the cells under stress conditions. We constructed Azospirillum brasilense, labeled with reporter genes (gus/gfp, mCherry) and examined the plant tissue localization along with a morphological conversion into the c-form upon its initial interaction with onion seedlings (Allium cepa L.). The PHB granules in the A. brasilense cells were easily detected under fluorescence as “black holes”, rendering it possible to monitor the morphological conversion from vegetative to the c-form cells. The results showed that the A. brasilense cells on the surface of the roots and bulbs (underground stem) began converting at three days following inoculation and that the cell conversion was significantly advanced with time along with the cell population increase. The endophytic infection of A. brasilense into the bulb tissues was also confirmed, although these likely constituted vegetative cells. Moreover, the morphological conversion into the c-form was induced under nitrogen-restricted conditions. Analysis of the biochemical properties of the A. brasilense cells during cell conversion revealed that the acetylene reduction activity correlated positively with the PHB accumulation in the cells converting into the c-form under nitrogen-restricted conditions. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

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16 pages, 3936 KiB

Open AccessArticle

The Algal Symbiont Modifies the Transcriptome of the Scleractinian Coral Euphyllia paradivisa during Heat Stress

by Dalit Meron, Keren Maor-Landaw, Eviatar Weizman, Hiba Waldman Ben-Asher, Gal Eyal, Ehud Banin, Yossi Loya and Oren Levy

Microorganisms 2019, 7(8), 256; https://doi.org/10.3390/microorganisms7080256 - 12 Aug 2019

Cited by 11 | Viewed by 5641

Abstract

The profound mutualistic symbiosis between corals and their endosymbiotic counterparts, Symbiodiniaceae algae, has been threatened by the increase in seawater temperatures, leading to breakdown of the symbiotic relationship—coral bleaching. To characterize the heat-stress response of the holobiont, we generated vital apo-symbiotic Euphyllia paradivisa corals that lacked the endosymbiotic algae. Using RNA sequencing, we analyzed the gene expression of these apo-symbionts vs. symbiotic ones, to test the effect of the algal presence on the tolerance of the coral. We utilized literature-derived lists of “symbiosis differentially expressed genes” and “coral heat-stress genes” in order to compare between the treatments. The symbiotic and apo-symbiotic samples were segregated into two separate groups with several different enriched gene ontologies. Our findings suggest that the presence of endosymbionts has a greater negative impact on the host than the environmental temperature conditions experienced by the holobiont. The peak of the stress reaction was identified as 28 °C, with the highest number of differentially expressed genes. We suggest that the algal symbionts increase coral holobiont susceptibility to elevated temperatures. Currently, we can only speculate whether coral species, such as E. paradivisa, with the plasticity to also flourish as apo-symbionts, may have a greater chance to withstand the upcoming global climate change challenge. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

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16 pages, 858 KiB

Open AccessArticle

Effects of Chestnut Tannin Extract, Vescalagin and Gallic Acid on the Dimethyl Acetals Profile and Microbial Community Composition in Rumen Liquor: An In Vitro Study

by Federica Mannelli, Matteo Daghio, Susana P. Alves, Rui J. B. Bessa, Sara Minieri, Luciana Giovannetti, Giuseppe Conte, Marcello Mele, Anna Messini, Stefano Rapaccini, Carlo Viti and Arianna Buccioni

Microorganisms 2019, 7(7), 202; https://doi.org/10.3390/microorganisms7070202 - 18 Jul 2019

Cited by 20 | Viewed by 4199

Abstract

The addition of polyphenol extracts in ruminant diets is an effective strategy to modulate rumen microflora. The aim of this in vitro trial was to study the effects of chestnut tannin extract (CHT), vescalagin (VES) and gallic acid (GAL) on dietary fibre degradability and on the dimethyl acetals (DMA) profile and microbial community composition of rumen liquor. Four diets (basal diet; basal diet plus CHT; basal diet plus VES; basal diet plus GAL) were fermented for 24 h using ewe rumen liquor. At the end of the fermentation, the microbial communities were characterized by sequencing the 16S rRNA gene. The DMA profile was analyzed by gas chromatography. Chestnut tannin extract did not affect fibre degradability, whereas VES and GAL showed a detrimental effect. The presence of CHT, VES and GAL influenced the concentration of several DMA (i.e., 12:0, 13:0, 14:0, 15:0, 18:0 and 18:1 trans-11), whereas the composition of the microbial community was marginally affected. The inclusion of CHT led to the enrichment of the genera Anaerovibrio, Bibersteinia, Escherichia/Shigella, Pseudobutyrivibrio and Streptococcus. The results of this study support the hypothesis that the activity of CHT is due to the synergistic effect of all components rather than the property of a single component. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

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15 pages, 1426 KiB

Open AccessArticle

Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria

by Sabina Zoledowska, Luana Presta, Marco Fondi, Francesca Decorosi, Luciana Giovannetti, Alessio Mengoni and Ewa Lojkowska

Microorganisms 2019, 7(4), 101; https://doi.org/10.3390/microorganisms7040101 - 5 Apr 2019

Cited by 11 | Viewed by 4647

Abstract

Understanding plant–microbe interactions is crucial for improving plants’ productivity and protection. Constraint-based metabolic modeling is one of the possible ways to investigate the bacterial adaptation to different ecological niches and may give insights into the metabolic versatility of plant pathogenic bacteria. We reconstructed a raw metabolic model of the emerging plant pathogenic bacterium Pectobacterium parmentieri SCC3193 with the use of KBase. The model was curated by using inParanoind and phenotypic data generated with the use of the OmniLog system. Metabolic modeling was performed through COBRApy Toolbox v. 0.10.1. The curated metabolic model of P. parmentieri SCC3193 is highly reliable, as in silico obtained results overlapped up to 91% with experimental data on carbon utilization phenotypes. By mean of flux balance analysis (FBA), we predicted the metabolic adaptation of P. parmentieri SCC3193 to two different ecological niches, relevant for the persistence and plant colonization by this bacterium: soil and the rhizosphere. We performed in silico gene deletions to predict the set of essential core genes for this bacterium to grow in such environments. We anticipate that our metabolic model will be a valuable element for defining a set of metabolic targets to control infection and spreading of this plant pathogen. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

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Review

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21 pages, 1195 KiB

Open AccessReview

The Varied Role of Efflux Pumps of the MFS Family in the Interplay of Bacteria with Animal and Plant Cells

by Martina Pasqua, Milena Grossi, Alessandro Zennaro, Giulia Fanelli, Gioacchino Micheli, Frederic Barras, Bianca Colonna and Gianni Prosseda

Microorganisms 2019, 7(9), 285; https://doi.org/10.3390/microorganisms7090285 - 22 Aug 2019

Cited by 66 | Viewed by 6061

Abstract

Efflux pumps represent an important and large group of transporter proteins found in all organisms. The importance of efflux pumps resides in their ability to extrude a wide range of antibiotics, resulting in the emergence of multidrug resistance in many bacteria. Besides antibiotics, multidrug efflux pumps can also extrude a large variety of compounds: Bacterial metabolites, plant-produced compounds, quorum-sensing molecules, and virulence factors. This versatility makes efflux pumps relevant players in interactions not only with other bacteria, but also with plant or animal cells. The multidrug efflux pumps belonging to the major facilitator superfamily (MFS) are widely distributed in microbial genomes and exhibit a large spectrum of substrate specificities. Multidrug MFS efflux pumps are present either as single-component transporters or as tripartite complexes. In this review, we will summarize how the multidrug MFS efflux pumps contribute to the interplay between bacteria and targeted host cells, with emphasis on their role in bacterial virulence, in the colonization of plant and animal host cells and in biofilm formation. We will also address the complexity of these interactions in the light of the underlying regulatory networks required for the effective activation of efflux pump genes. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

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13 pages, 259 KiB

Open AccessReview

Symbiosis in Sustainable Agriculture: Can Olive Fruit Fly Bacterial Microbiome Be Useful in Pest Management?

by Tânia Nobre

Microorganisms 2019, 7(8), 238; https://doi.org/10.3390/microorganisms7080238 - 3 Aug 2019

Cited by 10 | Viewed by 6169

Abstract

The applied importance of symbiosis has been gaining recognition. The relevance of symbiosis has been increasing in agriculture, in developing sustainable practices, including pest management. Insect symbiotic microorganisms’ taxonomical and functional diversity is high, and so is the potential of manipulation of these microbial partners in suppressing pest populations. These strategies, which rely on functional organisms inhabiting the insect, are intrinsically less susceptible to external environmental variations and hence likely to overcome some of the challenges posed by climate change. Rates of climate change in the Mediterranean Basin are expected to exceed global trends for most variables, and this warming will also affect olive production and impact the interactions of olives and their main pest, the obligate olive fruit fly (Bactrocera oleae). This work summarizes the current knowledge on olive fly symbiotic bacteria towards the potential development of symbiosis-based strategies for olive fruit fly control. Particular emphasis is given to Candidatus Erwinia dacicola, an obligate, vertically transmitted endosymbiont that allows the insect to cope with the olive-plant produced defensive compound oleuropein, as a most promising target for a symbiosis disruption approach. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

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16 pages, 1080 KiB

Open AccessReview

Green Technology: Bacteria-Based Approach Could Lead to Unsuspected Microbe–Plant–Animal Interactions

by Daniela Bulgari, Matteo Montagna, Emanuela Gobbi and Franco Faoro

Microorganisms 2019, 7(2), 44; https://doi.org/10.3390/microorganisms7020044 - 6 Feb 2019

Cited by 11 | Viewed by 5501

Abstract

The recent and massive revival of green strategies to control plant diseases, mainly as a consequence of the Integrated Pest Management (IPM) rules issued in 2009 by the European Community and the increased consumer awareness of organic products, poses new challenges for human health and food security that need to be addressed in the near future. One of the most important green technologies is biocontrol. This approach is based on living organisms and how these biocontrol agents (BCAs) directly or indirectly interact as a community to control plant pathogens and pest. Although most BCAs have been isolated from plant microbiomes, they share some genomic features, virulence factors, and trans-kingdom infection abilities with human pathogenic microorganisms, thus, their potential impact on human health should be addressed. This evidence, in combination with the outbreaks of human infections associated with consumption of raw fruits and vegetables, opens new questions regarding the role of plants in the human pathogen infection cycle. Moreover, whether BCAs could alter the endophytic bacterial community, thereby leading to the development of new potential human pathogens, is still unclear. In this review, all these issues are debated, highlighting that the research on BCAs and their formulation should include these possible long-lasting consequences of their massive spread in the environment. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

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