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Agronomy
Special Issues
Management of Agricultural Microbiomes towards Sustainability and Restoration
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Management of Agricultural Microbiomes towards Sustainability and Restoration

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Soil and Plant Nutrition".

Deadline for manuscript submissions: closed (5 March 2022) | Viewed by 13883

Special Issue Editors

Dr. Blanca R. López

E-Mail Website
Guest Editor
1. Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico
2. Bashan Institute of Science, Auburn, AL, USA
Interests: bacterial endophytes; microbial inoculants; plant–soil interaction; microbial communities
Special Issues, Collections and Topics in MDPI journals
Dr. Luz E. De-Bashan

E-Mail Website
Guest Editor
Bashan Institute of Sciences, 1730 Post Oak Ct, Auburn, AL 36830, USA
Interests: plant–bacteria interaction; microbial inoculants; plant growth promoting bacteria; microbial-assisted restoration of degraded soils
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

During the last century, crop production has been characterized by the excessive use of synthetic fertilizers, pesticides, and agricultural practices that challenge the resilience of agroecosystems, leading in many cases to soil degradation and desertification, intensified by climate change. Microorganisms are nutrient cycling drivers and essential players in agroecological processes that influence soil fertility and improve crop performance against pests and environmental stress. Currently, comprehensive studies using omic technologies elucidate the diversity and function of microbial assemblages across agricultural components (soils, water) and different trophic levels (plants, soil mesofauna, herbivores), thus enabling the potential use of microbiomes as a biotechnological tool for agroecosystems sustainability and restoration.

This Special Issue aims to gather transdisciplinary contributions with innovative research, methodological proposals, and research ideas on agricultural microbiomes, focused on (but not restricted to) the following topics:

  • Methodological and experimental approaches that assess microbiomes across multitrophic levels (interactions) in degraded and recovered agroecosystems;
  • Management of agricultural microbiomes to address issues such as pest management or soil restoration;
  • Culture approaches (culturomics);
  • Microbiome-based biostimulants and their effect on plants, animals, and other components of the agroecosystem;
  • Microbial tools to revert soil degradation in agroecosystems.

We seek regular research papers, communications, short notes, reviews with research proposals, and original ideas.

Dr. Blanca R. López
Dr. Luz E. de-Bashan
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

  • agricultural microbiomes
  • soil degradation
  • restoration
  • multitrophic interactions

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Published Papers (4 papers)

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Research

14 pages, 1463 KiB  
Article
Impact of Azospirillum sp. B510 on the Rhizosphere Microbiome of Rice under Field Conditions
by Michiko Yasuda, Khondoker M. G. Dastogeer, Elsie Sarkodee-Addo, Chihiro Tokiwa, Tsuyoshi Isawa, Satoshi Shinozaki and Shin Okazaki
Agronomy 2022, 12(6), 1367; https://doi.org/10.3390/agronomy12061367 - 5 Jun 2022
Cited by 15 | Viewed by 4219
Abstract
There has been increasing attention toward the influence of biofertilizers on the composition of microbial communities associated with crop plants. We investigated the impact of Azospirillum sp. B510, a bacterial strain with nitrogen-fixing ability, on the structure of bacterial and fungal communities within [...] Read more.
There has been increasing attention toward the influence of biofertilizers on the composition of microbial communities associated with crop plants. We investigated the impact of Azospirillum sp. B510, a bacterial strain with nitrogen-fixing ability, on the structure of bacterial and fungal communities within rice plant rhizospheres by amplicon sequencing at two sampling stages (the vegetative and harvest stages of rice). Principal coordinate analysis (PCoA) demonstrated a significant community shift in the bacterial microbiome when the plants were inoculated with B510 at the vegetative stage, which was very similar to the effect of chemical N-fertilizer application. This result suggested that the inoculation with B510 strongly influenced nitrogen uptake by the host plants under low nitrogen conditions. Least discriminant analysis (LDA) showed that the B510 inoculation significantly increased the N2-fixing Clostridium, Aeromonas and Bacillus populations. In contrast, there was no apparent influence of B510 on the fungal community structure. The putative functional properties of bacteria were identified through PICRUSt2, and this hinted that amino acid, sugar and vitamin production might be related to B510 inoculation. Our results indicate that B510 inoculation influenced the bacterial community structure by recruiting other N2-fixing bacteria in the absence of nitrogen fertilizer. Full article
(This article belongs to the Special Issue Management of Agricultural Microbiomes towards Sustainability and Restoration)
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13 pages, 1939 KiB  
Article
Effect of Plant Growth-Promoting Bacteria Azospirillum brasilense on the Physiology of Radish (Raphanus sativus L.) under Waterlogging Stress
by Gisselle Salazar-Garcia, Helber Enrique Balaguera-Lopez and Juan Pablo Hernandez
Agronomy 2022, 12(3), 726; https://doi.org/10.3390/agronomy12030726 - 17 Mar 2022
Cited by 3 | Viewed by 3684
Abstract
Stress due to waterlogging is considered an abiotic factor that negatively affects crop production, which, together with the excessive fertilization of crops, reduces cost-effectiveness and generates the need to create sustainable alternatives economically and environmentally. The effect of inoculation with Azospirillum brasilense on [...] Read more.
Stress due to waterlogging is considered an abiotic factor that negatively affects crop production, which, together with the excessive fertilization of crops, reduces cost-effectiveness and generates the need to create sustainable alternatives economically and environmentally. The effect of inoculation with Azospirillum brasilense on the physiology of the Raphanus sativus var. Crimson Giant subjected to waterlogging, was evaluated. Stomatal conductance, chlorophyll concentration and chlorophyll a fluorescence were analyzed to establish this effect, corroborating the beneficial effect of inoculation with A. brasilense in radish under waterlogging stress. The stomatal conductance of inoculated and waterlogged treatments presented the same values as the control plants, and photosystem II efficiency was favored in inoculated and waterlogged treatments (0.6 Fv/Fm) compared to non-inoculated and waterlogged treatments (0.3 Fv/Fm). The results suggested that this increased efficiency was due to the preservation of photosynthetic pigments in the tissues, allowing the preservation of stomatal conductance and a reduction in the amount of energy dissipated in the form of heat (fluorescence) due to inoculation with A. brasilense. Therefore, plant growth-promoting bacteria are responsible for activating and improving some physiological mechanisms of the plant. Full article
(This article belongs to the Special Issue Management of Agricultural Microbiomes towards Sustainability and Restoration)
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14 pages, 26869 KiB  
Article
Effects of Nutrient Levels and Rice Cultivation on Taxonomic and Functional Diversity of Bacterial Communities in Flooded Soils of the Hanon Maar Crater, Korea
by Jinu Eo and Myung-Hyun Kim
Agronomy 2022, 12(3), 651; https://doi.org/10.3390/agronomy12030651 - 7 Mar 2022
Cited by 2 | Viewed by 2330
Abstract
Agricultural land use may deteriorate soil bacterial diversity and function in an agroecosystem. This study aimed to explore the impact of agricultural disturbance on the taxonomic and functional diversity of soil bacteria using a high-throughput sequencing method. We examined the bacterial community diversity [...] Read more.
Agricultural land use may deteriorate soil bacterial diversity and function in an agroecosystem. This study aimed to explore the impact of agricultural disturbance on the taxonomic and functional diversity of soil bacteria using a high-throughput sequencing method. We examined the bacterial community diversity in five types of flooded soils in the Hanon Maar Crater from two types of canals characterized by different nutrient levels and three field types with a different rice cultivation history. Proteobacteria (43.2%), Chloroflexi (19.8%), Acidobacteria (15.8%), Actinobacteria (5.1%), and Nitrospirae (5.0%) were the dominant phyla (>5%). The relative abundance of Actinobacteria was 7.1 times greater in the abandoned fields than in the polluted canal. Alpha diversity indices of taxonomic diversity showed strong negative correlations with C, N, and NH4+ levels. The 1.7-fold greater number of operational taxonomic units (OTUs) in abandoned fields than in paddy fields may be caused by factors other than nutrients. Functional analysis revealed that 11 putative functions, including cellulolysis and ligninolysis, were significantly affected by soil management. Functional diversity indices showed negative correlations with electrical conductivity (EC) and NH4+. Nitrogen input had a greater effect on bacterial taxonomic diversity than on functional diversity. Available P was positively correlated with the diversity indices. Taken together, these results suggest that keeping land fallow for more than 5 years and monitoring of C, N, and P levels are practical approaches for restoring taxonomic diversity but not functional diversity of soil bacteria. Our study demonstrated a decoupled response of taxonomic and functional diversity to rice cultivation, highlighting the necessity of further studies on the impact of decoupling on the stability of ecosystem functioning. Full article
(This article belongs to the Special Issue Management of Agricultural Microbiomes towards Sustainability and Restoration)
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13 pages, 1489 KiB  
Article
Use of Acyl-Homoserine Lactones Leads to Improved Growth of Ginseng Seedlings and Shifts in Soil Microbiome Structure
by Jerald-Conrad Ibal, Min-Kyu Park, Gun-Seok Park, Byung-Kwon Jung, Tae-Hyung Park, Min-Sueng Kim, Gi-Ung Kang, Yeong-Jun Park and Jae-Ho Shin
Agronomy 2021, 11(11), 2177; https://doi.org/10.3390/agronomy11112177 - 28 Oct 2021
Cited by 7 | Viewed by 2837
Abstract
Panax ginseng is a well-known medicinal plant that achieves strong resistance against plant pathogens while growing in the wild. Due to the high market demand for ginseng as a health food source, ginseng cultivation is prevalent in South Korea. However, continuous monocropping creates [...] Read more.
Panax ginseng is a well-known medicinal plant that achieves strong resistance against plant pathogens while growing in the wild. Due to the high market demand for ginseng as a health food source, ginseng cultivation is prevalent in South Korea. However, continuous monocropping creates problems like irregular growth or vulnerability to crop diseases. Quorum sensing (QS) deals with the intracellular communication of bacteria and plays a role in dynamic changes in the soil microbiome. Here, we investigated how acyl-homoserine lactone (AHL) signaling molecules in QS (C8, C10, and C12) improve plant growth and induce shifts in the soil microbiome. To assess the effects, we recorded root and shoot growth of ginseng seedlings and checked the changes in the soil microbiome during different time points (0, 2, 4, and 8) after 8 weeks of growth. We observed that soils treated with N-decanoyl-L-homoserine lactone (C10) showed the most pronounced effects. Very striking was that C10 had the lowest alpha diversity. Using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), we observed a high number of QS-related functional genes, with the highest count occurring in the untreated planted soil (W). Together with the known direct and beneficial effects of AHLs on plant development, AHLs treated mono-cropped soil showed trends in the microbiome community. Full article
(This article belongs to the Special Issue Management of Agricultural Microbiomes towards Sustainability and Restoration)
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