Soil Fungi in Sustainable Agriculture

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

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 18317

Special Issue Editors

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
Special Issues, Collections and Topics in MDPI journals
Laboratório de Microbiologia e Fitopatologia, Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Monte Carmelo 38500-000, Brazil
Interests: soil health; soil microbiology; biofertilizer; microbial biomass; plant beneficial microorganisms
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soil is the most complex living system containing different organisms involved in specific ecosystem services. Soil provides a natural habitat to organisms such as bacteria, archaea, fungi, protozoans, and nematodes, but bacteria and fungi in particular are by far most numerous and involved in organic matter decomposition, biogeochemical cycling processes, soil formation and structure, and plant growth and health. It has been estimated that one gram of soil contains as many as 1010–1011 bacteria and up to 200 m fungal hyphae, but the number of bacteria in the mycosphere is higher than in bulk soil, indicating the effect of fungi within complex interactions with bacteria. Different free-living and symbiotic fungi play an important role in growth and health of plants and improving their stress tolerance. In addition, fungi take part in soil bioremediation, water absorption, nutrient mobilization and uptake, soil formation and aggregation, and control of plant pathogens. However, fungi are relatively understudied, and we know very little not only regarding specific fungal interactions with other soil organisms but also which are the factors that determine the fungal role in plant microbiota structure, dynamics, and functions. Another multidisciplinary task is learning how to explore fungi more effectively in the frame of sustainable agriculture following the 3-P strategy (prebiotics, probiotics, and postbiotics).

This Special Issue will collect studies on a wide range of soil/plant beneficial and pathogenic fungi, their interactions with below- and above-ground organisms, and their role in nutrient mobilization, plant nutrient acquisition, bioremediation, and biocontrol potential. Special attention will be paid to works on methods of selection/isolation of fungi, their characteristics, production and formulation as biofertilizers, biocontrol, and bioremediation agents. Another group of contributions is related to determination of the soil fungal diversity.

Prof. Dr. Nikolay Bojkov Vassilev
Dr. Gilberto de Oliveira Mendes
Guest Editors

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Keywords

  • plant beneficial microorganisms
  • plant–fungi interactions
  • biofertilizers
  • inoculants
  • biocontrol agents

Published Papers (8 papers)

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Editorial

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5 pages, 198 KiB  
Editorial
Soil Fungi in Sustainable Agriculture
Microorganisms 2024, 12(1), 163; https://doi.org/10.3390/microorganisms12010163 - 13 Jan 2024
Viewed by 479
Abstract
It is widely accepted that the continuously growing human population needs rapid solutions to respond to the increased global demand for high agricultural productivity [...] Full article
(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture)

Research

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14 pages, 1068 KiB  
Article
Crop Productivity Boosters: Native Mycorrhizal Fungi from an Old-Growth Grassland Benefits Tomato (Solanum lycopersicum) and Pepper (Capsicum annuum) Varieties in Organically Farmed Soils
Microorganisms 2023, 11(8), 2012; https://doi.org/10.3390/microorganisms11082012 - 04 Aug 2023
Viewed by 647
Abstract
This paper investigates the response of five tomato and five pepper varieties to native arbuscular mycorrhizal (AM) fungal inoculation in an organic farming system. The field experiment was conducted across a growing season at a working organic farm in Lawrence, KS, USA. The [...] Read more.
This paper investigates the response of five tomato and five pepper varieties to native arbuscular mycorrhizal (AM) fungal inoculation in an organic farming system. The field experiment was conducted across a growing season at a working organic farm in Lawrence, KS, USA. The researchers hypothesized that native AM fungi inoculation would improve crop biomass production for both crop species, but that the magnitude of response would depend on crop cultivar. The results showed that both crops were significantly positively affected by inoculation. AM fungal inoculation consistently improved total pepper biomass throughout the experiment (range of +2% to +8% depending on the harvest date), with a +3.7% improvement at the final harvest for inoculated plants. An interaction between pepper variety and inoculation treatment was sometimes observed, indicating that some pepper varieties were more responsive to AM fungi than others. Beginning at the first harvest, tomatoes showed a consistent positive response to AM fungal inoculation among varieties. Across the experiment, AM fungi-inoculated tomatoes had +10% greater fruit biomass, which was driven by a +20% increase in fruit number. The study highlights the potential benefits of using native AM fungi as a soil amendment in organic farmed soils to improve pepper and tomato productivity. Full article
(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture)
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25 pages, 3976 KiB  
Article
Continued Organic Fertigation after Basal Manure Application Does Not Impact Soil Fungal Communities, Tomato Yield or Soil Fertility
Microorganisms 2023, 11(7), 1715; https://doi.org/10.3390/microorganisms11071715 - 30 Jun 2023
Cited by 1 | Viewed by 997
Abstract
There is currently a limited understanding of the complex response of fungal microbiota diversity to organic fertigation. In this work, a 2-year field trial with organic tomato crops in a soil previously amended with fresh sheep manure was conducted. Two hypotheses were compared: [...] Read more.
There is currently a limited understanding of the complex response of fungal microbiota diversity to organic fertigation. In this work, a 2-year field trial with organic tomato crops in a soil previously amended with fresh sheep manure was conducted. Two hypotheses were compared: (i) fertigation with organic liquid fertilizers versus (ii) irrigation with water. At the end of both years, soils were analyzed for physical–chemical parameters and mycobiome variables. Plate culture and DNA metabarcoding methods were performed in order to obtain a detailed understanding of soil fungal communities. Fertigation did not increase any of the physical–chemical parameters. Concerning soil fungal communities, differences were only found regarding the identification of biomarkers. The class Leotiomycetes and the family Myxotrichaceae were identified as biomarkers in the soil fungal community analyzed by means of DNA metabarcoding of the “fertigation” treatment at the end of Year 1. The Mortierella genus was detected as a biomarker in the “water” treatment, and Mucor was identified in the “fertigation” treatment in the cultivable soil fungi at the end of Year 2. In both years, tomato yield and fruit quality did not consistently differ between treatments, despite the high cost of the fertilizers added through fertigation. Full article
(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture)
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12 pages, 1497 KiB  
Article
Response of Sagebrush Steppe Grass Species to AMF Inoculum Sources and Biochar
Microorganisms 2023, 11(5), 1113; https://doi.org/10.3390/microorganisms11051113 - 25 Apr 2023
Viewed by 1173
Abstract
The sagebrush steppe has presented increasing levels of degradation. The addition of arbuscular mycorrhizal fungi (AMF) and biochar have been suggested to restore ecosystems. However, little is known about their effects on sagebrush steppe plants. We tested three sources of AMF inoculum: soil [...] Read more.
The sagebrush steppe has presented increasing levels of degradation. The addition of arbuscular mycorrhizal fungi (AMF) and biochar have been suggested to restore ecosystems. However, little is known about their effects on sagebrush steppe plants. We tested three sources of AMF inoculum: soil from a disturbed site (Inoculum A), soil from an undisturbed site (Inoculum B), and commercial inoculum (Inoculum C), all with and without biochar, to test if they could mediate growth of Pseudoroegneria spicata (native perennial), Taeniatherum caput-medusae (early seral; exotic annual) and Ventenata dubia (early seral; exotic annual) under greenhouse conditions. We measured AMF colonization and biomass. We hypothesized that the plant species would be differently affected by the inoculum types. The colonization of T. caput-medusae and V. dubia was greatest when inoculated with Inoculum A (38.8% and 19.6%). In contrast, the colonization of P. spicata was greatest with Inoculum B and Inoculum C (32.1% and 32.2). Biochar decreased biomass production but increased colonization with Inoculum A for P. spicata and V. dubia and with Inoculum C for T. caput-medusae. This study reveals the response of early and late seral sagebrush steppe grass species to contrasting sources of AMF and suggests that late seral plant species respond better to late seral inocula. Full article
(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture)
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15 pages, 4901 KiB  
Article
Phosphorus-Solubilizing Capacity of Mortierella Species Isolated from Rhizosphere Soil of a Poplar Plantation
Microorganisms 2022, 10(12), 2361; https://doi.org/10.3390/microorganisms10122361 - 29 Nov 2022
Cited by 9 | Viewed by 2165
Abstract
Phosphorus is one of the main nutrients necessary for plant growth and development. Phosphorus-dissolving microorganisms may convert insoluble phosphorus in soil into available phosphorus that plants can easily absorb and utilize. In this study, four phosphorus-solubilizing fungi (L3, L4, L5, and L12) were [...] Read more.
Phosphorus is one of the main nutrients necessary for plant growth and development. Phosphorus-dissolving microorganisms may convert insoluble phosphorus in soil into available phosphorus that plants can easily absorb and utilize. In this study, four phosphorus-solubilizing fungi (L3, L4, L5, and L12) were isolated from the rhizosphere soil of a poplar plantation in Dongtai, Jiangsu Province, China. Phylogenetic analysis based on the internal transcribed spacer (ITS) and large subunit (LSU) of the ribosomal DNA sequences showed that the ITS and 28S sequences of isolates were the most similar to those of Mortierella. Morphological observation showed that most colonies grew in concentric circles and produced spores under different culture conditions. These results and further microscopic observations showed that these isolated fungi belonged to the genus Mortierella. Pikovskaya (PKO) medium, in which tricalcium phosphate was the sole phosphorus source, was used to screen strain L4 with the best phosphorus-solubilizing effect for further study. When the carbon source was glucose, the nitrogen source was ammonium chloride, the pH was 5, and the available phosphorus content was the highest. By exploring the possible mechanism of phosphorus release by phosphorus-solubilizing fungi, it was found that strain L4 produces several organic acids, such as oxalic acid, lactic acid, acetic acid, succinic acid, tartaric acid, malic acid, and citric acid. At 24 h, the alkaline phosphatase and acid phosphatase activities reached 154.72 mol/(L·h) and 120.99 mol/(L·h), respectively. Full article
(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture)
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12 pages, 1402 KiB  
Article
Aspergillus niger as a Biological Input for Improving Vegetable Seedling Production
Microorganisms 2022, 10(4), 674; https://doi.org/10.3390/microorganisms10040674 - 22 Mar 2022
Cited by 12 | Viewed by 4151
Abstract
This study evaluated the potential of Aspergillus niger as an inoculant for growth promotion of vegetable seedlings. Seven vegetable species were evaluated in independent experiments carried out in 22 + 1 factorial schemes, with two doses of conidia (102 and 10 [...] Read more.
This study evaluated the potential of Aspergillus niger as an inoculant for growth promotion of vegetable seedlings. Seven vegetable species were evaluated in independent experiments carried out in 22 + 1 factorial schemes, with two doses of conidia (102 and 106 per plant) applied in two inoculation methods (seed treatment and in-furrow granular application), plus an uninoculated control. Experiments were carried out in a greenhouse. Growth parameters evaluated were shoot length, stem diameter, root volume, total root length, shoot and root fresh mass, shoot and root dry mass, and total dry mass. Regardless of the dose and inoculation method, seedlings inoculated with A. niger showed higher growth than uninoculated ones for all crops. The highest relative increase promoted by the fungus was observed for aboveground parts, increasing the production of shoot fresh mass of lettuce (61%), kale (40%), scarlet eggplant (101%), watermelon (38%), melon (16%), pepper (92%), and tomato (42%). Aspergillus niger inoculation also increased seedling root growth of lettuce, pepper, scarlet eggplant, watermelon, and tomato. This research shows that A. niger boosts the growth of all analyzed vegetables, appearing as a promising bio-input for vegetable seedling production. Full article
(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture)
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Review

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20 pages, 2591 KiB  
Review
Review on Performance of Aspergillus and Penicillium Species in Biodegradation of Organochlorine and Organophosphorus Pesticides
Microorganisms 2023, 11(6), 1485; https://doi.org/10.3390/microorganisms11061485 - 02 Jun 2023
Cited by 2 | Viewed by 1655
Abstract
The use of pesticides in agricultural practices raises concerns considering the toxic effects they generate in the environment; thus, their sustainable application in crop production remains a challenge. One of the frequently addressed issues regarding their application includes the development of a sustainable [...] Read more.
The use of pesticides in agricultural practices raises concerns considering the toxic effects they generate in the environment; thus, their sustainable application in crop production remains a challenge. One of the frequently addressed issues regarding their application includes the development of a sustainable and ecofriendly approach for their degradation. Since the filamentous fungi can bioremediate various xenobiotics owing to their efficient and versatile enzymatic machinery, this review has addressed their performance in the biodegradation of organochlorine and organophosphorus pesticides. It is focused particularly on fungal strains belonging to the genera Aspergillus and Penicillium, since both are ubiquitous in the environment, and often abundant in soils contaminated with xenobiotics. Most of the recent reviews on microbial biodegradation of pesticides focus primarily on bacteria, and the soil filamentous fungi are mentioned only marginally there. Therefore, in this review, we have attempted to demonstrate and highlight the exceptional potential of aspergilli and penicillia in degrading the organochlorine and organophosphorus pesticides (e.g., endosulfan, lindane, chlorpyrifos, and methyl parathion). These biologically active xenobiotics have been degraded by fungi into various metabolites efficaciously, or these are completely mineralized within a few days. Since they have demonstrated high rates of degradation activity, as well as high tolerance to pesticides, most of the Aspergillus and Penicillium species strains listed in this review are excellent candidates for the remediation of pesticide-contaminated soils. Full article
(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture)
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14 pages, 756 KiB  
Review
Fungi, P-Solubilization, and Plant Nutrition
Microorganisms 2022, 10(9), 1716; https://doi.org/10.3390/microorganisms10091716 - 26 Aug 2022
Cited by 15 | Viewed by 5966
Abstract
The application of plant beneficial microorganisms is widely accepted as an efficient alternative to chemical fertilizers and pesticides. It was shown that annually, mycorrhizal fungi and nitrogen-fixing bacteria are responsible for 5 to 80% of all nitrogen, and up to 75% of P [...] Read more.
The application of plant beneficial microorganisms is widely accepted as an efficient alternative to chemical fertilizers and pesticides. It was shown that annually, mycorrhizal fungi and nitrogen-fixing bacteria are responsible for 5 to 80% of all nitrogen, and up to 75% of P plant acquisition. However, while bacteria are the most studied soil microorganisms and most frequently reported in the scientific literature, the role of fungi is relatively understudied, although they are the primary organic matter decomposers and govern soil carbon and other elements, including P-cycling. Many fungi can solubilize insoluble phosphates or facilitate P-acquisition by plants and, therefore, form an important part of the commercial microbial products, with Aspergillus, Penicillium and Trichoderma being the most efficient. In this paper, the role of fungi in P-solubilization and plant nutrition will be presented with a special emphasis on their production and application. Although this topic has been repeatedly reviewed, some recent views questioned the efficacy of the microbial P-solubilizers in soil. Here, we will try to summarize the proven facts but also discuss further lines of research that may clarify our doubts in this field or open new perspectives on using the microbial and particularly fungal P-solubilizing potential in accordance with the principles of the sustainability and circular economy. Full article
(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture)
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