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Anaerobic Soil Disinfestation: A Tool for Non-Fumigant-Based Integrated Soil-Borne Disease and Pest Management

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A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Pest and Disease Management".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 14998

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Dr. Joji Muramoto

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Department of Environmental Studies, University of California, Santa Cruz 1156 High Street, Santa Cruz, CA 95064, USA
Interests: soil health; agroecology; non-fumigant alternatives

Prof. Dr. Carol Shennan

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Guest Editor

Department of Environmental Studies, University of California, Santa Cruz, CA 95064, USA
Interests: agroecology; integrated fertility and soil-borne disease management
Special Issues, Collections and Topics in MDPI journals

Dr. Erin Rosskopf

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U.S. Horticultural Research Laboratory, 2001 South Rock Road, Ft. Pierce, FL 34945, USA
Interests: soil disinfestation; fungal plant pathogens; weed management; plant nutrition; post-harvest quality

Dr. Noriaki Momma

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Guest Editor

Institute for Horticultural Plant Breeding, 2-5-1 Kamishiki, Matsudo, Chiba 270-2221, Japan
Interests: disease control; breeding for disease resistance

Special Issue Information

Dear Colleagues,

Since its development in early 2000, anaerobic soil disinfestation (ASD), also known as biological soil disinfestation or reductive soil disinfestation, has proven to be a promising non-fumigant approach for soil-borne disease management in high-value crops worldwide. Although the actual commercial scale adoption of ASD remains limited to small farms, buffer zone applications, and some organic berry productions, this approach will play a crucial role in the future of non-fumigant-based soil-borne disease and pest management strategies, which are desperately needed on a global scale. Due to the biological mechanisms involved, ASD’s effects vary depending on factors such as soil type, temperature, previous cropping history, potential for anaerobiosis, type and rate of carbon sources applied, and target pathogens. This Special Issue invites papers from developed and developing countries on cutting edge research facilitating broader adoption and understanding of ASD. In particular, we welcome papers on the development of environmental thresholds for suppressing a range of soil-borne pests by ASD, studies on mechanisms of disease and weed suppression and plant growth enhancement by ASD, potential adverse and positive environmental impacts of ASD, the integrated use of ASD with other non-fumigant-based tactics, the current status of ASD adoption in different parts of the world, and potential limitations and barriers to adopting ASD from stakeholders’ perspectives.

Dr. Joji Muramoto
Prof. Dr. Carol Shennan
Dr. Erin Rosskopf
Dr. Noriaki Momma
Guest Editors

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Keywords

anaerobic soil disinfestation
non-fumigant alternatives
soil-borne disease management
integrated pest management
greenhouse gas emission
barriers to adoption
post-harvest quality

Published Papers (8 papers)

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16 pages, 722 KiB

Open AccessArticle

Brewer’s Spent Grain with Yeast Amendment Shows Potential for Anaerobic Soil Disinfestation of Weeds and Pythium irregulare

by Danyang Liu, Jayesh Samtani, Charles Johnson, Xuemei Zhang, David M. Butler and Jeffrey Derr

Agronomy 2023, 13(8), 2081; https://doi.org/10.3390/agronomy13082081 - 08 Aug 2023

Cited by 1 | Viewed by 1546

Abstract

Anaerobic soil disinfestation (ASD) is a promising alternative to chemical fumigation for controlling soilborne plant pathogens and weeds. This study investigated the impact of brewer’s spent grain (BSG), a locally available carbon source, on various weed species and the oomycete pathogen Pythium irregulare in ASD. Two greenhouse studies were conducted using BSG and yeast at full and reduced rates in a completely randomized design with four replicates and two runs per study. In both studies, ASD treatments significantly decreased the seed viability of all weed species and the Pythium irregulare inoculum, while promoting higher cumulative anaerobicity compared to the non-treated control. The addition of yeast had a notable effect when combined with BSG but not with rice bran. When used in reduced carbon rates, yeast supplementation enhanced the efficacy of BSG, providing comparable control to the full rate for most weed species, including redroot pigweed, white clover, and yellow nutsedge. Interestingly, no ASD treatment affected the soil temperature. Furthermore, BSG treatments caused higher concentrations of volatile fatty acids compared to ASD with rice bran and the non-treated control. This finding suggests that the inclusion of yeast in ASD shows potential for reducing the carbon input required for effective soil disinfestation. Full article

(This article belongs to the Special Issue Anaerobic Soil Disinfestation: A Tool for Non-Fumigant-Based Integrated Soil-Borne Disease and Pest Management)

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19 pages, 16950 KiB

Open AccessArticle

Integrated Pathogen Management in Stevia Using Anaerobic Soil Disinfestation Combined with Different Fungicide Programs in USA, Mexico, and Paraguay

by Andres D. Sanabria-Velazquez, Guillermo A. Enciso-Maldonado, Marco Maidana-Ojeda, Jose F. Diaz-Najera, Sergio Ayvar-Serna, Lindsey D. Thiessen and H. David Shew

Agronomy 2023, 13(5), 1358; https://doi.org/10.3390/agronomy13051358 - 12 May 2023

Viewed by 1753

Abstract

Stevia is a semi-perennial crop grown to obtain the diterpene glycosides in its leaves, which are processed to manufacture non-caloric sweeteners. Anaerobic soil disinfestation (ASD) and fungicide application were evaluated for the management of stevia stem rot (SSR) and Septoria leaf spot (SLS) in lab and field experiments. In 2019 and 2021, experiments using carbon sources for ASD were carried out in microplots at NCSU (Clayton, NC, USA). In 2020/21 and 2021/22 seasons, field experiments were conducted at CSAEGRO, Mexico (MX) and CEDIT, Paraguay (PY) using a 2 × 3 factorial design with two ASD treatments and three fungicide treatments. ASD treatments included soil amended with cornmeal (MX) or wheat bran (PY) at a rate of 20.2 Mg ha⁻¹, molasses at 10.1 Mg ha⁻¹, and non-amended controls. Fungicide applications included chemical (azoxystrobin), organic (pyroligneous acid, PA), and a non-treated control. ASD was effective in reducing sclerotia viability of Sclerotium rolfsii in laboratory assays (p < 0.0001) and microplot trials (p < 0.0001) in NC. During field trials, the viability of sclerotia was significantly reduced (p < 0.0001) in soils amended with cornmeal + molasses or wheat bran + molasses as carbon sources for ASD. While there was no significant effectiveness of ASD in reducing SLS in 2020 and 2021 or SSR in MX 2020 field trials (p = 0.83), it did exhibit efficacy on SSR in 2021 (p < 0.001). The application of fungicides was significantly effective in reducing SSR (p = 0.01) and SLS (p = 0.001), with azoxystrobin being the most consistent and PA not being statistically different from the control or azoxystrobin. The effects of ASD on fresh yield were inconsistent, exhibiting significant effects in Mexican fields in 2020 but not in 2021. During Paraguayan field trials, ASD only significantly interacted with fungicide applications in the dry yield in 2022. In the 2020/21 MX and 2020 PY field trials, fungicides were significantly effective in enhancing dry leaf yields, with azoxystrobin showing the highest consistency among treatments and PA variable control. In conclusion, utilizing ASD alongside organic fungicides can be a valuable tool for stevia farmers when the use of chemical fungicides is limited. Further research is required to enhance consistency and reduce the costs associated with these treatments under diverse edaphoclimatic conditions. Full article

(This article belongs to the Special Issue Anaerobic Soil Disinfestation: A Tool for Non-Fumigant-Based Integrated Soil-Borne Disease and Pest Management)

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20 pages, 6464 KiB

Open AccessArticle

Analysis of Trace Volatile Compounds Emitted from Flat Ground and Formed Bed Anaerobic Soil Disinfestation in Strawberry Field Trials on California’s Central Coast

by Kali Prescott, Stefanie Kortman, Josue Duque, Joji Muramoto, Carol Shennan, Gloria Greenstein and Arlene L. M. Haffa

Agronomy 2023, 13(5), 1190; https://doi.org/10.3390/agronomy13051190 - 23 Apr 2023

Cited by 1 | Viewed by 1342

Abstract

Anaerobic soil disinfestation (ASD) is emerging globally as an alternative to fumigant pesticides. To investigate ASD mechanisms, we monitored microbially produced volatile organic compounds (VOCs) and other volatile gases in situ using Fourier Transform Infrared Spectroscopy. Study plots infested with Fusarium oxysporum, Macrophomina phaseolina, and/or Verticillium dahliae included: organic flat ground (fASD, 6.7 + 13.5 megagrams per hectare, Mg/ha, rice bran/broccoli) and uncovered soil treated with mustard seed meal (MSM, 3.4 Mg/ha) at one site performed in fall of 2018; formed bed (bASD, 20 Mg/harice bran), control (UTC) and fumigant (FUM) at a second field site in fall of 2019 and 2021. Here, we present VOC diversity and temporal distribution. fASD generated 39 VOCs and GHGS, including known pathogen suppressors: dimethyl sulfide, dimethyl disulfide, and n-butylamine. bASD produced 17 VOCs and greenhouses gases (GHGs), 12 of which were also detected in fASD but in greater concentrations. Plant mortality and wilt score (fASD: 3.75% ± 4.79%, 2.8 ± 0.8; MSM: 6.25% ± 12.50%, 2.7 ± 0.3; bASD: 61.27% ± 11.26%, 4.1 ± 0.5; FUM: 13.89% ± 7.17%, 2.3 ± 0.2; UTC: 76.63% ± 25.11%, 4.3 ± 1.0) were significantly lower for fASD and MSM versus bASD and UTC (p < 0.05). Only FUM was not statistically different from fASD and MSM, and was significantly lower than UTC and bASD (bASD-FUM, p < 0.05; UTC-FUM, p < 0.05). The cumulative strawberry yield from bASD-treated plots was not different from FUM or UTC (bASD: 60.3 ± 13.6; FUM: 79.4 ± 9.19; UTC: 42.9 ± 12.4 Mg/ha). FUM yield was significantly greater than UTC (p = 0.005). These results, and to a far greater extent, additional challenges faced during both bASD trials, suggest that bASD is not as effective or as feasible at maintaining overall plant health as fASD or traditional fumigants. However, differences in management practices and environmental conditions at both sites across years cannot be fully excluded from consideration and many of our observations remain qualitative in nature. Full article

(This article belongs to the Special Issue Anaerobic Soil Disinfestation: A Tool for Non-Fumigant-Based Integrated Soil-Borne Disease and Pest Management)

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14 pages, 5367 KiB

Open AccessArticle

Anaerobic Soil Disinfestation Promotes Soil Microbial Stability and Antagonistic Bacteria Abundance in Greenhouse Vegetable Production Systems

by Jing Hu, Li Wan, Waqas Qasim, Haofeng Lv, Yiming Zhao, Guoyuan Li, Klaus Butterbach-Bahl and Shan Lin

Agronomy 2023, 13(3), 939; https://doi.org/10.3390/agronomy13030939 - 22 Mar 2023

Cited by 2 | Viewed by 1778

Abstract

Excessive water and fertiliser inputs, as well as long-term monocropping, not only cause resource waste and environmental pollution but also drive soil degradation and the occurrence of soil-borne diseases. Anaerobic soil disinfestation (ASD) is a widely used technique in greenhouse vegetable production to replace the use of agrochemicals in disinfestation and improve product quality. While the short-term effects of ASD on the soil microbial community have been well documented in the past 15 years, only a few studies have investigated the multiseason effects of ASD, particularly on the soil microbial community composition and stability, as well as on pathogens and antagonistic microorganisms. Field experiments were conducted in three adjacent greenhouses used for tomato production for at least 20 years. Three treatments were included: CK (control: no irrigation, no plastic film covering, incorporation of chicken manure), ASD (irrigation, plastic film covering, and incorporation of rice husks), and ASD+M (ASD plus incorporation of chicken manure). Results showed that (1) ASD significantly reduced the diversity of soil bacteria and fungi and improved the complexity and stability of the soil bacterial community at the end of the ASD, but the soil microbial diversity recovered to the level before the experiment after 1.5 years. (2) Compared with CK, ASD significantly increased the relative abundance of antagonistic bacteria Bacillus, Paenibacillus and Streptomyces, decreased the relative abundance of pathogens Fusarium and the quantity of nematodes and could still effectively eliminate soil pathogens after 1.5 years. (3) Chicken manure application did not increase the pathogenic microorganisms Fusarium and nematodes, but it significantly decreased the relative abundance of antagonistic bacteria. Our results highlight that ASD not only showed an inhibitory effect on soil-borne diseases after 1.5 years but also significantly increased the relative abundance of antagonistic bacteria. However, the additional incorporation of chicken manure for ASD should be avoided due to its negative effects on the abundance of antagonistic bacteria and its contribution to environmental pollution due to N leaching and increased emissions of GHG N₂O. Full article

(This article belongs to the Special Issue Anaerobic Soil Disinfestation: A Tool for Non-Fumigant-Based Integrated Soil-Borne Disease and Pest Management)

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15 pages, 1629 KiB

Open AccessEditor’s ChoiceArticle

Fungicidal Activity of Caproate Produced by Clostridium sp. strain E801, a Bacterium Isolated from Cocopeat Medium Subjected to Anaerobic Soil Disinfestation

by Shota Shirane, Noriaki Momma, Toshiyuki Usami, Chiharu Suzuki, Tomoyuki Hori, Tomo Aoyagi and Seigo Amachi

Agronomy 2023, 13(3), 747; https://doi.org/10.3390/agronomy13030747 - 03 Mar 2023

Cited by 3 | Viewed by 1811

Abstract

Anaerobic soil disinfestation (ASD) consists of the application of labile organic materials to soil, flooding, and covering the soil surface with plastic film. Anaerobic soil disinfestation is a widely used ecofriendly alternative to chemical fumigation for eliminating soil-borne plant pathogens. However, the exact mode of action of ASD has not been elucidated. In particular, the potential role of anaerobic soil bacteria in disinfestation is unclear. In this study, we isolated a predominant bacterium designated as strain E801 from cocopeat medium after laboratory-scale ASD with ethanol as the carbon source. The strain was closely related with Clostridium kluyveri, and fermentatively produced butyrate and caproate from ethanol and acetate. Interestingly, the culture supernatant of strain E801 strongly suppressed the growth of Fusarium oxysporum f. sp. lycopersici (Fol) in a pH-dependent manner. Among the volatile fatty acids produced by E801, only caproate showed significant growth suppression at pHs below 5.5. In addition, caproate eliminated Fol conidia completely at pHs 5.5 and 5.0 and suppressed Fol growth even at a low temperature (15 °C). Furthermore, cocopeat medium amended with caproate eliminated Fol conidia completely within 6 days. These results suggest that caproate is one of the key disinfestation factors in ethanol-based ASD and that the direct application of caproate to soil could be a promising strategy for rapid and stable soil disinfestation. Full article

(This article belongs to the Special Issue Anaerobic Soil Disinfestation: A Tool for Non-Fumigant-Based Integrated Soil-Borne Disease and Pest Management)

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20 pages, 1662 KiB

Open AccessEditor’s ChoiceArticle

Evaluation of Anaerobic Soil Disinfestation for Environmentally Sustainable Weed Management

by Ram B. Khadka, Andres D. Sanabria-Velazquez, John Cardina and Sally A. Miller

Agronomy 2022, 12(12), 3147; https://doi.org/10.3390/agronomy12123147 - 12 Dec 2022

Cited by 2 | Viewed by 2262

Abstract

In anaerobic soil disinfestation (ASD), soil amended with a carbon source undergoes anaerobic conditions accompanied by changes in microbial community composition and an increase in the concentration of organic acids, primarily acetic and butyric acids, and gases that are deleterious to plant pathogens, insects, and potentially to weeds. The purpose of this study was to explore the efficacy of ASD with different carbon sources on inactivation of propagules of a variety of weed species. Germination and viability of propagules of common lambsquarters (Chenopodium album L.), black nightshade (Solanum nigrum L.), yellow nutsedge (Cyperus esculentus L.), common pokeweed (Phytolacca decandra L.), barnyardgrass (Echinochloa crus-galli L.), dandelion (Taraxacum officinale (Weber)), and redroot pigweed (Amaranthus retroflexus L.) were tested using different rates of four carbon sources: molasses, wheat bran, mustard greens biomass, and raw chicken manure. Wheat bran was the most effective carbon source for inactivation of all weed propagules, followed by molasses and mustard greens biomass. Carbon sources were mixed with soil, which was irrigated to saturation and covered with plastic to promote anaerobic conditions for three weeks. Chicken manure inactivated all the tested species except A. retroflexus compared to the anaerobic control. Rates of carbon sources applied in soil were weakly but significantly correlated (r > 0.42 and p < 0.04) with weed seed mortality or germination inhibition (E. crus-galli) for all the tested carbon sources and weed species except for chicken manure for C. album, A. retroflexus, and S. nigrum. Laboratory tests to confirm organic acid toxicity showed that 1000 µL L⁻¹ acetic plus 1000 µL L⁻¹ butyric acids for at least 60 h inhibited of sprouting of C. esculentus tubers and E. crusgalli seeds, whereas 120 h or exposure was required to inhibit C. album seed germination. Anaerobic soil disinfestation effectively suppressed weed seed germination and viability when wheat bran, molasses and mustard greens biomass were used as carbon sources. This approach could be adopted for weed management in organic systems or any farming system where priority is given to environmentally sustainable practices. Full article

(This article belongs to the Special Issue Anaerobic Soil Disinfestation: A Tool for Non-Fumigant-Based Integrated Soil-Borne Disease and Pest Management)

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14 pages, 2562 KiB

Open AccessPerspective

Comprehensive Control System for Ginger Bacterial Wilt Disease Based on Anaerobic Soil Disinfestation

by Mitsuo Horita, Yuso Kobara, Kazutaka Yano, Kazusa Hayashi, Yoshihide Nakamura, Kazuhiro Iiyama and Tomoka Oki

Agronomy 2023, 13(7), 1791; https://doi.org/10.3390/agronomy13071791 - 03 Jul 2023

Cited by 2 | Viewed by 2412

Abstract

Bacterial wilt is a soil-borne disease that causes severe damage in ginger-growing regions of Japan (eight prefectures in the Shikoku, Kyushu, and Honshu regions). Because the pathogen Ralstonia pseudosolanacearum usually lives in deeper soil and infects host plants via the roots, it is not easy to eliminate even with chemical pesticides (such as soil fumigants). In our previous study, we found that anaerobic soil disinfestation with diluted ethanol (Et-ASD) effectively eliminated this pathogen. We conducted field experiments to confirm the effectiveness of Et-ASD in a ginger monoculture system. Eight trials were conducted in seven different ginger fields from spring to autumn. Excluding one trial in early spring, seven trials in summer successfully eliminated the pathogen from the field soil (below the detection limit by the developed sensitive bio-PCR method), and no disease recurrence was observed after ASD treatment. In addition, other useful methods for controlling the disease were explored, including proper field management after the disease outbreak and the disinfection of seed rhizomes. Based on these results, a comprehensive control system for bacterial wilt disease in ginger was developed. Full article

(This article belongs to the Special Issue Anaerobic Soil Disinfestation: A Tool for Non-Fumigant-Based Integrated Soil-Borne Disease and Pest Management)

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7 pages, 235 KiB

Open AccessProject Report

Carbon Sources for Anaerobic Soil Disinfestation in Southern California Strawberry

by Oleg Daugovish, Maripaula Valdes-Berriz, Joji Muramoto, Carol Shennan, Margherita Zavatta and Peter Henry

Agronomy 2023, 13(6), 1635; https://doi.org/10.3390/agronomy13061635 - 19 Jun 2023

Viewed by 1126

Abstract

Anaerobic soil disinfestation (ASD) has been adopted in over 900 ha in California strawberry production as an alternative to chemical fumigation. Rice bran, the predominant carbon source for ASD, has become increasingly expensive. In 2021–22 and the 2022–23 field studies, we evaluated 20–30% lower-priced wheat middlings (Midds) and dried distillers’ grain (DDG) at 21,800 kg ha⁻¹ (in 2021) and 17,000 kg ha⁻¹ (in 2022) as alternative carbon sources to rice bran. The study was placed at Santa Paula, California in September of each season in preparation for strawberry planting in October. Soil and air temperatures were 18–26 °C during that time. After the incorporation of carbon sources into the top 30 cm of bed soil, beds were reshaped, and irrigation drip lines were installed and covered with totally impermeable film (TIF) to prevent gas exchange. Beds were irrigated to saturate the bed soil within 48 h after TIF installation. Anaerobic conditions were measured with soil redox potential (Eh) sensors placed at 15 cm depth in all plots. Both DDG and Midds plots maintained Eh at −180 to 0 mV during the two ASD weeks, while untreated soil was aerobic at 200 to 400 mV. Permeable bags with inocula of Macrophomina phaseolina, a lethal soil-borne pathogen of strawberry, and tubers of a perennial weed Cyperus esculentus were placed 15 cm deep in the soil at ASD initiation and retrieved two weeks later for analyses. Two weeks after that, holes were cut to aerate beds and ‘Victor’ or ‘Fronteras’ bare-root strawberries were transplanted into them. ASD with DDG reduced viable microsclerotia of M. phaseolina by 49% in the first season and 75 to 85% with both carbon sources in the second season. Both ASD treatments reduced tuber germination of C. esculentus 86–90% compared to untreated soil in one of two years. Additionally, Midds and DDG provided greater sufficiency of plant-available nitrogen and phosphorus compared to untreated soil with synthetic pre-plant fertilizer and improved fruit yields by 11–29%. ASD with these carbon sources can suppress soil pathogens and weeds and help sustain organic strawberry production in California. Full article

(This article belongs to the Special Issue Anaerobic Soil Disinfestation: A Tool for Non-Fumigant-Based Integrated Soil-Borne Disease and Pest Management)

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