The Role of Soil Amendments in Shaping Soil and Plant-Associated Microbiomes

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: closed (31 May 2021) | Viewed by 22931

Special Issue Editors

Newe Yaar Research Center, Agricultural Research Organization (ARO), Ramat Yishay 30095, Israel
Interests: systems biology; microbial communities; metabolic networks; genomics
Department of Plant Pathology, Stellenbosch University, South Africa; Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA 98801, USA
Interests: the role of microbes in ecosystem health; plant-microbe and microbe-microbe interactions; engineering disease-suppressive microbial consortia
Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA 98801, USA
Interests: the role of microbes in ecosystem health; plant-microbe and microbe-microbe interactions; microbial carbon and energy use efficiency

Special Issue Information

Dear Colleagues,

Soil amendments generally refer to various organic inputs based on livestock manure, green manure, and cover crops that are extensively utilized in organic agricultural systems for soil-borne disease management. Soil-amendment-based strategies typically utilize effective nutritional sources to either stimulate disease-suppressing populations or directly suppress specific pathogenic elements in soil. The use of such strategies is consistent with accumulating evidence indicating that plant health and soil fertility are to a large extent governed by the broader microbial consortia in soil. Accordingly, successful application of amendment-based approaches provides both a conceptual and practical paradigm for improving food production in ways that also reduce negative impacts on the environment. To date, however, very few such protocols have been found that outperform conventional practices. The main goal of the upcoming Special Issue is to review cutting-edge studies investigating the influence of amendment-based practices on soil- and plant-associated communities from the rhizosphere and endosphere to phyllosphere. A broader understanding and consideration of how these altered microbiomes may enhance or diminish plant health will support the development of more sustainable and effective amendment-based approaches.

Dr. Shiri Freilich
Guest Editor

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Keywords

  • Sustainable agriculture 
  • Microbial communities 
  • Systems biology 
  • Soil amendments

Published Papers (9 papers)

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Research

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17 pages, 1631 KiB  
Article
Water Relations, Gas Exchange, Chlorophyll Fluorescence and Electrolyte Leakage of Ectomycorrhizal Pinus halepensis Seedlings in Response to Multi-Heavy Metal Stresses (Pb, Zn, Cd)
by Chadlia Hachani, Mohammed S. Lamhamedi, Abdenbi Zine El Abidine, Mejda Abassi, Damase P. Khasa and Zoubeir Béjaoui
Microorganisms 2022, 10(1), 57; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010057 - 28 Dec 2021
Cited by 7 | Viewed by 1794
Abstract
The success of mine site restoration programs in arid and semi-arid areas poses a significant challenge and requires the use of high-quality seedlings capable of tolerating heavy metal stresses. The effect of ectomycorrhizal fungi on different physiological traits was investigated in Pinus halepensis [...] Read more.
The success of mine site restoration programs in arid and semi-arid areas poses a significant challenge and requires the use of high-quality seedlings capable of tolerating heavy metal stresses. The effect of ectomycorrhizal fungi on different physiological traits was investigated in Pinus halepensis seedlings grown in soil contaminated with heavy metals (Pb-Zn-Cd). Ectomycorrhizal (M) and non-ectomycorrhizal (NM) seedlings were subjected to heavy metals stress (C: contaminated, NC: control or non-contaminated) soils conditions for 12 months. Gas exchange, chlorophyll fluorescence, water relations parameters derived from pressure–volume curves and electrolyte leakage were evaluated at 4, 8 and 12 months. Ectomycorrhizal symbiosis promoted stronger resistance to heavy metals and improved gas exchange parameters and water-use efficiency compared to the non-ectomycorrhizal seedlings. The decrease in leaf osmotic potentials (Ψπ100: osmotic potential at saturation and Ψπ0: osmotic potential with loss of turgor) was higher for M-C seedling than NM-C ones, indicating that the ectomycorrhizal symbiosis promotes cellular osmotic adjustment and protects leaf membrane cell against leakage induced by Pb, Zn and Cd. Our results suggest that the use of ectomycorrhizal symbiosis is among the promising practices to improve the morphophysiological quality of seedlings produced in forest nurseries, their performance and their tolerance to multi-heavy metal stresses. Full article
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11 pages, 2252 KiB  
Article
NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data
by Ofir Tal, Rotem Bartuv, Maria Vetcos, Shlomit Medina, Jiandong Jiang and Shiri Freilich
Microorganisms 2021, 9(9), 1838; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091838 - 30 Aug 2021
Cited by 5 | Viewed by 2677
Abstract
The study of microbial activity can be viewed as a triangle with three sides: environment (dominant resources in a specific habitat), community (species dictating a repertoire of metabolic conversions) and function (production and/or utilization of resources and compounds). Advances in metagenomics enable a [...] Read more.
The study of microbial activity can be viewed as a triangle with three sides: environment (dominant resources in a specific habitat), community (species dictating a repertoire of metabolic conversions) and function (production and/or utilization of resources and compounds). Advances in metagenomics enable a high-resolution description of complex microbial communities in their natural environments and support a systematic study of environment-community-function associations. NetCom is a web-tool for predicting metabolic activities of microbial communities based on network-based interpretation of assembled and annotated metagenomics data. The algorithm takes as an input, lists of differentially abundant enzymatic reactions and generates the following outputs: (i) pathway associations of differently abundant enzymes; (ii) prediction of environmental resources that are unique to each treatment, and their pathway associations; (iii) prediction of compounds that are produced by the microbial community, and pathway association of compounds that are treatment-specific; (iv) network visualization of enzymes, environmental resources and produced compounds, that are treatment specific (2 and 3D). The tool is demonstrated on metagenomic data from rhizosphere and bulk soil samples. By predicting root-specific activities, we illustrate the relevance of our framework for forecasting the impact of soil amendments on the corresponding microbial communities. NetCom is available online. Full article
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15 pages, 3847 KiB  
Article
Root-Associated Microbiomes, Growth and Health of Ornamental Geophytes Treated with Commercial Plant Growth-Promoting Products
by Gavriel Friesem, Noam Reznik, Michal Sharon Cohen, Nir Carmi, Zohar Kerem and Iris Yedidia
Microorganisms 2021, 9(8), 1785; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081785 - 23 Aug 2021
Viewed by 1959
Abstract
The microbial community inhabiting a plant’s root zone plays a crucial role in plant health and protection. To assess the ability of commercial plant growth-promoting products to enhance the positive effects of this environment, two products containing beneficial soil bacteria and a product [...] Read more.
The microbial community inhabiting a plant’s root zone plays a crucial role in plant health and protection. To assess the ability of commercial plant growth-promoting products to enhance the positive effects of this environment, two products containing beneficial soil bacteria and a product containing plant extracts were tested on Zantedeschia aethiopica and Ornithogalum dubium. The products were tested in two different growing media: a soil and a soilless medium. The effects of these products on Pectobacterium brasiliense, the causal agent of soft rot disease, were also evaluated in vitro, and on naturally occurring infections in the greenhouse. The growing medium was found to have the strongest effect on the microbial diversity of the root-associated microbiome, with the next-strongest effect due to plant type. These results demonstrate that either a single bacterial strain or a product will scarcely reach the level that is required to influence soil microbial communities. In addition, the microbes cultured from these products, could not directly inhibit Pectobacterium growth in vitro. We suggest density-based and functional analyses in the future, to study the specific interactions between plants, soil type, soil microbiota and relevant pathogens. This should increase the effectiveness of bio-supplements and soil disinfestation with natural products, leading to more sustainable, environmentally friendly solutions for the control of bacterial plant diseases. Full article
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27 pages, 2083 KiB  
Article
Analysis of Environmental Variables and Carbon Input on Soil Microbiome, Metabolome and Disease Control Efficacy in Strawberry Attributable to Anaerobic Soil Disinfestation
by Shashika S. Hewavitharana, Emmi Klarer, Joji Muramoto, Carol Shennan and Mark Mazzola
Microorganisms 2021, 9(8), 1638; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081638 - 31 Jul 2021
Cited by 11 | Viewed by 2045
Abstract
Charcoal rot and Fusarium wilt, caused by Macrophomina phaseolina and Fusarium oxysporum f. sp. fragariae, respectively, are major soil-borne diseases of strawberry that have caused significant crop losses in California. Anaerobic soil disinfestation has been studied as an industry-level option to replace [...] Read more.
Charcoal rot and Fusarium wilt, caused by Macrophomina phaseolina and Fusarium oxysporum f. sp. fragariae, respectively, are major soil-borne diseases of strawberry that have caused significant crop losses in California. Anaerobic soil disinfestation has been studied as an industry-level option to replace soil fumigants to manage these serious diseases. Studies were conducted to discern whether Gramineae carbon input type, incubation temperature, or incubation duration influences the efficacy of this disease control tactic. In experiments conducted using ‘low rate’ amendment applications at moderate day/night temperatures (24/18 °C), and carbon inputs (orchard grass, wheat, and rice bran) induced an initial proliferation and subsequent decline in soil density of the Fusarium wilt pathogen. This trend coincided with the onset of anaerobic conditions and a corresponding generation of various anti-fungal compounds, including volatile organic acids, hydrocarbons, and sulfur compounds. Generation of these metabolites was associated with increases in populations of Clostridium spp. Overall, carbon input and incubation temperature, but not incubation duration, significantly influenced disease suppression. All Gramineae carbon inputs altered the soil microbiome and metabolome in a similar fashion, though the timing and maximum yield of specific metabolites varied with input type. Fusarium wilt and charcoal rot suppression were superior when anaerobic soil disinfestation was conducted using standard amendment rates of 20 t ha−1 at elevated temperatures combined with a 3-week incubation period. Findings indicate that anaerobic soil disinfestation can be further optimized by modulating carbon source and incubation temperature, allowing the maximum generation of antifungal toxic volatile compounds. Outcomes also indicate that carbon input and environmental variables may influence treatment efficacy in a target pathogen-dependent manner which will require pathogen-specific optimization of treatment protocols. Full article
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22 pages, 2379 KiB  
Article
Organic Amendments Alter Soil Hydrology and Belowground Microbiome of Tomato (Solanum lycopersicum)
by Taylor Readyhough, Deborah A. Neher and Tucker Andrews
Microorganisms 2021, 9(8), 1561; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081561 - 22 Jul 2021
Cited by 8 | Viewed by 2717
Abstract
Manure-derived organic amendments are a cost-effective tool that provide many potential benefits to plant and soil health including fertility, water retention, and disease suppression. A greenhouse experiment was conducted to evaluate how dairy manure compost (DMC), dairy manure compost-derived vermicompost (VC), and dehydrated [...] Read more.
Manure-derived organic amendments are a cost-effective tool that provide many potential benefits to plant and soil health including fertility, water retention, and disease suppression. A greenhouse experiment was conducted to evaluate how dairy manure compost (DMC), dairy manure compost-derived vermicompost (VC), and dehydrated poultry manure pellets (PP) impact the tripartite relationship among plant growth, soil physiochemical properties, and microbial community composition. Of tomato plants with manure-derived fertilizers amendments, only VC led to vigorous growth through the duration of the experiment, whereas DMC had mixed impacts on plant growth and PP was detrimental. Organic amendments increased soil porosity and soil water holding capacity, but delayed plant maturation and decreased plant biomass. Composition of bacterial communities were affected more by organic amendment than fungal communities in all microhabitats. Composition of communities outside roots (bulk soil, rhizosphere, rhizoplane) contrasted those within roots (endosphere). Distinct microbial communities were detected for each treatment, with an abundance of Massilia, Chryseolinea, Scedosporium, and Acinetobacter distinguishing the control, vermicompost, dairy manure compost, and dehydrated poultry manure pellet treatments, respectively. This study suggests that plant growth is affected by the application of organic amendments not only because of the soil microbial communities introduced, but also due to a synergistic effect on the physical soil environment. Furthermore, there is a strong interaction between root growth and the spatial heterogeneity of soil and root-associated microbial communities. Full article
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13 pages, 4728 KiB  
Article
Effect of Fungicide Application on Lowbush Blueberries Soil Microbiome
by Austin W. Lloyd, David Percival and Svetlana N. Yurgel
Microorganisms 2021, 9(7), 1366; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071366 - 23 Jun 2021
Cited by 9 | Viewed by 2244
Abstract
Lowbush blueberries (Vaccinium sp.) are perennial crops produced throughout eastern Canada and Maine through management of wild populations. Given the constraints of this cropping system, the application of fungicides is critical to reducing disease pressure and ensuring consistent yields. However, as plant [...] Read more.
Lowbush blueberries (Vaccinium sp.) are perennial crops produced throughout eastern Canada and Maine through management of wild populations. Given the constraints of this cropping system, the application of fungicides is critical to reducing disease pressure and ensuring consistent yields. However, as plant health is intertwined with soil health, it is important to consider the impact of fungicides on microbial communities. To understand the effects of fungicides in this context, bacterial and fungal microbial communities from fungicide-treated plots, as well as untreated control plots (UTG) were analyzed using amplicon sequencing. The fungicides, considered collectively as a combined treatment group (CTG), lead to a loss in fungal richness. One family, Clavariaceae, had an increased abundance under prothioconazole relative to UTG. This finding may be significant as taxa in Clavariaceae have been thought to potentially form ericoid mycorrhizae with Vaccinium. Five functional pathways and 74 enzymes differed significantly in relative abundance between CTG and UTG including enzymes associated with soil nutrient cycles. Most notably, enzymes corresponding to the breakdown of halogen-organic compounds had an increased abundance in CTG, suggesting bacterial fungicide degradation. Some enzymes associated with soil nutrient cycles differed significantly, possibly implying changes to nutrient pathways due to fungicide treatment. Full article
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24 pages, 4397 KiB  
Article
Impact of Cellulose-Rich Organic Soil Amendments on Growth Dynamics and Pathogenicity of Rhizoctonia solani
by Anna Clocchiatti, Silja Emilia Hannula, Muhammad Syamsu Rizaludin, Maria P. J. Hundscheid, Paulien J. A. klein Gunnewiek, Mirjam T. Schilder, Joeke Postma and Wietse de Boer
Microorganisms 2021, 9(6), 1285; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061285 - 12 Jun 2021
Cited by 9 | Viewed by 3484
Abstract
Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study [...] Read more.
Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study explores these scenarios, with a focus on the pathogenic fungus Rhizoctonia solani. Saprotrophic growth of R. solani on cellulose-rich materials was tested in vitro. This confirmed paper pulp as a highly suitable substrate for R. solani, whereas its performance on wood sawdusts varied with tree species. In two pot experiments, the effects of amendment of R. solani-infected soil with cellulose-rich materials on performance of beetroot seedlings were tested. All deciduous sawdusts and paper pulp stimulated soil fungal biomass, but only oak, elder and beech sawdusts reduced damping-off of beetroot. Oak sawdust amendment gave a consistent stimulation of saprotrophic Sordariomycetes fungi and of seedling performance, independently of the time between amendment and sowing. In contrast, paper pulp caused a short-term increase in R. solani abundance, coinciding with increased disease severity for beet seedlings sown immediately after amendment. However, damping-off of beetroot was reduced if plants were sown two or four weeks after paper pulp amendment. Cellulolytic bacteria, including Cytophagaceae, responded to paper pulp during the first two weeks and may have counteracted further spread of R. solani. The results showed that fungus-stimulating, cellulose-rich amendments have potential to be used for suppression of R. solani. However, such amendments require a careful consideration of material choice and application strategy. Full article
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24 pages, 2576 KiB  
Article
Comparative Analysis of the Apple Root Transcriptome as Affected by Rootstock Genotype and Brassicaceae Seed Meal Soil Amendment: Implications for Plant Health
by Likun Wang, Tracey S. Somera, Heidi Hargarten, Loren Honaas and Mark Mazzola
Microorganisms 2021, 9(4), 763; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040763 - 06 Apr 2021
Cited by 3 | Viewed by 2163
Abstract
Brassicaceae seed meal (SM) soil amendment has been utilized as an effective strategy to control the biological complex of organisms, which includes oomycetes, fungi, and parasitic nematodes, that incites the phenomenon termed apple replant disease. Soil-borne disease control attained in response to Brassicaceae [...] Read more.
Brassicaceae seed meal (SM) soil amendment has been utilized as an effective strategy to control the biological complex of organisms, which includes oomycetes, fungi, and parasitic nematodes, that incites the phenomenon termed apple replant disease. Soil-borne disease control attained in response to Brassicaceae SM amendment is reliant on multiple chemical and biological attributes, including specific SM-generated modifications to the soil/rhizosphere microbiome. In this study, we conducted a comparative analyses of apple root gene expression as influenced by rootstock genotype combined with a seed meal (SM) soil amendment. Apple replant disease (ARD) susceptible (M.26) and tolerant (G.210) rootstocks cultivated in SM-amended soil exhibited differential gene expression relative to corresponding non-treated control (NTC) orchard soil. The temporal dynamics of gene expression indicated that the SM-amended soil system altered the trajectory of the root transcriptome in a genotype-specific manner. In both genotypes, the expression of genes related to plant defense and hormone signaling were altered in SM-amended soil, suggesting SM-responsive phytohormone regulation. Altered gene expression was temporally associated with changes in rhizosphere microbiome density and composition in the SM-treated soil. Gene expression analysis across the two rootstocks cultivated in the pathogen-infested NTC soil showed genotype-specific responses indicative of different defensive strategies. These results are consistent with previously described resistance mechanisms of ARD “tolerant” rootstock cultivars and also add to our understanding of the multiple mechanisms by which SM soil amendment and the resulting rhizosphere microbiome affect apple rootstock physiology. Future studies which assess transcriptomic and metagenomic data in parallel will be important for illuminating important connections between specific rhizosphere microbiota, gene-regulation, and plant health. Full article
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Review

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18 pages, 1176 KiB  
Review
Irreplaceable Role of Amendment-Based Strategies to Enhance Soil Health and Disease Suppression in Potato Production
by Jianjun Hao and Katherine Ashley
Microorganisms 2021, 9(8), 1660; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081660 - 03 Aug 2021
Cited by 5 | Viewed by 2783
Abstract
Soilborne diseases are a major constraining factor to soil health and plant health in potato production. In the toolbox of crop management, soil amendments have shown benefits to control these diseases and improve soil quality. Most amendments provide nutrients to plants and suppress [...] Read more.
Soilborne diseases are a major constraining factor to soil health and plant health in potato production. In the toolbox of crop management, soil amendments have shown benefits to control these diseases and improve soil quality. Most amendments provide nutrients to plants and suppress multiple soilborne pathogens. Soil amendments are naturally derived materials and products and can be classified into fresh or living plants, organic or inorganic matters, and microbial supplements. Fresh plants have unique functions and continuously exude chemicals to interact with soil microbes. Organic and inorganic matter contain high levels of nutrients, including nitrogen and carbon that plants and soil microorganisms need. Soil microorganisms, whether being artificially added or indigenously existing, are a key factor in plant health. Microbial communities can be considered as a biological reactor in an ecosystem, which suppress soilborne pathogens in various mechanisms and turn soil organic matter into absorbable forms for plants, regardless of amendment types. Therefore, soil amendments serve as an energy input, nutrient source, and a driving force of microbial activities. Advanced technologies, such as microbiome analyses, make it possible to analyze soil microbial communities and soil health. As research advances on mechanisms and functions, amendment-based strategies will play an important role in enhancing soil health and disease suppression for better potato production. Full article
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