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Beneficial Microbiomes in Agriculture and Human Health: The Food Connection

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

Deadline for manuscript submissions: closed (15 March 2023) | Viewed by 48052

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Prof. Dr. Annamaria Bevivino

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Leading Guest Editor

Territorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, 00123 Rome, Italy
Interests: food-associated bacteria; microbial ecology; soil microorganisms; plant-growth-promoting bacteria; bacterial-host interaction; plant-microbe interactions
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Prof. Dr. Maria Maddalena Del Gallo

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Co-Guest Editor

Department of Life, Health and Environmental Sciences (MeSVA), Università degli Studi dell'Aquila, L'Aquila, Italy
Interests: microbial ecology; environmental microbiology; soil biodiversity; geomicrobiology; biological nitrogen-fixation; plant growth promoting microorganisms
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Many studies support the role of beneficial microbiomes for improving agri-food production and human health. Only during the last decade, we have begun to gain insights into the composition and functional of microbiomes as a consequence of major advances in High Throughput DNA sequencing (HTS) technologies. Microbiomes occupy a central position in the “One Health” framework. They can colonize almost all biological niches including plants and humans providing benefits to the planet as a whole and everything that lives on and in it. Plant-associated bacteria can be found in fact on leaves, roots or in the internal tissues as well as human-associated bacteria can reside on or within human. The application of beneficial microbes into agriculture can contribute to providing healthy food in a sustainable manner by reducing the amount of fertilizer, pesticides and herbicides. Given the food link, microbes from vegetable-diet can also have a direct and indirect effects on human health.

In this special Issue, we kindly invite the research community to submit original research papers and reviews that provide newest insights into the structure and dynamics of the core microbiomes across the food system (from soil to plants, and from foods to human) and to better investigate how we can use or manipulate microbiomes for achieving enhanced crop production and/or improving human health.

Prof. Dr. Annamaria Bevivino
Prof. Dr. Maria Maddalena Del Gallo
Guest Editors

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Keywords

plant growth-promoting microorganisms
probiotics
sustainable agriculture
food system
plant-food microbiome
gut microbiome
host-microbe interaction
human health
dysbiosis
heathy diet

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Published Papers (9 papers)

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Research

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19 pages, 3724 KiB

Open AccessArticle

Glomerales Dominate Arbuscular Mycorrhizal Fungal Communities Associated with Spontaneous Plants in Phosphate-Rich Soils of Former Rock Phosphate Mining Sites

by Amandine Ducousso-Détrez, Robin Raveau, Joël Fontaine, Mohamed Hijri and Anissa Lounès-Hadj Sahraoui

Microorganisms 2022, 10(12), 2406; https://doi.org/10.3390/microorganisms10122406 - 5 Dec 2022

Cited by 4 | Viewed by 2514

Abstract

Arbuscular mycorrhizal fungi (AMF) are key drivers of soil functioning. They interact with multiple soil parameters, notably, phosphorus (P). In this work, AMF communities of native plants grown spontaneously on former mining sites either enriched (P sites) or not enriched with P (nP sites) by mining cuttings of rock phosphate (RP) were studied. No significant differences were observed in the root mycorrhizal rates of the plants when comparing P and nP sites. The assessment of AMF diversity and community structure using Illumina MiSeq metabarcoding and targeting 18S rDNA in roots and rhizospheric soils showed a total of 318 Amplicon Sequence Variants (ASVs) of Glomeromycota phylum. No significant difference in the diversity was found between P and nP sites. Glomeraceae species were largely dominant, formed a fungal core of 26 ASVs, and were persistent and abundant in all sites. In the P soils, eight ASVs were identified by indicator species analysis. A trend towards an increase in Diversisporaceae and Claroideoglomeraceae and a reduction in Paraglomeraceae and Glomeraceae were noticed. These results provide new insights into AMF ecology in former RP mining sites; they document that P concentration is a driver of AMF community structures in soils enriched in RP long term but also suggest an influence of land disturbance, ecosystem self-restoration, and AMF life history strategies as drivers of AMF community profiles. Full article

(This article belongs to the Special Issue Beneficial Microbiomes in Agriculture and Human Health: The Food Connection)

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16 pages, 2262 KiB

Open AccessArticle

Dual Action of Beauveria bassiana (Hypocreales; Cordycipitaceae) Endophytic Stains as Biocontrol Agents against Sucking Pests and Plant Growth Biostimulants on Melon and Strawberry Field Plants

by Spiridon Mantzoukas, Eufrosini Daskalaki, Foteini Kitsiou, Vasileios Papantzikos, Dimitrios Servis, Stergios Bitivanos, George Patakioutas and Panagiotis A. Eliopoulos

Microorganisms 2022, 10(11), 2306; https://doi.org/10.3390/microorganisms10112306 - 21 Nov 2022

Cited by 8 | Viewed by 2935

Abstract

Entomopathogenic fungi (EPF) can colonize plant tissues and serve crops not only as biopesticides but also as biostimulants that promote plant growth and trigger defense mechanisms. In this context, field trials were conducted evaluating two commercial strains of the entomopathogen Beauveria bassiana (Hypocreales: Cordycipitaceae), GHA (Botanigard) and PPRI 5339 (Velifer^® ES) and a wild strain (AP0101) isolated from Achaia, Greece. The three strains were investigated in the field for their endophytic effects on melon Cucumis melo (Cucurbitales: Cucurbitaceae) and strawberry Fragaria sp. (Rosales: Rosaceae) plants and in particular for their ability to colonize plant tissues, control infestations of sucking insects Aphis gossypii (Hemiptera: Aphididae), Chaetosiphon fragaefolii (Hemiptera: Aphididae) and Frankliniella occidentalis (Thysanoptera: Thripidae), and improve plant growth parameters (plant height, number of flowers and fruits). All experimental fungal strains successfully colonized both plants. A significant decrease in the aphid and thrip populations was observed in the treated plants compared to the untreated control. As for plant growth, the number of flowers and fruits was significantly increased in plants treated with B. bassiana strains AP0101 and PPRI 5339. Our results clearly indicate that fungal endophytes can efficiently act as dual action agents demonstrating both insecticidal and growth-promoting effects. Full article

(This article belongs to the Special Issue Beneficial Microbiomes in Agriculture and Human Health: The Food Connection)

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21 pages, 1444 KiB

Open AccessArticle

Coriander (Coriandrum sativum L.) in Combination with Organic Amendments and Arbuscular Mycorrhizal Inoculation: An Efficient Option for the Phytomanagement of Trace Elements-Polluted Soils

by Joël Fontaine, Jérome Duclercq, Natacha Facon, Dorothée Dewaele, Frédéric Laruelle, Benoit Tisserant and Anissa Lounès-Hadj Sahraoui

Microorganisms 2022, 10(11), 2287; https://doi.org/10.3390/microorganisms10112287 - 17 Nov 2022

Cited by 4 | Viewed by 2155

Abstract

The cultivation of coriander (Coriandrum sativum L.) destined for essential oils production was recently presented as an innovative and economically viable alternative for the phytomanagement of trace elements (TE)-polluted soils. However, Cd accumulation in shoots has proven to be an obstacle in the valorization of the distillation residues and the development of these phytotechnologies. The present study aimed to evaluate the effect of arbuscular mycorrhizal fungus (Funneliformis mosseae) inoculation and organic amendment application on the soil TE bioavailability and plant uptake, as well as on the soil quality and health improvement. The application of compost and sewage sludge improved the growth of coriander and Cd and Zn immobilization in soil, resulting in reduced Cd plant uptake. A synergistic effect of arbuscular mycorrhizal fungi (AMF) inoculation and organic amendments was observed in the decrease in the extractable soil Cd and Zn concentrations, but not in the Cd plant uptake. Despite a significant decrease in Cd accumulation in shoots, coriander retained its accumulative phenotype, with a metal bioconcentration factor close to 1. Furthermore, both the vegetation and the organic amendments improved the soil quality and health by increasing its microbial biomass, as estimated by phospholipid fatty acids, soil enzyme activities (dehydrogenase, phosphatase, β-glucosidase, and cellubiosidase), and the bacterial metabolic function and diversity. The findings demonstrate the potential of C. sativum, particularly in combination with organic amendments and AMF inoculation, for the phytomanagement of TE-polluted soils and soil quality and health improvement. Full article

(This article belongs to the Special Issue Beneficial Microbiomes in Agriculture and Human Health: The Food Connection)

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16 pages, 3337 KiB

Open AccessArticle

Microbial Consortium Associated with Crustacean Shells Composting

by Svetlana N. Yurgel, Muhammad Nadeem and Mumtaz Cheema

Microorganisms 2022, 10(5), 1033; https://doi.org/10.3390/microorganisms10051033 - 16 May 2022

Cited by 4 | Viewed by 2701

Abstract

Soil microbes play an essential role in the biodegradation of crustacean shells, which is the process of sustainable bioconversion to chitin derivatives ultimately resulting in the promotion of plant growth properties. While a number of microorganisms with chitinolytic properties have been characterized, little is known about the microbial taxa that participate in this process either by active chitin degradation or by facilitation of this activity through nutritional cooperation and composting with the chitinolytic microorganisms. In this study, we evaluated the transformation of the soil microbiome triggered by close approximation to the green crab shell surface. Our data indicate that the microbial community associated with green crab shell matter undergoes significant specialized changes, which was reflected in a decreased fungal and bacterial Shannon diversity and evenness and in a dramatic alteration in the community composition. The relative abundance of several bacterial and fungal genera including bacteria Flavobacterium, Clostridium, Pseudomonas, and Sanguibacter and fungi Mortierella, Mycochlamys, and Talaromyces were increased with approximation to the shell surface. Association with the shell triggered significant changes in microbial cooperation that incorporate microorganisms that were previously reported to be involved in chitin degradation as well as ones with no reported chitinolytic activity. Our study indicates that the biodegradation of crab shells in soil incorporates a consortium of microorganisms that might provide a more efficient way for bioconversion. Full article

(This article belongs to the Special Issue Beneficial Microbiomes in Agriculture and Human Health: The Food Connection)

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22 pages, 2625 KiB

Open AccessArticle

Genomic, Antimicrobial, and Aphicidal Traits of Bacillus velezensis ATR2, and Its Biocontrol Potential against Ginger Rhizome Rot Disease Caused by Bacillus pumilus

by Leiqin Liang, Yajuan Fu, Sangsang Deng, Yan Wu and Meiying Gao

Microorganisms 2022, 10(1), 63; https://doi.org/10.3390/microorganisms10010063 - 29 Dec 2021

Cited by 16 | Viewed by 3425

Abstract

Ginger rhizome rot disease, caused by the pathogen Bacilluspumilus GR8, could result in severe rot of ginger rhizomes and heavily threaten ginger production. In this study, we identified and characterized a new Bacillus velezensis strain, designated ATR2. Genome analysis revealed B. velezensis ATR2 harbored a series of genes closely related to promoting plant growth and triggering plant immunity. Meanwhile, ten gene clusters involved in the biosynthesis of various secondary metabolites (surfactin, bacillomycin, fengycin, bacillibactin, bacilysin, difficidin, macrolactin, bacillaene, plantazolicin, and amylocyclicin) and two clusters encoding a putative lipopeptide and a putative phosphonate which might be explored as novel bioactive compounds were also present in the ATR2 genome. Moreover, B. velezensis ATR2 showed excellent antagonistic activities against multiple plant pathogenic bacteria, plant pathogenic fungi, human pathogenic bacteria, and human pathogenic fungus. B. velezensis ATR2 was also efficacious in control of aphids. The antagonistic compound from B. velezensis ATR2 against B.pumilus GR8 was purified and identified as bacillomycin D. In addition, B. velezensis ATR2 exhibited excellent biocontrol efficacy against ginger rhizome rot disease on ginger slices. These findings showed the potential of further applications of B. velezensis ATR2 as a biocontrol agent in agricultural diseases and pests management. Full article

(This article belongs to the Special Issue Beneficial Microbiomes in Agriculture and Human Health: The Food Connection)

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21 pages, 2574 KiB

Open AccessArticle

Bacterial Communities in the Embryo of Maize Landraces: Relation with Susceptibility to Fusarium Ear Rot

by Alessandro Passera, Alessia Follador, Stefano Morandi, Niccolò Miotti, Martina Ghidoli, Giovanni Venturini, Fabio Quaglino, Milena Brasca, Paola Casati, Roberto Pilu and Davide Bulgarelli

Microorganisms 2021, 9(11), 2388; https://doi.org/10.3390/microorganisms9112388 - 19 Nov 2021

Cited by 8 | Viewed by 3471

Abstract

Locally adapted maize accessions (landraces) represent an untapped resource of nutritional and resistance traits for breeding, including the shaping of distinct microbiota. Our study focused on five different maize landraces and a reference commercial hybrid, showing different susceptibility to fusarium ear rot, and whether this trait could be related to particular compositions of the bacterial microbiota in the embryo, using different approaches. Our cultivation-independent approach utilized the metabarcoding of a portion of the 16S rRNA gene to study bacterial populations in these samples. Multivariate statistical analyses indicated that the microbiota of the embryos of the accessions grouped in two different clusters: one comprising three landraces and the hybrid, one including the remaining two landraces, which showed a lower susceptibility to fusarium ear rot in field. The main discriminant between these clusters was the frequency of Firmicutes, higher in the second cluster, and this abundance was confirmed by quantification through digital PCR. The cultivation-dependent approach allowed the isolation of 70 bacterial strains, mostly Firmicutes. In vivo assays allowed the identification of five candidate biocontrol strains against fusarium ear rot. Our data revealed novel insights into the role of the maize embryo microbiota and set the stage for further studies aimed at integrating this knowledge into plant breeding programs. Full article

(This article belongs to the Special Issue Beneficial Microbiomes in Agriculture and Human Health: The Food Connection)

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23 pages, 4819 KiB

Open AccessArticle

Microbial Diversity in the Phyllosphere and Rhizosphere of an Apple Orchard Managed under Prolonged “Natural Farming” Practices

by Ying-Hong He, Charith Raj Adkar-Purushothama, Tsutae Ito, Asuka Shirakawa, Hideki Yamamoto, Akiko Kashiwagi, Ayumu Tatewaki, Misato Fujibayashi, Shuichi Sugiyama, Katsuhiko Yaginuma, Tomoya Akahira, Shingen Yamamoto, Seiya Tsushima, Yuko Matsushita and Teruo Sano

Microorganisms 2021, 9(10), 2056; https://doi.org/10.3390/microorganisms9102056 - 29 Sep 2021

Cited by 3 | Viewed by 3447

Abstract

Microbial diversity in an apple orchard cultivated with natural farming practices for over 30 years was compared with conventionally farmed orchards to analyze differences in disease suppression. In this long-term naturally farmed orchard, major apple diseases were more severe than in conventional orchards but milder than in a short-term natural farming orchard. Among major fungal species in the phyllosphere, we found that Aureobasidium pullulans and Cryptococcus victoriae were significantly less abundant in long-term natural farming, while Cladosporium tenuissimum predominated. However, diversity of fungal species in the phyllosphere was not necessarily the main determinant in the disease suppression observed in natural farming; instead, the maintenance of a balanced, constant selection of fungal species under a suitable predominant species such as C. tenuissimum seemed to be the important factors. Analysis of bacteria in the phyllosphere revealed Pseudomonas graminis, a potential inducer of plant defenses, predominated in long-term natural farming in August. Rhizosphere metagenome analysis showed that Cordyceps and Arthrobotrys, fungal genera are known to include insect- or nematode-infecting species, were found only in long-term natural farming. Among soil bacteria, the genus Nitrospira was most abundant, and its level in long-term natural farming was more than double that in the conventionally farmed orchard. Full article

(This article belongs to the Special Issue Beneficial Microbiomes in Agriculture and Human Health: The Food Connection)

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15 pages, 34229 KiB

Open AccessArticle

Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds

by Yasuko Yoneda, Kyosuke Yamamoto, Ayaka Makino, Yasuhiro Tanaka, Xian-Ying Meng, Junko Hashimoto, Kazuo Shin-ya, Noriyuki Satoh, Manabu Fujie, Tadashi Toyama, Kazuhiro Mori, Michihiko Ike, Masaaki Morikawa, Yoichi Kamagata and Hideyuki Tamaki

Microorganisms 2021, 9(6), 1133; https://doi.org/10.3390/microorganisms9061133 - 24 May 2021

Cited by 28 | Viewed by 7276

Abstract

Duckweeds are small, fast growing, and starch- and protein-rich aquatic plants expected to be a next generation energy crop and an excellent biomaterial for phytoremediation. Despite such an importance, very little is known about duckweed–microbe interactions that would be a key biological factor for efficient industrial utilization of duckweeds. Here we first report the duckweed growth promoting ability of bacterial strains belonging to the phylum Acidobacteria, the members of which are known to inhabit soils and terrestrial plants, but their ecological roles and plant–microbe interactions remain largely unclear. Two novel Acidobacteria strains, F-183 and TBR-22, were successfully isolated from wild duckweeds and phylogenetically affiliated with subdivision 3 and 6 of the phylum, respectively, based on 16S rRNA gene sequence analysis. In the co-culture experiments with aseptic host plants, the F-183 and TBR-22 strains visibly enhanced growth (frond number) of six duckweed species (subfamily Lemnoideae) up to 1.8–5.1 times and 1.6–3.9 times, respectively, compared with uninoculated controls. Intriguingly, both strains also increased the chlorophyll content of the duckweed (Lemna aequinoctialis) up to 2.4–2.5 times. Under SEM observation, the F-183 and TBR-22 strains were epiphytic and attached to the surface of duckweed. Taken together, our findings suggest that indigenous plant associated Acidobacteria contribute to a healthy growth of their host aquatic plants. Full article

(This article belongs to the Special Issue Beneficial Microbiomes in Agriculture and Human Health: The Food Connection)

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22 pages, 1041 KiB

Open AccessReview

Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety

by Marta Bertola, Andrea Ferrarini and Giovanna Visioli

Microorganisms 2021, 9(7), 1400; https://doi.org/10.3390/microorganisms9071400 - 28 Jun 2021

Cited by 87 | Viewed by 16386

Abstract

Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health. Full article

(This article belongs to the Special Issue Beneficial Microbiomes in Agriculture and Human Health: The Food Connection)

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