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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 (31 January 2021) | Viewed by 42120

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Prof. Dr. Nikolay Vassilev

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Department of Chemical Engineering, Institute of Biotechnology, Faculty of Sciences, University of Granada, c/Fuentenueva s/n, E-18071 Granada, Spain
Interests: industrial microbiology; bioreactors and fermentation processes; cell and enzyme immobilization; biotechnological production of enzymes, organic acids, biofuels; plant microbiome; plant-microbial interactions; microbial mineral dissolution; production and formulation of soil inoculants
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Dr. Eligio Malusà

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The National Institute of Horticultural Research, 96-100 Skierniewice, Poland
Interests: biocontrol; entomopathogenic fungi; soil-borne pests management
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microorganisms constantly interact with plants supplying macro- and micronutrients, fostering plant growth and controlling microbial pathogens as well as increasing plant resistance against abiotic stress factors. Managing microbial communities in soil–plant systems is currently one of the main scientific challenges and a promising tool to optimize crop production and quality. These challenges are related to the isolation, selection, characterization, production, formulation, and development of field application techniques of microbial inoculants. However, it is now also understood that a deep analysis of the existing soil–microbiome–plant relationships is necessary to take into consideration to assure an effective and sustainable use of microbial products. Furthermore, prebiotic, probiotic, and postbiotic approaches to enhance soil quality and facilitate microbial functions of existing and formulated beneficial microorganisms have to be encompassed in the research to fully appraise the mechanisms utilized by plants for recruiting microbial specific functions. These research fields, together with commercial and legislation requirements, as well as safety measures in manipulating microbial products, are expected (welcomed) to be the subject of the Special Issue, which is open for research works and review papers on the recent trends in the field of microbial-based plant nutrition.

Prof. Dr. Nikolay Bojkov Vassilev
Prof. Dr. Eligio Malusà
Guest Editors

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Keywords

plant beneficial microorganisms
plant–microbiome interactions
techniques for biofertilizers production, formulation and delivery
management and assessment (monitoring) of microbial communities

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Published Papers (9 papers)

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Editorial

Jump to: Research, Review

3 pages, 195 KiB

Open AccessEditorial

Special Issue: Microorganisms and Plant Nutrition

by Nikolay Vassilev and Eligio Malusà

Microorganisms 2021, 9(12), 2571; https://doi.org/10.3390/microorganisms9122571 - 13 Dec 2021

Cited by 3 | Viewed by 2418

Abstract

Plant-beneficial microorganisms affect plant nutrition and health, as a key part of prebiotic-, probiotic-, and symbiotic-based interactions [...] Full article

(This article belongs to the Special Issue Microorganisms and Plant Nutrition)

Research

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15 pages, 22590 KiB

Open AccessArticle

Shift of Dominant Species in Plant Community and Soil Chemical Properties Shape Soil Bacterial Community Characteristics and Putative Functions: A Case Study on Topographic Variation in a Mountain Pasture

by Jinu Eo, Myung-Hyun Kim, Min-Kyeong Kim and Soon-Kun Choi

Microorganisms 2021, 9(5), 961; https://doi.org/10.3390/microorganisms9050961 - 29 Apr 2021

Cited by 10 | Viewed by 2618

Abstract

Reducing management intensity according to the topography of pastures can change the dominant plant species from sown forages to weeds. It is unclear how changes in species dominance in plant community drive spatial variation in soil bacterial community characteristics and functions in association with edaphic condition. Analysing separately the effects of both plant communities and soil chemical properties on bacterial community is crucial for understanding the biogeographic process at a small scale. In this paper, we investigated soil bacterial responses in five plant communities (two forage and three weed), where >65% of the coverage was by one or two species. The structure and composition of the bacterial communities in the different microbiome were analysed using sequencing and their characteristics were assessed using the Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Firmicutes and Planctomycetes responded only to one specific plant community, and each plant community harboured unique operational taxonomic units (OTUs) at the species level. There were a large percentage of uniquely absent OTUs for specific plant communities, suggesting that a negative effect is critical in the relationship between plants and bacteria. Bacterial diversity indices were influenced more by soil chemical properties than by plant communities. Some putative functions related to C and N recycling including nitrogen fixation were correlated with pH, electrical conductivity (EC) and nutrient levels, and this also implied that some biological functions, such as ureolysis and carbon metabolism, may decline when fertilisation intensity is reduced. Taken together, these results suggest that a shift of dominant species in plant community exerts individual effects on the bacterial community composition, which is different from the effect of soil chemical properties. Full article

(This article belongs to the Special Issue Microorganisms and Plant Nutrition)

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19 pages, 991 KiB

Open AccessArticle

Plant-Growth Endophytic Bacteria Improve Nutrient Use Efficiency and Modulate Foliar N-Metabolites in Sugarcane Seedling

by Matheus Aparecido Pereira Cipriano, Raquel de Paula Freitas-Iório, Maurício Rocha Dimitrov, Sara Adrián López de Andrade, Eiko Eurya Kuramae and Adriana Parada Dias da Silveira

Microorganisms 2021, 9(3), 479; https://doi.org/10.3390/microorganisms9030479 - 25 Feb 2021

Cited by 31 | Viewed by 4398

Abstract

Beneficial plant–microbe interactions lead to physiological and biochemical changes that may result in plant-growth promotion. This study evaluated the effect of the interaction between sugarcane and endophytic bacterial strains on plant physiological and biochemical responses under two levels of nitrogen (N) fertilization. Six strains of endophytic bacteria, previously selected as plant growth-promoting bacteria (PGPB), were used to inoculate sugarcane mini stalks, with and without N fertilization. After 45 days, biomass production; shoot nutrient concentrations; foliar polyamine and free amino acid profiles; activities of nitrate reductase and glutamine synthase; and the relative transcript levels of the GS1, GS2, and SHR5 genes in sugarcane leaves were determined. All six endophytic strains promoted sugarcane growth, increasing shoot and root biomass, plant nutritional status, and the use efficiency of most nutrients. The inoculation-induced changes at the biochemical level altered the foliar free amino acid and polyamine profiles, mainly regarding the relative concentrations of citrulline, putrescine, glycine, alanine, glutamate, glutamine, proline, and aspartate. The transcription of GS1, GS2, and SHR5 was higher in the N fertilized seedlings, and almost not altered by endophytic bacterial strains. The endophytic strains promoted sugarcane seedlings growth mainly by improving nutrient efficiency. This improvement could not be explained by their ability to induce the production of amino acid and polyamine composts, or GS1, GS2, and SHR5, showing that complex interactions may be associated with enhancement of the sugarcane seedlings’ performance by endophytic bacteria. The strains demonstrated biotechnological potential for sugarcane seedling production. Full article

(This article belongs to the Special Issue Microorganisms and Plant Nutrition)

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19 pages, 4305 KiB

Open AccessArticle

Agroecological Service Crops Drive Plant Mycorrhization in Organic Horticultural Systems

by Alessandra Trinchera, Elena Testani, Giancarlo Roccuzzo, Gabriele Campanelli and Corrado Ciaccia

Microorganisms 2021, 9(2), 410; https://doi.org/10.3390/microorganisms9020410 - 16 Feb 2021

Cited by 13 | Viewed by 2857

Abstract

Mycorrhizal symbiosis represents a valuable tool for increasing plant nutrient uptake, affecting system biodiversity, ecosystem services and productivity. Introduction of agroecological service crops (ASCs) in cropping systems may determine changes in weed community, that can affect the development of the mycorrhizal mycelial network in the rhizosphere, favoring or depressing the cash crop mycorrhization. Two no-till Mediterranean organic horticultural systems were considered: one located in central Italy, where organic melon was transplanted on four winter-cereals mulches (rye, spelt, barley, wheat), one located in southern Italy (Sicily), where barley (as catch crop) was intercropped in an organic young orange orchard, with the no tilled, unweeded systems taken as controls. Weed “Supporting Arbuscular Mycorrhiza” (SAM) trait, weed density and biodiversity indexes, mycorrhization of coexistent plants in the field, the external mycelial network on roots were analyzed by scanning electron microscopy, crop P uptake, yield and quality were evaluated. We verified that cereals, used as green mulches or intercropped, may drive the weed selection in favor of the SAM species, and promote the mycelial network, thus significantly increasing the mycorrhization, the P uptake, the yield and quality traits of the cash crop. This is a relevant economic factor when introducing sustainable cropping practices and assessing the overall functionality of the agroecosystem. Full article

(This article belongs to the Special Issue Microorganisms and Plant Nutrition)

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17 pages, 1361 KiB

Open AccessArticle

Microbial Communities in Soils and Endosphere of Solanum tuberosum L. and their Response to Long-Term Fertilization

by Martina Kracmarova, Jana Karpiskova, Ondrej Uhlik, Michal Strejcek, Jirina Szakova, Jiri Balik, Katerina Demnerova and Hana Stiborova

Microorganisms 2020, 8(9), 1377; https://doi.org/10.3390/microorganisms8091377 - 8 Sep 2020

Cited by 22 | Viewed by 3610

Abstract

An understanding of how fertilization influences endophytes is crucial for sustainable agriculture, since the manipulation of the plant microbiome could affect plant fitness and productivity. This study was focused on the response of microbial communities in the soil and tubers to the regular application of manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and chemical fertilizer (NPK; 330-90-300 kg N-P-K/ha). Unfertilized soil was used as a control (CF), and the experiment was set up at two distinct sites. All fertilization treatments significantly altered the prokaryotic and fungal communities in soil, whereas the influence of fertilization on the community of endophytes differed for each site. At the site with cambisol, prokaryotic and fungal endophytes were significantly shifted by MF and SF3 treatments. At the site with chernozem, neither the prokaryotic nor fungal endophytic communities were significantly associated with fertilization treatments. Fertilization significantly increased the relative abundance of the plant-beneficial bacteria Stenotrophomonas, Sphingomonas and the arbuscular mycorrhizal fungi. In tubers, the relative abundance of Fusarium was lower in MF-treated soil compared to CF. Although fertilization treatments clearly influenced the soil and endophytic community structure, we did not find any indication of human pathogens being transmitted into tubers via organic fertilizers. Full article

(This article belongs to the Special Issue Microorganisms and Plant Nutrition)

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13 pages, 1908 KiB

Open AccessArticle

Does Biological Denitrification Inhibition (BDI) in the Field Induce an Increase in Plant Growth and Nutrition in Apium graveolens L. Grown for a Long Period?

by William Galland, Florence Piola, Céline Mathieu, Lyna Bouladra, Laurent Simon and Feth el Zahar Haichar

Microorganisms 2020, 8(8), 1204; https://doi.org/10.3390/microorganisms8081204 - 7 Aug 2020

Cited by 8 | Viewed by 3182

Abstract

Intensive agriculture uses a lot of nitrogen fertilizers to increase crop productivity. These crops are in competition with soil-denitrifying microorganisms that assimilate nitrogen in the form of nitrate and transform it into N₂O, a greenhouse gas, or N₂. However, certain plant species exude secondary metabolites, called procyanidins, which inhibit denitrifiers and increase the nitrate pool in the soil available for plant nutrition. This phenomenon is called biological denitrification inhibition. Previously, we showed that the addition of exogenous procyanidins to a lettuce crop induces denitrifier inhibition and increases nitrate content in the soil, affecting lettuce morphological traits. Here, the effects of procyanidin amendments in the field on a more long-term and nitrogen-consuming crop species such as celery were tested. The effects of procyanidin amendment on celery growth with those of conventional ammonium nitrate amendments were, therefore, compared. Denitrification activity, nitrate concentration, the abundance of denitrifying bacteria in the soil, and traits related to celery growth were measured. It was shown that the addition of procyanidins inhibits denitrifiers and increases the soil nitrate level, inducing an improvement in celery morphological traits. In addition, procyanidin amendment induces the lowest nitrogen concentration in tissues and reduces N₂O emissions. Full article

(This article belongs to the Special Issue Microorganisms and Plant Nutrition)

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22 pages, 1469 KiB

Open AccessArticle

Role of Beneficial Microorganisms and Salicylic Acid in Improving Rainfed Agriculture and Future Food Safety

by Naeem Khan, Asghari Bano and José Alfredo Curá

Microorganisms 2020, 8(7), 1018; https://doi.org/10.3390/microorganisms8071018 - 9 Jul 2020

Cited by 60 | Viewed by 5870

Abstract

Moisture stress in rainfed areas has significant adverse impacts on plant growth and yield. Plant growth promoting rhizobacteria (PGPR) plays an important role in the revegetation and rehabilitation of rainfed areas by modulating plant growth and metabolism and improving the fertility status of the rhizosphere soils. The current study explored the positive role of PGPR and salicylic acid (SA) on the health of the rhizosphere soil and plants grown under rainfed conditions. Maize seeds of two different varieties, i.e., SWL-2002 (drought tolerant) and CZP-2001 (drought sensitive), were soaked for 4 h prior to sowing in 24-h old culture of Planomicrobium chinense strain P1 (accession no. MF616408) and Bacillus cereus strain P2 (accession no. MF616406). The foliar spray of SA (150 mg/L) was applied on 28-days old seedlings. The combined treatment of the consortium of PGPR and SA not only alleviated the adverse effects of low moisture stress of soil in rainfed area but also resulted in significant accumulation of leaf chlorophyll content (40% and 24%), chlorophyll fluorescence (52% and 34%) and carotenoids (57% and 36%) in the shoot of both the varieties. The PGPR inoculation significantly reduced lipid peroxidation (33% and 23%) and decreased the proline content and antioxidant enzymes activities (32% and 38%) as compared to plants grown in rainfed soil. Significant increases (>52%) were noted in the contents of Ca, Mg, K Cu, Co, Fe and Zn in the shoots of plants and rhizosphere of maize inoculated with the PGPR consortium. The soil organic matter, total nitrogen and C/N ratio were increased (42%), concomitant with the decrease in the bulk density of the rhizosphere. The PGPR consortium, SA and their combined treatment significantly enhanced the IAA (73%) and GA (70%) contents but decreased (55%) the ABA content of shoot. The rhizosphere of plants treated with PGPR, SA and consortium showed a maximum accumulation (>50%) of IAA, GA and ABA contents, the sensitive variety had much higher ABA content than the tolerant variety. It is inferred from the results that rhizosphere soil of treated plants enriched with nutrients content, organic matter and greater concentration of growth promoting phytohormones, as well as stress hormone ABA, which has better potential for seed germination and establishment of seedlings for succeeding crops. Full article

(This article belongs to the Special Issue Microorganisms and Plant Nutrition)

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Review

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18 pages, 655 KiB

Open AccessReview

Fermentation Strategies to Improve Soil Bio-Inoculant Production and Quality

by Maria Vassileva, Eligio Malusà, Lidia Sas-Paszt, Pawel Trzcinski, Antonia Galvez, Elena Flor-Peregrin, Stefan Shilev, Loredana Canfora, Stefano Mocali and Nikolay Vassilev

Microorganisms 2021, 9(6), 1254; https://doi.org/10.3390/microorganisms9061254 - 9 Jun 2021

Cited by 40 | Viewed by 11890

Abstract

The application of plant beneficial microorganisms has been widely accepted as an efficient alternative to chemical fertilizers and pesticides. Isolation and selection of efficient microorganisms, their characterization and testing in soil-plant systems are well studied. However, the production stage and formulation of the final products are not in the focus of the research, which affects the achievement of stable and consistent results in the field. Recent analysis of the field of plant beneficial microorganisms suggests a more integrated view on soil inoculants with a special emphasis on the inoculant production process, including fermentation, formulation, processes, and additives. This mini-review describes the different groups of fermentation processes and their characteristics, bearing in mind different factors, both nutritional and operational, which affect the biomass/spores yield and microbial metabolite activity. The characteristics of the final products of fermentation process optimization strategies determine further steps of development of the microbial inoculants. Submerged liquid and solid-state fermentation processes, fed-batch operations, immobilized cell systems, and production of arbuscular mycorrhiza are presented and their advantages and disadvantages are discussed. Recommendations for further development of the fermentation strategies for biofertilizer production are also considered. Full article

(This article belongs to the Special Issue Microorganisms and Plant Nutrition)

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10 pages, 290 KiB

Open AccessReview

Aspegillus terreus: From Soil to Industry and Back

by Maria Vassileva, Eligio Malusá, Bettina Eichler-Löbermann and Nikolay Vassilev

Microorganisms 2020, 8(11), 1655; https://doi.org/10.3390/microorganisms8111655 - 25 Oct 2020

Cited by 15 | Viewed by 3748

Abstract

Aspergillus terreus is an important saprophytic filamentous fungus that can be found in soils. Like many other soil microorganisms, A. terreus demonstrates multiple functions and offers various important metabolites, which can be used in different fields of human activity. The first application of A. terreus on an industrial level is the production of itaconic acid, which is now considered as one of the most important bioproducts in the Green Chemistry field. The general schemes for itaconic acid production have been studied, but in this mini-review some lines of future research are presented based on analysis of the published results. A. terreus is also intensively studied for its biocontrol activity and plant growth-promoting effect. However, this microorganism is also known to infect important crops such as, amongst others, rice, wheat, potato, sugar cane, maize, and soybean. It was suggested, however, that the balance between positive vs. negative effects is dependent on the soil-plant-inoculant dose system. A. terreus has frequently been described as an important human pathogen. Therefore, its safety manipulation in biotechnological processes for the production of itaconic acid and some drugs and its use in soil-plant systems should be carefully assessed. Some suggestions in this direction are discussed, particularly concerning the uses in crop production. Full article

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