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Beneficial Soil Microorganisms for Improved Plant Performance and Resilience in Sustainable Agricultural Systems

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A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Farming Sustainability".

Deadline for manuscript submissions: closed (31 July 2022) | Viewed by 21257

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Special Issue Editors

Prof. Dr. Helena Freitas

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Guest Editor

Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
Interests: agroecology; ecology; forest and agriculture; ecology and management of exotic and invasive species; nature conservation; biodiversity; ecosystem services; tolerance to stress and bioremediation; environmental policy; microbial ecology
Special Issues, Collections and Topics in MDPI journals

Dr. Rui S. Oliveira

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Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
Interests: plant-microbe interactions; mycorrhiza; plant beneficial bacteria; sustainable agriculture; phytoremediation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Intensive agriculture relies on increased use of chemical fertilizers, pesticides and water resources. However, such high-input farming practices are neither sustainable nor environmentally desirable, leading ultimately to public health issues. Moreover, these detrimental effects are predicted to magnify under the warmer, drier climate of the future.

Achieving agricultural sustainability is one of the major challenges of mankind. Several groups of soil microorganisms with their wide range of plant beneficial traits have great potential to be used as agronomic tools that can contribute to mitigating the deleterious effects of intensive farming and progress towards agricultural sustainability.

The interest in applying beneficial microbes for improving plant performance has been steadily growing and their exploration in agroecosystems has never been so relevant and timely. In this context, this Special Issue welcomes recent advances on the roles of beneficial soil microorganisms in sustainable cropping systems. Topics include but are not limited to:

Crop yield enhancement by soil microbes;
Influence of beneficial soil microbes in improving the nutritional value of crop foods;
Microbe-assisted mitigation of plant abiotic stresses (e.g., drought, salinity) related to climate change;
Contribution of soil microbes for increasing crop tolerance to biotic stresses caused by pathogenic bacteria, fungi, viruses, nematodes, insects, arachnids and weeds;
Soil microbial diversity and its relation to crop performance;
Microbial formulations for agricultural applications;
Inoculation methods of beneficial soil microbes.

Prof. Dr. Helena Freitas
Dr. Rui Oliveira
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. Agronomy 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 2600 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

mycorrhizal fungi
plant growth promoting bacteria
rhizobia
Trichoderma
plant–microbe interactions
crop yield
nutritional value
abiotic stresses
biotic stresses
climate change
microbial diversity
microbial formulations
inoculation methods

Published Papers (7 papers)

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Research

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14 pages, 2239 KiB

Open AccessArticle

Diversity and Potential Function of the Bacterial Rhizobiome Associated to Physalis Ixocarpa Broth. in a Milpa System, in Michoacan, Mexico

by Daniella Ariza-Mejía, Guadalupe Oyoque-Salcedo, Valentina Angóa-Pérez, Hortencia G. Mena-Violante, Dioselina Álvarez-Bernal and Jesús R. Torres-García

Agronomy 2022, 12(8), 1780; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12081780 - 28 Jul 2022

Cited by 3 | Viewed by 1663

Abstract

Michoacan state has a long history in plant domestication’s. Physalis ixocarpa is a native plant that growth associated to maize crops from this region. Due to the domestication process includes the adaptation to environmental factors, we ask if (1) Does P. ixocarpa has the capacity of association with bacterial communities of the zone where it was domesticated? and (2) Does the rhizobiome of this plant can increase the potential functions in the soil? An experiment was established in a traditional milpa system. Samples of rhizobiome from corn, P. ixocarpa, P. philadelphica, and soil were sequenced using Next Generation Sequencing in the region 16S. The potential function, metabolic pathway reconstruction and participation of each bacteria genus was inferred using iVikodak platform. A total of 34 Phyla and 795 genera were identified. Purine metabolism’s was the principal function, where all rhizobiomes showed similar metabolic pathways. However, the difference among plant species is the participation of the distinct genera in the Purine metabolism. We conclude that the rhizobiome of P. ixocarpa maintains the capacity of bacterial association in the region and shows complementarity for the soil functions. Therefore, their utilization can be helpful in zones where the agricultural practices have degraded microbiological soil conditions. Full article

(This article belongs to the Special Issue Beneficial Soil Microorganisms for Improved Plant Performance and Resilience in Sustainable Agricultural Systems)

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13 pages, 1138 KiB

Open AccessArticle

Different Green Manures (Vicia villosa and Brassica juncea) Construct Different Fungal Structures, Including Plant-Growth-Promoting Effects, after Incorporation into the Soil

by Waleed Asghar and Ryota Kataoka

Agronomy 2022, 12(2), 323; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12020323 - 26 Jan 2022

Cited by 5 | Viewed by 2612

Abstract

The application of green manure to soil improves soil health by increasing biological activity. However, little attention has been paid to the effects of different green manures on the microbiological community and soil function after incorporation. Here, it was found that the green manures of Vicia villosa (leguminous) and Brassica juncea (non-leguminous) have different fungal structures, despite the soil originally being the same. Moreover, some isolated strains showed plant-growth-promoting abilities. Three strains (H1: Penicillium spp., H2: Clonostachys spp., and H3: Trichoderma spp.) from leguminous-manure-incorporated soil and four strains (B1: Purpureocillium spp., B4: Taifanglania spp., B6: Trichoderma spp., and B10: Aspergillus spp.) from non-leguminous-manure-incorporated soil showed the potential for plant growth enhancement. Plant-growth-promoting traits revealed that four strains possessed phosphate solubilization and siderophore production, although none of them showed the ability to produce indole-3-acetic acid (IAA)-like compounds with/without tryptophan. In addition, higher extracellular enzyme activities—including endoglucanase and β-glucosidase activities—were also detected in the soil-incorporated green manures. In conclusion, this study suggests that different fungal structures appeared when different green manures were applied, which promoted plant growth. This indicates the potential benefits of promoting the incorporation of green manure into the soil. Full article

(This article belongs to the Special Issue Beneficial Soil Microorganisms for Improved Plant Performance and Resilience in Sustainable Agricultural Systems)

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17 pages, 2372 KiB

Open AccessArticle

Early Effects of Fertilizer and Herbicide Reduction on Root-Associated Biota in Oil Palm Plantations

by Aisjah R. Ryadin, Dennis Janz, Dominik Schneider, Aiyen Tjoa, Bambang Irawan, Rolf Daniel and Andrea Polle

Agronomy 2022, 12(1), 199; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12010199 - 14 Jan 2022

Cited by 4 | Viewed by 3020

Abstract

To secure high yield, tropical oil palm plantations are fertilized, and understory vegetation is controlled by chemical clearing with herbicides. These treatments cause a drastic turnover of soil microbes and cause loss of beneficial mycorrhizal fungi. Here, we tested if reduced fertilization and weeding instead of conventional treatments restored beneficial ecological groups associated with roots. We conducted our study one year after the start of the reduced management in large-scale oil palm plantations. We hypothesized that reduced fertilizer application and weeding result in shifts of the root-associated species composition because changes in the management regimes affect belowground biomass and nutrients in soil and roots. Alternatively, we hypothesized that the legacy of massive soil fertilization and herbicide application preclude compositional shifts of root-associated biota within short time periods. We did not find any significant treatment effects on root nutrient contents, root biomass, and nutrients in soil. At the level of species (based on operational taxonomic units obtained by Illumina sequencing) or phyla, no significant effects of reduced management were observed. However, distinct functional groups showed early responses to the treatments: nematodes decreased in response to weeding; yeasts and ectomycorrhizal-multitrophic fungi increased under fertilizer treatments; arbuscular mycorrhizal fungi increased under fertilizer reduction. Since the responsive ecological groups were represented by low sequence abundances, their responses were masked by very high sequence abundances of saprotrophic and pathotrophic fungi. Thus, the composition of the whole root-associated community was unaffected by reduced management. In conclusion, our results show that changes in management regimes start to re-wire critical constituents of soil–plant food webs. Full article

(This article belongs to the Special Issue Beneficial Soil Microorganisms for Improved Plant Performance and Resilience in Sustainable Agricultural Systems)

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15 pages, 1639 KiB

Open AccessArticle

Changes in Soil-Borne Communities of Arbuscular Mycorrhizal Fungi during Natural Regrowth of Abandoned Cattle Pastures Are Indicative of Ecosystem Restoration

by Carlos H. Rodríguez-León, Clara P. Peña-Venegas, Armando Sterling, Herminton Muñoz-Ramirez and Yeny R. Virguez-Díaz

Agronomy 2021, 11(12), 2468; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11122468 - 03 Dec 2021

Cited by 3 | Viewed by 2817

Abstract

Natural restoration of ecosystems includes the restoration of plant-microbial associations; however, few studies had documented those changes in tropical ecosystems. With the aim to contribute to understand soil microbial changes in a natural regrowth succession of degraded pastures that were left for natural restoration, we studied changes in arbuscular mycorrhizal (AM) fungal communities. Arbuscular mycorrhizal fungi (AMF) establish a mutualistic symbiosis with plants, improving plant nutrition. Amplification of the small subunit rRNA with specific primers and subsequent Illumina sequencing were used to search soil-borne AM fungal communities in four successional natural regrowth stages in two landscapes (hill and mountain) with soil differences, located in the Andean-Amazonian transition. Molecular results corroborated the results obtained previously by spores-dependent approaches. More abundance and virtual taxa of AMF exist in the soil of degraded pastures and early natural regrowth stages than in old-growth or mature forest soils. Although changes in AM fungal communities occurred similarly over the natural regrowth chronosequence, differences in soil texture between landscapes was an important soil feature differentiating AM fungal community composition and richness. Changes in soil-borne AM fungal communities reflect some signals of environmental restoration that had not been described before, such as the reduction of Glomus dominance and the increase of Paraglomus representativeness in the AM fungal community during the natural regrowth chronosequence. Full article

(This article belongs to the Special Issue Beneficial Soil Microorganisms for Improved Plant Performance and Resilience in Sustainable Agricultural Systems)

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18 pages, 2323 KiB

Open AccessArticle

Growth Promotion of Rapeseed (Brassica napus L.) and Blackleg Disease (Leptosphaeria maculans) Suppression Mediated by Endophytic Bacteria

by Nikola Lipková, Juraj Medo, Renata Artimová, Jana Maková, Jana Petrová, Soňa Javoreková and Jaroslav Michalko

Agronomy 2021, 11(10), 1966; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11101966 - 29 Sep 2021

Cited by 9 | Viewed by 2216

Abstract

Rapeseed is an important oil crop strongly dependent on high agrochemical inputs. Some pathogens, including Leptosphaeria maculans, cause blackleg disease and can drastically decrease yields. Microbial inoculants seem to be a promising solution to these problems. However, a selection of potent bacterial strains able to improve growth and/or suppress disease is needed. Endophytic bacteria (n = 38) isolated from rapeseed plants with exceptionally good growth were screened for plant growth promoting (PGP) traits and L. maculans antifungal activity. A majority of isolates (35) showed the ability to produce siderophores, 17 isolates solubilized phosphate, and 28 isolates inhibited the growth of L. maculans. The six most promising isolates belonging to Bacillus genera were characterized in detail and compared to two previously published PGP strains. Plant growth measured as total weight and root length of rapeseed seedlings was stimulated by all isolates in comparison to control. The best isolate, 1L6, preliminary identified as Bacillus pumilus showed the highest phosphate solubilization, IAA and HCN production, and growth promotion of plants. Isolates with high antifungal activity in screening showed good potential to suppress disease on plants, with 87% reduction of lesions caused by L. maculans. These strains are good candidates to be explored under field use either solely or in combination. Full article

(This article belongs to the Special Issue Beneficial Soil Microorganisms for Improved Plant Performance and Resilience in Sustainable Agricultural Systems)

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12 pages, 1203 KiB

Open AccessArticle

Beneficial Soil Microbes Negatively Affect Spider Mites and Aphids in Pepper

by Maria L. Pappas, Konstantinos Samaras, Ioannis Koufakis and George D. Broufas

Agronomy 2021, 11(9), 1831; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11091831 - 13 Sep 2021

Cited by 5 | Viewed by 3092

Abstract

Beneficial soil microbes have long been recognized for their ability to improve plant growth, to antagonize pathogens and to prime plants against biotic stressors. Nevertheless, their ability to enhance plant resistance against arthropod pests remains largely unexplored, especially in crop plants such as pepper. Herein, we assessed the effects of several fungal and bacterial species/strains applied in the soil on the performance of key pests of pepper plants. Specifically, we recorded the impact of pepper inoculation with commercial strains of beneficial bacteria (Bacillus amyloliquefaciens and Pseudomonas spp.) as well as fungi (Trichoderma spp. and Cordyceps fumosorosea) on the population growth of the green peach aphid, Myzus persicae, and the two-spotted spider mite, Tetranychus urticae. Furthermore, we recorded the effects of microbial inoculation on plant growth parameters, such as stem and root weight. We found that both pests can be negatively affected by microbial inoculation: spider mites laid up to 40% fewer eggs, and the number of aphids were up to 50% less on pepper-inoculated plants, depending on the microbe. We also recorded a variation among the tested microbes in their impact on herbivore performance, but no significant effects were found on plant biomass. Our results add to the growing literature that beneficial soil microbes may be capable of exerting biocontrol capabilities against aboveground herbivorous pests possibly, among other means, via the elicitation of plant defense responses. Full article

(This article belongs to the Special Issue Beneficial Soil Microorganisms for Improved Plant Performance and Resilience in Sustainable Agricultural Systems)

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Review

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20 pages, 1826 KiB

Open AccessEditor’s ChoiceReview

Overview of the Role of Rhizobacteria in Plant Salt Stress Tolerance

by Miguel Ayuso-Calles, José David Flores-Félix and Raúl Rivas

Agronomy 2021, 11(9), 1759; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11091759 - 31 Aug 2021

Cited by 31 | Viewed by 4581

Abstract

Salinity is one of the main causes of abiotic stress in plants, resulting in negative effects on crop growth and yield, especially in arid and semi-arid regions. The effects of salinity on plant growth mainly generate osmotic stress, ion toxicity, nutrient deficiency, and oxidative stress. Traditional approaches for the development of salt-tolerant crops are expensive and time-consuming, as well as not always being easy to implement. Thus, the use of plant growth-promoting bacteria (PGPB) has been reported as a sustainable and cost-effective alternative to enhance plant tolerance to salt stress. In this sense, this review aims to understand the mechanisms by which PGPB help plants to alleviate saline stress, including: (i) changes in the plant hormonal balance; (ii) release of extracellular compounds acting as chemical signals for the plant or enhancing soil conditions for plant development; (iii) regulation of the internal ionic content of the plant; or iv) aiding in the synthesis of osmoprotectant compounds (which reduce osmotic stress). The potential provided by PGPB is therefore an invaluable resource for improving plant tolerance to salinity, thereby facilitating an increase in global food production and unravelling prospects for sustainable agricultural productivity. Full article

(This article belongs to the Special Issue Beneficial Soil Microorganisms for Improved Plant Performance and Resilience in Sustainable Agricultural Systems)

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