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Lin YM, Li MH, Dai CY, Liu Y, Zhang WP, Yang Q, Cui XM, Yang Y. Dazomet fumigation modification of the soil microorganism community and promotion of Panax notoginseng growth. Front Microbiol 2024; 15:1443526. [PMID: 39132142 PMCID: PMC11309993 DOI: 10.3389/fmicb.2024.1443526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 07/08/2024] [Indexed: 08/13/2024] Open
Abstract
Introduction Panax notoginseng, a medicinal herb in China, is attacked by several pathogens during its cultivation. Dazomet (DZ) is a soil fumigant that is effective in controlling soil-borne pathogens, but its long-term effects on P. notoginseng growth and soil properties are unknown. Methods We conducted field experiments over two consecutive years to assess the impact of three concentrations of DZ fumigation (35 kg/666.7 m2, 40 kg/666.7 m2, and 45 kg/666.7 m2) on soil physicochemical properties, microbial diversity, and P. notoginseng growth. Correlation analyses were performed between microbial community changes and soil properties, and functional predictions for soil microorganisms were conducted. Results DZ fumigation increased total nitrogen, total phosphorus, total potassium, available phosphorus, available potassium, and ammonia nitrogen levels in the soil. DZ fumigation promoted the nutrient accumulation and improvement of agronomic traits of P. notoginseng, resulted in a 2.83-3.81X yield increase, with the highest total saponin content increasing by 24.06%. And the 40 kg/666.7 m2 treatment had the most favorable impact on P. notoginseng growth and saponin accumulation. After DZ fumigation, there was a decrease in the relative abundance of pathogenic fungi such as Fusarium, Plectosphaerella, and Ilyonectria, while beneficial bacteria such as Ramlibacter, Burkholderia, and Rhodanobacteria increased. The effects of fumigation on soil microorganisms and soil physicochemical properties persisted for 18 months post-fumigation. DZ fumigation enhanced the relative abundance of bacteria involved in the biosynthesis of secondary metabolites and arbuscular mycorrhizal fungi, reduced the relative abundance of plant-animal pathogenic fungi, reduced the occurrence of soil-borne diseases. Conclusion In conclusion, DZ fumigation enhanced soil physicochemical properties, increased the proportion of beneficial bacteria in the soil, and rebalanced soil microorganism populations, consequently improving the growth environment of P. notoginseng and enhancing its growth, yield, and quality. This study offers a theoretical foundation for DZ fumigation as a potential solution to the continuous cropping issue in perennial medicinal plants such as P. notoginseng.
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Affiliation(s)
- Ya-meng Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
| | - Ming-hua Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
| | - Chun-yan Dai
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
| | - Yuan Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
| | - Wen-ping Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
| | - Qian Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
| | - Xiu-ming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
| | - Ye Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
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Gu G, Murphy CM, Zheng J, Nou X, Rideout SL, Strawn LK. Effects of Fumigation on the Reduction of Salmonella enterica in Soil. Foodborne Pathog Dis 2023; 20:563-569. [PMID: 37738333 PMCID: PMC11079441 DOI: 10.1089/fpd.2023.0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023] Open
Abstract
Due to the phaseout of methyl bromide (MeBr), there is a need for broad-spectrum soil fumigation alternatives for pest management. Little is known about the impact of fumigation alternatives on foodborne pathogens, such as Salmonella, in agricultural soils. This study investigated the effect of MeBr alternative fumigants on Salmonella reduction in soil. Sandy loam soil was collected from a conventional farmed vegetable field and inoculated with either Salmonella Newport J1892 or Typhimurium ATCC 14028 (5.9 ± 0.3 log10 colony-forming unit [CFU]/g). Each of the four fumigants labeled for pest management (1,3-dichloropropene, chloropicrin, dimethyl disulfide, and metam sodium) was applied at labeled maximum application field levels to soil in pots and stored for a 2-week period. Sterile water was used as a control. Following the 2-week period, Salmonella concentrations in soil samples were enumerated at 1, 7, 14, and 21 days postfumigation. The mean concentration of Salmonella Newport was significantly higher than that of Salmonella Typhimurium 1 day after fumigation (p = 0.015). Fumigation using 1,3-dichloropropene or dimethyl disulfide significantly reduced Salmonella Newport and Salmonella Typhimurium concentrations, compared with the sterile water control. The rate of Salmonella reduction in soil treated with dimethyl disulfide was higher (0.17 ± 0.02 log10 CFU/g/day), compared with soil treated with the other fumigants (0.10-0.12 log10 CFU/g/day). Due to the reduction of Salmonella, alternative fumigation treatments may mitigate potential Salmonella contamination in soil within farm environments.
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Affiliation(s)
- Ganyu Gu
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, USA
- Environmental Microbial and Food Safety Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, USA
| | - Claire M. Murphy
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Xiangwu Nou
- Environmental Microbial and Food Safety Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, USA
| | - Steven L. Rideout
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Laura K. Strawn
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
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Li Y, Lu D, Xia Y, Xu X, Huang H, Mei X, Yang M, Li J, Zhu S, Liu Y, Zhang Z. Effects of allyl isothiocyanate fumigation on medicinal plant root knot disease control, plant survival, and the soil bacterial community. BMC Microbiol 2023; 23:278. [PMID: 37775764 PMCID: PMC10542678 DOI: 10.1186/s12866-023-02992-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 08/22/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Allyl isothiocyanate (AITC) is a natural product with high volatility that is used as a biofumigant to alleviate soil-borne plant diseases, and problems such as root knot nematodes (RKNs) that necessitate continuous cropping. However, little research has assessed the effects of AITC fumigation on medicinal plants. RESULTS AITC significantly reduced the population of RKNs in soil (p < 0.0001) and showed an excellent RKN disease control effect within 6 months after sowing Panax notoginseng (p < 0.0001). The seedling survival rate of 2-year-old P. notoginseng was approximately 1.7-fold higher after soil treatment with AITC (p = 0.1008). 16S rRNA sequencing indicated that the AITC treatment affected bacterial richness rather than diversity in consecutively cultivated (CC) soil. Furthermore, biomarkers with statistical differences between AITC-treated and untreated CC soil showed that Pirellulales (order), Pirellulaceae (family), Pseudomonadaceae (family), and Pseudomonas (genus) played important roles in the AITC-treated group. In addition, the microbiome functional phenotypes predicted using the BugBase tool suggested that AITC treatment is more conducive to improving CC soil through changes in the bacterial community structure. Crucially, our research also suggested that AITC soil treatment significantly increases soil organic matter (p = 0.0055), total nitrogen (p = 0.0054), and available potassium (p = 0.0373), which promotes the survival of a succeeding medicinal plant (Polygonatum kingianum). CONCLUSION AITC is an ecologically friendly soil treatment that affects the top 10 bacterial richness but not diversity. It could also provide a basis for a useful agricultural soil management measure to alleviate soil sickness.
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Affiliation(s)
- Yingbin Li
- Department of Pesticide Science, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Daqing Lu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yan Xia
- Department of Pesticide Science, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xinjing Xu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Huichuan Huang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xinyue Mei
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Min Yang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jianqiang Li
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, 100193, China
| | - Shusheng Zhu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yixiang Liu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Zhiping Zhang
- Department of Horticulture, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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Lu Q, Bunn R, Whitney E, Feng Y, DeVetter LW, Tao H. Arbuscular mycorrhizae influence raspberry growth and soil fertility under conventional and organic fertilization. Front Microbiol 2023; 14:1083319. [PMID: 37260690 PMCID: PMC10227501 DOI: 10.3389/fmicb.2023.1083319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/25/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction Introducing beneficial soil biota such as arbuscular mycorrhizal fungi (AMF) to agricultural systems may improve plant performance and soil fertility. However, whether bioinocula species composition affects plant growth and soil fertility, and whether fertilizer source influences AMF colonization have not been well characterized. The objectives of this research were to: (1) assess if AMF bioinocula of different species compositions improve raspberry (Rubus idaeus L.) performance and characteristics of soil fertility and (2) evaluate the impact of fertilizer source on AMF colonization. Methods Five bioinocula with different AMF species compositions and three fertilizer sources were applied to tissue culture raspberry transplants in a randomized complete block design with eight replicates. Plants were grown in a greenhouse for 14 weeks and plant growth, tissue nutrient concentrations, soil fertility, and AMF root colonization were measured. Results Shoot K and Zn concentrations as well as soil pH and K concentration increased in the Commercial Mix 1 treatment (Glomus, Gigaspora, and Paraglomus AMF species) compared to the non-inoculated control. RFI (raspberry field bioinoculum; uncharacterized AMF and other microbiota) increased soil organic matter (SOM), estimated nitrogen release (ENR), and soil copper (Cu) concentration compared to the non-inoculated control. Furthermore, plants receiving the Mix 1 or RFI treatments, which include more AMF species, had greater AMF root colonization than the remaining treatments. Plants receiving organic fertilizer had significantly greater AMF colonization than conventionally fertilized plants. Conclusion Taken together, our data indicate that coupling organic fertilizers and bioinocula that include diverse AMF species may enhance raspberry growth and soil fertility.
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Affiliation(s)
- Qianwen Lu
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, United States
| | - Rebecca Bunn
- Department of Environmental Sciences, Western Washington University, Bellingham, WA, United States
| | - Erika Whitney
- Department of Environmental Sciences, Western Washington University, Bellingham, WA, United States
| | - Yuanyuan Feng
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Lisa Wasko DeVetter
- Northwestern Washington Research and Extension Center, Washington State University, Mount Vernon, WA, United States
| | - Haiying Tao
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, United States
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Sim JXF, Drigo B, Doolette CL, Vasileiadis S, Donner E, Karpouzas DG, Lombi E. Repeated applications of fipronil, propyzamide and flutriafol affect soil microbial functions and community composition: A laboratory-to-field assessment. CHEMOSPHERE 2023; 331:138850. [PMID: 37146771 DOI: 10.1016/j.chemosphere.2023.138850] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/07/2023]
Abstract
Pesticides play an important role in conventional agriculture by controlling pests, weeds, and plant diseases. However, repeated applications of pesticides may have long lasting effects on non-target microorganisms. Most studies have investigated the short-term effects of pesticides on soil microbial communities at the laboratory scale. Here, we assessed the ecotoxicological impact of fipronil (insecticide), propyzamide (herbicide) and flutriafol (fungicide) on (i) soil microbial enzymatic activities, (ii) potential nitrification, (iii) abundance of the fungal and bacterial community and key functional genes (nifH, amoA, chiA, cbhl and phosphatase) and (iii) diversity of bacteria, fungi, ammonia oxidizing bacteria (AOB) and archaea (AOA) after repeated pesticide applications in laboratory and field experiments. Our results showed that repeated applications of propyzamide and flutriafol affected the soil microbial community structure in the field and had significant inhibitory effects on enzymatic activities. The abundances of soil microbiota affected by pesticides recovered to levels similar to the control following a second application, suggesting that they might be able to recover from the pesticide effects. However, the persistent pesticide inhibitory effects on soil enzymatic activities suggests that the ability of the microbial community to cope with the repeated application was not accompanied by functional recovery. Overall, our results suggest that repeated pesticide applications may influence soil health and microbial functionalities and that more information should be collected to inform risk-based policy development.
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Affiliation(s)
- Jowenna X F Sim
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia.
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Casey L Doolette
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis, 41500, Greece
| | - Erica Donner
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis, 41500, Greece
| | - Enzo Lombi
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
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Heydari A, Kim ND, Biggs PJ, Horswell J, Gielen GJHP, Siggins A, Taylor MD, Bromhead C, Palmer BR. Co-Selection of Bacterial Metal and Antibiotic Resistance in Soil Laboratory Microcosms. Antibiotics (Basel) 2023; 12:antibiotics12040772. [PMID: 37107134 PMCID: PMC10135173 DOI: 10.3390/antibiotics12040772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/06/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Accumulation of heavy metals (HMs) in agricultural soil following the application of superphosphate fertilisers seems to induce resistance of soil bacteria to HMs and appears to co-select for resistance to antibiotics (Ab). This study aimed to investigate the selection of co-resistance of soil bacteria to HMs and Ab in uncontaminated soil incubated for 6 weeks at 25 °C in laboratory microcosms spiked with ranges of concentrations of cadmium (Cd), zinc (Zn) and mercury (Hg). Co-selection of HM and Ab resistance was assessed using plate culture on media with a range of HM and Ab concentrations, and pollution-induced community tolerance (PICT) assays. Bacterial diversity was profiled via terminal restriction fragment length polymorphism (TRFLP) assay and 16S rDNA sequencing of genomic DNA isolated from selected microcosms. Based on sequence data, the microbial communities exposed to HMs were found to differ significantly compared to control microcosms with no added HM across a range of taxonomic levels.
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Affiliation(s)
- Ali Heydari
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | - Nick D Kim
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | - Patrick J Biggs
- School of Natural Sciences, Massey University, Palmerston North 4410, New Zealand
- School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand
| | - Jacqui Horswell
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | | | - Alma Siggins
- School of Biological and Chemical Sciences and Ryan Institute, University of Galway, H91 TK33 Galway, Ireland
| | | | - Collette Bromhead
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | - Barry R Palmer
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
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Agyekum DVA, Kobayashi T, Dastogeer KMG, Yasuda M, Sarkodee-Addo E, Ratu STN, Xu Q, Miki T, Matsuura E, Okazaki S. Diversity and function of soybean rhizosphere microbiome under nature farming. Front Microbiol 2023; 14:1130969. [PMID: 36937301 PMCID: PMC10014912 DOI: 10.3389/fmicb.2023.1130969] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 02/10/2023] [Indexed: 03/05/2023] Open
Abstract
Nature farming is a farming system that entails cultivating crops without using chemical fertilizers and pesticides. The present study investigated the bacterial and fungal communities in the rhizosphere of soybean grown in conventional and nature farming soils using wild-type and non-nodulating mutant soybean. The effect of soil fumigant was also analyzed to reveal its perturbation of microbial communities and subsequent effects on the growth of soybean. Overall, the wild-type soybean exhibited a better growth index compared to mutant soybean and especially in nature farming. Nodulation and arbuscular mycorrhiza (AM) fungi colonization were higher in plants under nature farming than in conventionally managed soil; however, fumigation drastically affected these symbioses with greater impacts on plants in nature farming soil. The rhizosphere microbiome diversity in nature farming was higher than that in conventional farming for both cultivars. However, the diversity was significantly decreased after fumigation treatment with a greater impact on nature farming. Principal coordinate analysis revealed that nature farming and conventional farming soil harbored distinct microbial communities and that soil fumigation significantly altered the communities in nature farming soils but not in conventional farming soils. Intriguingly, some beneficial microbial taxa related to plant growth and health, including Rhizobium, Streptomyces, and Burkholderia, were found as distinct microbes in the nature farming soil but were selectively bleached by fumigant treatment. Network analysis revealed a highly complex microbial network with high taxa connectivity observed under nature farming soil than in conventional soil; however, fumigation strongly broke it. Overall, the results highlighted that nature farming embraced higher microbial diversity and the abundance of beneficial soil microbes with a complex and interconnected network structure, and also demonstrated the underlying resilience of the microbial community to environmental perturbations, which is critical under nature farming where chemical fertilizers and pesticides are not applied.
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Affiliation(s)
- Dominic V. A. Agyekum
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Tatsuyuki Kobayashi
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Khondoker M. G. Dastogeer
- Department of Plant Pathology, Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Michiko Yasuda
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Elsie Sarkodee-Addo
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Safirah T. N. Ratu
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Qicong Xu
- International Nature Farming Research Center, Nagano, Japan
| | - Takaaki Miki
- International Nature Farming Research Center, Nagano, Japan
| | - Eri Matsuura
- College of Agriculture, Ibaraki University, Mito, Japan
| | - Shin Okazaki
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Japan
- *Correspondence: Shin Okazaki,
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Castellano-Hinojosa A, Noling JW, Bui HX, Desaeger JA, Strauss SL. Effect of fumigants and non-fumigants on nematode and weed control, crop yield, and soil microbial diversity and predicted functionality in a strawberry production system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158285. [PMID: 36030874 DOI: 10.1016/j.scitotenv.2022.158285] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/26/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Fumigants are commonly used to control soil-borne pathogens of high-value crops, but they may also impact non-target soil microorganisms. Increasing interest in the use of sustainable management practices to control plant- and root-parasitic nematodes has resulted in the formulation of non-fumigant nematicides (chemicals or bionematicides) which are considered environmentally friendly alternatives to fumigants. However, the impact of these new products compared to standard fumigants on soil-borne pathogens, plant production, and the diversity and composition of non-target microbial communities in all crops remains unclear. To begin to address this knowledge gap, we examined the effect of fumigants commonly used in Florida (United States) strawberry production and newly formulated non-fumigant nematicides on nematode and weed control, plant growth, crop yield, and bacterial and fungal community diversity and predicted functionality. We found the standard fumigants increased crop yields and reduced weed pressure more than non-fumigants. Both fumigants and non-fumigants were an efficient management strategy to control sting nematodes. Treatments also impacted the abundance of specific beneficial and antagonistic taxa. Both fumigants and non-fumigants reduced soil bacterial and fungal diversity, an effect that remained for six months, thus suggesting a potential residual impact of these products on soil microorganisms. However, only fumigants altered soil microbial community composition and reduced network complexity, inducing a decrease or even a loss of some predicted bacterial and fungal functions, particularly during the first weeks after fumigation. Nevertheless, soil collected at the end of the season showed significant levels of root-knot nematode suppression in a growth chamber experiment, irrespective of the previous treatment. By linking the effect of fumigants and non-fumigants on soil-borne pests, plant and production, and the soil microbiome, this study increases our knowledge regarding the environmental impact of these products.
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Southwest Florida Research and Education Center, Department of Soil and Water Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL 34142, USA
| | - Joseph W Noling
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 14625 Co Rd 672, Wimauma, FL 33598, USA
| | - Hung Xuan Bui
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 14625 Co Rd 672, Wimauma, FL 33598, USA
| | - Johan A Desaeger
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 14625 Co Rd 672, Wimauma, FL 33598, USA
| | - Sarah L Strauss
- Southwest Florida Research and Education Center, Department of Soil and Water Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL 34142, USA.
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Li X, Skillman V, Dung J, Frost K. Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application. ENVIRONMENTAL MICROBIOME 2022; 17:59. [PMID: 36461097 PMCID: PMC9719244 DOI: 10.1186/s40793-022-00454-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Soil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented. RESULTS We found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil's previous fumigation exposure. CONCLUSIONS The legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.
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Affiliation(s)
- Xiaoping Li
- Virginia Tech, Hampton Roads Agricultural Research and Extension Center, Virginia Beach, VA, 23455, USA
| | - Victoria Skillman
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, 97838, USA
| | - Jeremiah Dung
- Central Oregon Agricultural Research and Extension Center, Oregon State University, Madras, OR, 97741, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97333, USA
| | - Kenneth Frost
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, 97838, USA.
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97333, USA.
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10
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Kadhim MM, Talib Abed Z, Rayid R, Abdullaha SA, Majdi A, Mahdi Rheima A, Hachim SK. The Cd-decorated AlN nanotube as a potential chemical sensor for chloropicrin: DFT studies. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Qasim W, Wan L, Lv H, Zhao Y, Hu J, Meng F, Lin S, Butterbach-Bahl K. Impact of anaerobic soil disinfestation on seasonal N 2O emissions and N leaching in greenhouse vegetable production system depends on amount and quality of organic matter additions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154673. [PMID: 35314244 DOI: 10.1016/j.scitotenv.2022.154673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Greenhouse vegetable production (GVP) systems in China receive excessive amounts of fertilizers (>1500 kg N ha-1 yr-1) and irrigation (>1200 mm yr-1), which results in severe soil degradation. Moreover, soil borne diseases are common as the same crop is planted continuously over years. Anaerobic soil disinfestation (ASD) is a method carried out every 3-4 years during the summer fallow period to combat soil-borne diseases and to improve soil health. The standard ASD practice, which is carried out before the cropping season, involves incorporation of organic matter (i.e. rice shells or straw) into the soil, covering of the soil with plastic films and soil irrigation until saturation. However, many farmers incorporate large amounts of organic nitrogen fertilizer for priming ASD. In this study, we investigated if incorporation of rice shells plus chicken manure (ASD+RM; farmers practice) provokes higher environmental N losses (N2O emissions and N leaching) during the ASD and the following tomato crop growing period as compared to the standard ASD practice (ASD+R: only rice shells) or a Control (fallow, but with incorporation of organic manure, standard in non-ASD years). Results showed that ASD+RM increased seasonal (ASD/fallow period plus tomato crop growing period) soil N2O emissions by a factor of 3 (ASD+RM: 14.1 kg N2O-N ha-1; ASD+R: 4.7 kg N2O-N ha-1), with 2/3 of emissions occurring during the 25 days long ASD period. Across all treatments, nitrate (NO3-) leaching dominated total N leaching (75%), with significantly lower rates observed for ASD+R as compared to ASD+RM. For both ASD treatments, total dissolved organic nitrogen (DON) leaching was a factor of two higher than for the Control. Crop productivity was not affected by ASD. Our findings imply that ASD+RM should be abandoned as the additional supply of manure N results in high environmental N losses without further increasing yields.
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Affiliation(s)
- Waqas Qasim
- Institute of Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Garmisch-Partenkirchen 82467, Germany; College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Li Wan
- Institute of Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Garmisch-Partenkirchen 82467, Germany; College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Haofeng Lv
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yiming Zhao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Jing Hu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Fanqiao Meng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Shan Lin
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; College of Life Science and Technology, Hubei Engineering University, Hubei 432000, China.
| | - Klaus Butterbach-Bahl
- Institute of Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Garmisch-Partenkirchen 82467, Germany; State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China.
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12
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Vincent IR, Paudel BR, Guo H, Rosskopf EN, Di Gioia F, Hong JC, McNear DH, Xu N, Anrecio L, Colee J, Zhao X. Spatial and Temporal Changes of Soil Microbial Communities in Field Tomato Production as Affected by Anaerobic Soil Disinfestation. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.838635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Anaerobic soil disinfestation (ASD) has been demonstrated as an effective alternative to pre-plant chemical soil fumigation (CSF) commonly used to control soilborne pathogens. However, the ASD effects on spatial and temporal changes in soil microbial communities remain poorly understood in production systems with low soilborne disease pressure. The objective of this study was to assess the influence of ASD treatments on soil microbial community composition at different soil depths during the spring tomato production season in Florida. Soil treatments included ASD using 6.9 m3 ha−1 of molasses with 11 Mg ha−1 of composted poultry litter (CPL) (ASD0.5), ASD with 13.9 m3 ha−1 of molasses and 22 Mg ha−1 CPL (ASD1.0), and chemical soil fumigation (CSF) using a mixture of 1,3-dichloropropene and chloropicrin. Soil microbial community composition was measured at soil depths of 0–15 and 15–30 cm using phospholipid fatty acid (PLFA) analysis at 0, 36, 76, and 99 days after transplanting (DAT). Fatty acid methyl esters were categorized into biomarker groups including total microbial biomass (TMB), G+ bacteria (G+), G− bacteria (G−), actinomycetes (Actino), arbuscular mycorrhizal fungi (AMF), protozoa, and general fungi (F). Soil concentrations of G+, Actino, F, AMF, and the ratio of F:bacteria (B) were significantly impacted by a soil treatment × soil depth × sampling time three-way interaction. All the microbial biomarkers were significantly affected by soil treatment × sampling depth two-way interactions except for protozoa and F:B ratio. Concentrations of TMB, Actino, AMF, F, G+, and G− bacteria were significantly increased in ASD treated soils at both 0–15 and 15–30 cm soil depths across different sampling times compared with CSF. In addition, the concentrations of G+ and G− bacteria, AMF, F, and TMB were higher at 0–15 vs. 15–30 cm soil depth under ASD treatments, whereas no soil depth differences were observed in CSF. Discriminant analysis further confirmed that soil microbial community composition was distinctly different in CSF compared with ASD treatments. The soil microbial profile was well-differentiated between the two soil depths under ASD treatments but not in CSF, while the enhancement of PLFA biomarkers by ASD decreased with increasing soil depth.
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13
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The Rhizosphere Microbiome of Ginseng. Microorganisms 2022; 10:microorganisms10061152. [PMID: 35744670 PMCID: PMC9231392 DOI: 10.3390/microorganisms10061152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
The rhizosphere of ginseng contains a wide range of microorganisms that can have beneficial or harmful effects on the plant. Root exudates of ginseng, particularly ginsenosides and phenolic acids, appear to select for particular microbial populations through their stimulatory and inhibitory activities, which may account for the similarities between the rhizosphere microbiomes of different cultivated species of Panax. Many practices of cultivation attempt to mimic the natural conditions of ginseng as an understory plant in hilly forested areas. However, these practices are often disruptive to soil, and thus the soil microbiome differs between wild and cultivated ginseng. Changes in the microbiome during cultivation can be harmful as they have been associated with negative changes of the soil physiochemistry as well as the promotion of plant diseases. However, isolation of a number of beneficial microbes from the ginseng rhizosphere indicates that many have the potential to improve ginseng production. The application of high-throughput sequencing to study the rhizosphere microbiome of ginseng grown under a variety of conditions continues to greatly expand our knowledge of the diversity and abundance of those organisms as well as their impacts of cultivation. While there is much more to be learnt, many aspects of the ginseng rhizosphere microbiome have already been revealed.
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Castellano-Hinojosa A, Boyd NS, Strauss SL. Impact of fumigants on non-target soil microorganisms: a review. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:128149. [PMID: 34999405 DOI: 10.1016/j.jhazmat.2021.128149] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Fumigants have been used for decades to control soil-borne pathogens of high-value crops, and increasing evidence indicates they can affect non-target soil microbial communities. Understanding the impacts of these products on soil microorganisms is of critical importance not only for evaluating their environmental safety, but also because soil microbial communities have a central role in soil quality and nutrient cycling, plant growth, and crop production. Thus, we conducted a systematic review and metanalysis study of fumigant impacts on non-target soil microorganisms. In general, we found that fumigation decreases the bacterial diversity and abundance of total bacteria and nitrogen-cycling genes by approximately 10-50% during the first four weeks after application compared to non-treated soils. These decreases appear transient and tend to diminish or disappear after four weeks. Increases in bacterial diversity and abundance can occur after fumigation but are less common. Fumigant application can also alter bacterial community composition during the first six weeks after treatment by significantly increasing and/or decreasing the relative abundance of bacterial taxa involved in key soil functions such as N-cycling and plant-growth promotion. Knowledge gaps and areas where future research efforts should be prioritized to improve our understanding of the impact of organic fumigants on non-target soil microorganisms are discussed.
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Southwest Florida Research and Education Center, Department of Soil and Water Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29 N, Immokalee, FL 34142, USA
| | - Nathan S Boyd
- Gulf Coast Research and Education Center, Department of Horticulture, Institute of Food and Agricultural Sciences, University of Florida, 14625 C.R. 672, Wimauma, FL 33598, USA
| | - Sarah L Strauss
- Southwest Florida Research and Education Center, Department of Soil and Water Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29 N, Immokalee, FL 34142, USA.
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15
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Oishi AA, Dhali P, Das A, Mondal S, Rad AS, Hasan MM. Study of the adsorption of chloropicrin on pure and Ga and Al doped B 12N 12: a comprehensive DFT and QTAIM investigation. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2053121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Adita Afrin Oishi
- Department of Physics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Palash Dhali
- Department of Physics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Antu Das
- Department of Physics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Samiran Mondal
- Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Ali Shokuhi Rad
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Md. Mehade Hasan
- Department of Physics, Jashore University of Science and Technology, Jashore, Bangladesh
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16
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Gupta A, Singh UB, Sahu PK, Paul S, Kumar A, Malviya D, Singh S, Kuppusamy P, Singh P, Paul D, Rai JP, Singh HV, Manna MC, Crusberg TC, Kumar A, Saxena AK. Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19053141. [PMID: 35270832 DOI: 10.3390/ijerph190531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 05/28/2023]
Abstract
Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.
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Affiliation(s)
- Amrita Gupta
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Udai B Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Pramod K Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Adarsh Kumar
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Pandiyan Kuppusamy
- ICAR-Central Institute for Research on Cotton Technology, Ginning Training Centre, Nagpur 440023, India
| | - Prakash Singh
- Department of Plant Breeding and Genetics, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon 802136, India
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, Truett McConnel University, 100 Alumni Dr., Cleveland, GA 30528, USA
| | - Jai P Rai
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Harsh V Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Madhab C Manna
- Soil Biology Division, ICAR-Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal 462038, India
| | - Theodore C Crusberg
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Arun Kumar
- Department of Agronomy, Bihar Agricultural University, Sabour, Bhagalpur 813210, India
| | - Anil K Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
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17
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Gupta A, Singh UB, Sahu PK, Paul S, Kumar A, Malviya D, Singh S, Kuppusamy P, Singh P, Paul D, Rai JP, Singh HV, Manna MC, Crusberg TC, Kumar A, Saxena AK. Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:3141. [PMID: 35270832 PMCID: PMC8910389 DOI: 10.3390/ijerph19053141] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 12/01/2022]
Abstract
Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.
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Affiliation(s)
- Amrita Gupta
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Udai B. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Pramod K. Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Adarsh Kumar
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Pandiyan Kuppusamy
- ICAR-Central Institute for Research on Cotton Technology, Ginning Training Centre, Nagpur 440023, India;
| | - Prakash Singh
- Department of Plant Breeding and Genetics, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon 802136, India;
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, Truett McConnel University, 100 Alumni Dr., Cleveland, GA 30528, USA;
| | - Jai P. Rai
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Harsh V. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Madhab C. Manna
- Soil Biology Division, ICAR-Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal 462038, India;
| | - Theodore C. Crusberg
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA;
| | - Arun Kumar
- Department of Agronomy, Bihar Agricultural University, Sabour, Bhagalpur 813210, India;
| | - Anil K. Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
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18
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Co-Selection of Heavy Metal and Antibiotic Resistance in Soil Bacteria from Agricultural Soils in New Zealand. SUSTAINABILITY 2022. [DOI: 10.3390/su14031790] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Accumulation of trace elements (including heavy metals) in soil from usage of superphosphate fertilisers induces resistance of soil bacteria to trace elements of environmental concern (TEoEC) and may co-select for resistance to antibiotics (Ab). This study aimed to investigate selection of co-resistance of soil bacteria to Cd, Zn and Hg, and Ab in soils with varied management histories. Genetic diversity of these bacteria and horizontal transfer of Cd resistance genes (cadA and czcA) were also investigated. Soils with either pastoral and arable management histories and either high levels of Cd and Zn, or indigenous bush with background levels of these TEoEC from the Waikato region, New Zealand were sampled. Plate culturing with a range of TEoEC and Ab concentrations, Pollution Induced Community Tolerance (PICT) assay, antibiotic sensitivity, terminal restriction fragment length polymorphism (TRFLP) and horizontal gene transfer (HGT) analyses were employed to investigate co-selection of TEoEC and Ab resistance. Higher levels of bacterial resistance to TEoEC and Ab correlated with higher levels of TEoEC in soil. Bacterial community structures were altered in soils with high TEoEC levels. Cd resistance genes were transferred from donor bacterial isolates, to recipients and the transconjugants also had resistance to Zn and/or Hg and a range of Ab.
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19
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Maïworé J, Ngoune LT, Koumba MK, Metayer I, Montet D, Durand N. Determination of bacterial population and the presence of pesticide residues from some Cameroonian smoked and dried fish. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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20
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Zhang X, Xue C, Fang D, He X, Wei M, Zhuo C, Jin J, Shen B, Li R, Ling N, Shen Q. Manipulating the soil microbiomes during a community recovery process with plant beneficial species for the suppression of Fusarium wilt of watermelon. AMB Express 2021; 11:87. [PMID: 34117935 PMCID: PMC8197695 DOI: 10.1186/s13568-021-01225-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/28/2021] [Indexed: 11/30/2022] Open
Abstract
Fusarium wilt is a devastating disease which impacts watermelon production. Soil fumigation using dazomet followed by biological organic fertilizer was applied to suppress the Fusarium wilt disease. We propose that fumigation suppresses the soil indigenous community, especially the soil-borne pathogens, while the utilization of bio-organic fertilizer facilitates the recovery of the soil microbiome to a beneficial, suppressive state through the introduction of plant growth-promoting microorganisms. Greenhouse experiment showed that applied biological organic fertilizer after dazomet fumigation effective restrain the disease incidence with a 93.6% disease control. Fumigation strongly decreased soil microbial diversity and altered relative taxa abundances, suggesting the possibility of niche release by the resident soil microbial community. Fumigation followed by bio-fertilizer transformed the soil microbial community composition and resulted in higher relative abundances of beneficial microbial groups such as Bacillus (8.5%) and Trichoderma (13.5%), coupled with lower Fusarium abundance compared to other treatments. Network analysis illustrated that soil fumigation decreased interactions within the soil microbial community with less nodes and links while bio-fertilizer addition promoted node interactions. In addition, bio-fertilizer addition after fumigation resulted in the beneficial species becoming the key network connectors. Collectively, fumigation appears to release the resident soil niche resulting in lower diversity while the beneficial microbes introduced by bio-fertilizer addition colonize these niches, leading to a more complex community with fewer pathogens that suppresses Fusarium wilt disease incidence.
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21
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Fang W, Song Z, Tao S, Zhang D, Huang B, Ren L, Cheng H, Yan D, Li Y, Cao A, Wang Q. Biochar mitigates the negative effect of chloropicrin fumigation on beneficial soil microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:139880. [PMID: 32531602 DOI: 10.1016/j.scitotenv.2020.139880] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/25/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
Chloropicrin (CP) is the most commonly used soil fumigant worldwide. Although CP effectively controls soilborne pathogens, it is also detrimental to beneficial soil microorganisms unless measures can be put in place to protect them from the effects of fumigation. In this study, we evaluated the ability of biochar made from the invasive weed Eupatorium adenophorum to mitigate the effects of CP fumigation on beneficial species. Our results showed that the addition of biochar to the soil effectively reduced the detrimental effects of CP on beneficial species and their ecological functions. Biochar added to CP-fumigated soil shortened the time to 28-84 days for microbial diversity and nitrogen cycle functions to be restored to unfumigated levels. At the same time, the inorganic nitrogen (NH4+-N, NO3--N) content and N2O production potential level in CP-fumigated soil returned to unfumigated levels relatively quickly, which showed that nitrogen metabolism improved with the addition of biochar. The mitigation effect of biochar in CP-fumigated soil was more evident at higher biochar amendment rates. Our results suggest that the addition of biochar to CP-fumigated soil significantly reduced the impact of CP on beneficial species and their ecological functions, and significantly shortened the time for beneficial species to recover to pre-fumigation levels. Field research is required to determine biochar's ability to mitigate the impact of CP and other fumigants on beneficial species and to quantify its benefits on crop quality and yield.
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Affiliation(s)
- Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhaoxin Song
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Laboratory of Integrated and Urban Phytopathology, University of Liege, Gembloux Agro-Bio Tech, Passage des deportes 2, 5030 Gembloux, Belgium
| | - Sha Tao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lirui Ren
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongyan Cheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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22
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Tang M, Li L, Wang X, You J, Li J, Chen X. Elevational is the main factor controlling the soil microbial community structure in alpine tundra of the Changbai Mountain. Sci Rep 2020; 10:12442. [PMID: 32709903 PMCID: PMC7381615 DOI: 10.1038/s41598-020-69441-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 07/07/2020] [Indexed: 12/31/2022] Open
Abstract
To reveal the self-coordination mechanism of the fragile ecosystem of alpine tundra, we explored the relationship between soil microorganisms and other elements. On the alpine tundra of the Changbai Mountain, different vegetation types, altitudes and soil properties were selected as driving factors of soil microbial community. Soil microbial community, C- and N-cycling functional microbial and fungal biomass were analyzed. Structural equation model was used to study the control of biotic and abiotic factors in rhizosphere soil microbial community. The results showed that the pH value of soil had the strongest direct impact on the diversity and community structure of soil microorganisms, and had significant correlation with most of the C- and N-cycling functional microbial; organic carbon and vegetation also have strongest direct effect on fungal biomass, but all of them were not main factors influence soil microbial community structure, the elevation was the main controlling factor. In addition, the elevation mainly through indirect action affects the soil microbial community by driving distribution of plant species, soil organic carbon and pH value. This finding highlighted that elevation was the main predictor to determine rhizosphere microbial community structure but not vegetation in alpine tundra of Changbai Mountain.
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Affiliation(s)
- Mingze Tang
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, School of Life Sciences, Jilin University, Changchun, 130112, China
| | - Lin Li
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, School of Life Sciences, Jilin University, Changchun, 130112, China
- Medical Technology Department, Qiqihar Medical University, Qiqihar, 161006, China
| | - Xiaolong Wang
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, School of Life Sciences, Jilin University, Changchun, 130112, China
- Medical Technology Department, Qiqihar Medical University, Qiqihar, 161006, China
| | - Jian You
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, School of Life Sciences, Jilin University, Changchun, 130112, China
| | - Jiangnan Li
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, School of Life Sciences, Jilin University, Changchun, 130112, China
| | - Xia Chen
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, School of Life Sciences, Jilin University, Changchun, 130112, China.
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The Evaluation of Egg-Parasitic Fungi Paraboeremia taiwanensis and Samsoniella sp. for the Biological Control of Meloidogyne enterolobii on Chinese Cabbage. Microorganisms 2020; 8:microorganisms8060828. [PMID: 32486332 PMCID: PMC7355667 DOI: 10.3390/microorganisms8060828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 11/17/2022] Open
Abstract
Meloidogyne enterolobii, an aggressive plant-parasitic nematode, has been causing great yield loss worldwide in recent years. With no resistant Chinese cabbage cultivar available currently, a biological control strategy is needed to offer an eco-friendly option for sustainable farming. In this study, the nematode suppression efficacy of two newly isolated fungi, Paraboeremia taiwanensis and Samsoniella sp., were evaluated against M. enterolobii and compared to the known biological control agents Hyalorbilia oviparasitica strain DoUCR50 and Purpureocillium lilacinum strain 251 (PL251). Both P. taiwanensis and Samsoniella sp. reduced 29–63% disease severity as effectively as the commercial product PL251 on Chinese cabbage in greenhouse trails. The in vitro egg infection rate was 47.83% by P. taiwanensis and 47.50% for Samsoniella sp., respectively. A special protocol for scanning electron microscope observation of the fungi-infected nematodes was established in this study, and the egg parasitism of the four fungi against M. enterolobii was further confirmed. For all fungi examined in this study, fungal hyphae were seen apparently penetrating into M. enterolobii eggs without destructive damage of the overall outer eggshell and the hyphae continued to grow within eggs after 6 days of infection. The results of this study imply a similar egg-parasitism mechanism for P. taiwanensis, Samsoniella sp., H. oviparasitica DoUCR50, and P. lilacinum PL251. It further enlightens the application potential of nematophagous fungi as biocontrol agents against plant-parasitic nematodes in vegetable crop management.
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24
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Huang B, Yan D, Wang Q, Fang W, Song Z, Cheng H, Li Y, Ouyang C, Han Q, Jin X, Cao A. Effects of Dazomet Fumigation on Soil Phosphorus and the Composition of phoD-Harboring Microbial Communities. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5049-5058. [PMID: 32134657 DOI: 10.1021/acs.jafc.9b08033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The soil phosphorus (P) cycle and P transformation are largely driven by the soil bacterial microbial community. However, little is known about the effects of dazomet (DZ) soil fumigation on soil P and soil microbial communities associated with P transformation. This research investigated P released from three farm soils as a result of DZ fumigation and changes in enzyme activity, gene abundance, and the encoding alkaline phosphatase PhoD microbial community. After DZ fumigation, we observed a briefly significant increase in the available P and the active P fractionation. The soil ALP activity, 16s rRNA abundance, and the phoD gene decreased significantly after DZ fumigation. The abundance and diversity of phoD-harboring microbes also decreased shortly after fumigation, increased significantly 14-28 days later, and then decreased again toward the end of the experimental period of 86 days. The shared OTUs between treatments became fewer with increasing time after fumigation. The changes in available P and the active P fractionation after DZ fumigation were significantly correlated with the abundance of the dominant phoD-harboring microbes. DZ fumigation promoted P mineralization in these farm soils and changed the composition of phoD-harboring microbial communities, which will benefit crops able to absorb and use P.
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Affiliation(s)
- Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhaoxin Song
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongyan Cheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Canbin Ouyang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Qingli Han
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Xi Jin
- IPPCAAS-BU Joint Research Centre for Soil Remediation, Baoding University, Hebei 071000, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
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25
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Huang B, Yan D, Ouyang C, Zhang D, Zhu J, Liu J, Li Y, Wang Q, Han Q, Cao A. Chloropicrin fumigation alters the soil phosphorus and the composition of the encoding alkaline phosphatase PhoD gene microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:135080. [PMID: 31818557 DOI: 10.1016/j.scitotenv.2019.135080] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
The transformation of phosphorus (P) compounds in soil depends largely on soil microbial communities and is sensitive to agricultural practices. However, the effects of soil fumigation on soil P, and microbes involved in P transformation, are unknown. Our results showed that chloropicrin (CP) fumigation significantly increased the available-P, Leached-P and active-P fractionation (inorganic P extracted from H2O, NaHCO3 and NaOH) in Shangdong and Miyun soils in the early stages of culture, while soil alkaline phosphatase (ALP) activity and phoD gene abundance decreased significantly. Leached-P in fumigated soil was positively correlated with increased active-P fractionation, indicating that it was an important source of soil Leached-P after fumigation. The changes in P-fractionation, Leached-P and ALP after fumigation were also significantly correlated with the composition of the microbial communities. CP fumigation briefly stimulated an increase in the abundance and diversity of phoD-harboring microbial communities and promoted the mineralization process of soil P. PICRUSt metagenomic analysis showed an increase in the relative abundance of microorganisms with involved in carbohydrate/lipid transport and metabolism functions after fumigation. These results suggest CP fumigation altered soil P transformation and phoD-harboring microbes that might lead to an increased risk of P enrichment in waterways.
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Affiliation(s)
- Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Canbin Ouyang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiahong Zhu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Qingli Han
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China.
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26
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Zhang D, Yan D, Fang W, Huang B, Wang X, Wang X, Zhu J, Liu J, Ouyang C, Li Y, Wang Q, Cao A. Chloropicrin alternated with biofumigation increases crop yield and modifies soil bacterial and fungal communities in strawberry production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 675:615-622. [PMID: 31035200 DOI: 10.1016/j.scitotenv.2019.04.222] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/12/2019] [Accepted: 04/14/2019] [Indexed: 06/09/2023]
Abstract
Chloropicrin (Pic) and biofumigation are both considered effective chemical and non-chemical alternatives to methyl bromide, respectively, for controlling crop-limiting soil-borne pests and diseases. In this study, we evaluated the effects of Pic alone and 'chloropicrin alternated with biofumigation' (CAB) on the soil's physico-chemical properties and strawberry yield, as well as their effects on soil bacterial and fungal communities. The contents of NO3--N, available phosphorus and potassium, and electrical conductivity were all significantly increased when CAB was used. In addition, CAB also significantly increased the strawberry marketable yield. High-throughput gene sequencing showed the species abundance of some soil bacteria and fungi was significantly increased such as the phyla Proteobacteria, Bacteroidetes, Actinobacteria and Ascomycota when CAB was used. However, CAB decreased the relative abundance of the phyla Firmicutes, Chloroflexi, Gemmatimonadete and Zygomycota. These results indicated that CAB could improve the physico-chemical properties of soil for strawberry production, increase the genetic diversity of microbes in the soil and enhance marketable fruit yield.
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Affiliation(s)
- Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xianli Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoning Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiahong Zhu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Canbin Ouyang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China.
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27
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Solanki MK, Abdelfattah A, Britzi M, Zakin V, Wisniewski M, Droby S, Sionov E. Shifts in the Composition of the Microbiota of Stored Wheat Grains in Response to Fumigation. Front Microbiol 2019; 10:1098. [PMID: 31156603 PMCID: PMC6533538 DOI: 10.3389/fmicb.2019.01098] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/30/2019] [Indexed: 01/21/2023] Open
Abstract
While the wheat-associated microbiome is of major agricultural importance, little is known about the alterations in wheat grain microbial community composition during storage. Characterization of the bacterial and fungal communities in stored wheat grains revealed the impact of phosphine fumigation, one of the most effective methods to eliminate insects in stored commodities, on the composition of the wheat grain microbiome. High-throughput amplicon sequencing of the bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region was used to analyze the wheat grain microbiome at different times over as 6 months period of storage. Higher bacterial diversity was found across the samples during the first (immediately after harvest) and second (3 months later) time points, with a predominance of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes. A two-fold decrease in the number of bacterial operational taxonomic units (OTUs) was observed in wheat grains at the last time point (6 months later), following phosphine treatment. In contrast to the effect of phosphine on bacteria, it did not affect fungal diversity in stored grains. The majority of fungal sequences were assigned to Ascomycota, followed by Basidiomycota, Glomeromycota, and unidentified fungi, which were evenly distributed throughout the storage period. Alpha and beta diversity analyses were confirmed by examination of the cultured microbial taxa obtained from the stored wheat grains. Mycotoxin analysis of wheat grains collected after phosphine fumigation revealed the presence of Fusarium toxins, primarily deoxynivalenol (DON). Several mycotoxigenic Fusarium spp. were also detected in the same samples. Results of the present study indicate that microbiome of stored, whole wheat grains was strongly affected by phosphine fumigation, which changed the structure of the microbial community leading to shifts in species composition toward mycotoxigenic strains. A better understanding of the complex interactions within the microbial communities of stored grains will assist in the development of novel biocontrol strategies to overcome mycotoxin contamination.
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Affiliation(s)
- Manoj Kumar Solanki
- Institute of Postharvest and Food Sciences, Agricultural Research Organization – The Volcani Center, Rishon LeZion, Israel
| | - Ahmed Abdelfattah
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Calabria, Italy
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Malka Britzi
- National Residue Control Laboratory, Kimron Veterinary Institute, Beit Dagan, Israel
| | - Varda Zakin
- Institute of Postharvest and Food Sciences, Agricultural Research Organization – The Volcani Center, Rishon LeZion, Israel
| | - Michael Wisniewski
- United States Department of Agriculture, Agricultural Research Service, Kearneysville, WV, United States
| | - Samir Droby
- Institute of Postharvest and Food Sciences, Agricultural Research Organization – The Volcani Center, Rishon LeZion, Israel
| | - Edward Sionov
- Institute of Postharvest and Food Sciences, Agricultural Research Organization – The Volcani Center, Rishon LeZion, Israel
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28
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Zhang D, Ji X, Meng Z, Qi W, Qiao K. Effects of fumigation with 1,3-dichloropropene on soil enzyme activities and microbial communities in continuous-cropping soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 169:730-736. [PMID: 30502523 DOI: 10.1016/j.ecoenv.2018.11.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
The compound 1,3-D (1,3-dichloropropene) is a potential candidate soil fumigant due to the restrictions on methyl bromide (MB). To date, little is known about the soil microbial community changes induced by 1,3-D fumigation. Therefore, soil properties, related soil enzymes, genes encoding the key enzymes of ammonia oxidation in both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) and bacterial diversity were investigated to assess the effects of 1,3-D fumigation on the soil microbial community. The results exhibited that fumigation with 1,3-D caused accumulation of NH4+-N, but it led to decrease in the rate of NO3--N, and the concentration of NO3--N gradually recovered. At 12 weeks after transplant (WAT) of tomato seedlings, the concentration of NH4+-N and NO3--N were not statistically significant between the 1,3-D treatment groups and the untreated control group. A similar tendency was found for organic matter, soil pH, urease and protease activities. Moreover, quantitative real-time PCR (qPCR) showed that 1,3-D decreased total bacterial abundance, AOA-amoA and AOB-amoA genes. In addition, Illumina MiSeq sequencing analysis revealed that soil bacterial community diversities were significantly reduced at earlier sampling time points, and at later sampling time points, soil bacterial diversity gradually recovered, there was no significant difference compared to the control group. The present study provides useful information to evaluate the environmental safety of 1,3-D.
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Affiliation(s)
- Dianli Zhang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Xiaoxue Ji
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Zhen Meng
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Wenzhe Qi
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Kang Qiao
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China.
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29
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Xiao WL, Wang ZX, Wu FZ, Zhou XG. Effects of soil improvement technology on soil quality in solar greenhouse. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:24093-24100. [PMID: 29948685 DOI: 10.1007/s11356-018-2321-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
Currently, cucumber cultivation is mainly through monoculture, as continuous culture leads to the decrease of crop yield and soil quality. In order to improve soil quality to achieve continuous monocultures, soil physicochemical properties, microbial biomass, content of phenolic compounds, and the size of bacterial, fungal, ammonia-oxidizing bacteria (AOB), and Fusarium oxysporum were first evaluated in cucumber monoculture solar greenhouse. Soil improvement technology, including catch wheat (CW), calcium cyanamide disinfection (LN), and straw reactor technology (SR) during summer fallow period, was compared with conventional fallow (CK). Results showed that CW, LN, and SR all significantly increased soil pH, and LN and SR increased soil electrical conductivity (EC); however, CW decreased soil EC. Meanwhile, LN increased soil available N content significantly and SR increased available P content significantly. CW had negative effect on the accumulation of soil available nutrients, conversely, CW and SR had positive effect on the accumulation of microbial biomass carbon (MBC). All the treatments increased the total phenol content in the soil compared with CK. While CW increased the size of bacteria, AOB in the soil inhibited fungal and wilt pathogen size. LN also increased the size of soil bacteria and reduced the size of fungi. The comprehensive evaluation of all treatments showed that CW could control soil nutrient loss and improve the continuous cropping soil, making the soil transform from fungi to bacteria type. All the treatments accelerate the accumulation of phenolic compound, while whether or not developing autotoxicity requires further investigation.
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Affiliation(s)
- Wan-Li Xiao
- Weifang University of Science and Technology, Facility Horticulture Laboratory of Universities in Shandong, Shouguang, Shandong Province, 262700, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, HarBin, Heilongjiang Province, 150030, China
| | - Zhe-Xin Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, HarBin, Heilongjiang Province, 150030, China
| | - Feng-Zhi Wu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, HarBin, Heilongjiang Province, 150030, China.
| | - Xin-Gang Zhou
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, HarBin, Heilongjiang Province, 150030, China
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30
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Hosseinian A, Gharachorloo A, Mohazzab Lighvani T, Delir Kheirollahi Nezhad P, Vessally E. The effect of electric field and Al doping on the sensitivity of hexa-peri
-hexabenzocoronene nanographene to chloropicrin. Appl Organomet Chem 2018. [DOI: 10.1002/aoc.4486] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Akram Hosseinian
- School of Engineering Science, College of Engineering; University of Tehran; PO Box 11365-4563 Tehran Iran
| | - Arezoo Gharachorloo
- Department of Chemistry; Payame Noor University; PO Box 19395-1697 Tehran Iran
| | | | | | - Esmail Vessally
- Department of Chemistry; Payame Noor University; PO Box 19395-1697 Tehran Iran
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Distinct impacts of reductive soil disinfestation and chemical soil disinfestation on soil fungal communities and memberships. Appl Microbiol Biotechnol 2018; 102:7623-7634. [PMID: 29931599 DOI: 10.1007/s00253-018-9107-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/28/2018] [Accepted: 05/08/2018] [Indexed: 01/12/2023]
Abstract
Soil disinfestation is an important agricultural practice to conquer soil-borne diseases and thereby ensure crop productivity. Reductive soil disinfestation (RSD) had been developed as an environmentally friendly alternative to chemical soil disinfestation (CSD). However, the differences between CSD and RSD on soil-borne pathogen suppression and fungal community structure remain poorly understood. In this work, five treatments, i.e., untreated soil (CK), CSD with 0.5 t ha-1 dazomet (DZ), RSD with 10 t ha-1 ethanol (ET), 15 t ha-1 sugarcane bagasse (SB), and 15 t ha-1 bean dregs (BD), were performed to investigate their influences on disinfestation efficiency, fungal abundance, diversity, and community structure via quantitative PCR and high-throughput sequencing. RSD-related treatments, especially the BD treatment, effectively alleviated soil acidification and salinization. The fungal abundance and microbial activity considerably increased in the BD treatment and significantly declined in the DZ treatment as compared to the CK treatment. Moreover, both CSD and RSD-related treatments significantly inhibited the population of Fusarium oxysporum and the relative abundance of genus Fusarium. Fungal community structure was notably altered by CSD and RSD practices. Furthermore, both CSD and RSD harbored a distinct unique microbiome, with the DZ treatment dominated by the genus Mortierella and BD treatment predominated by the genera Zopfiella, Chaetomium, and Penicillium. Taken together, these results indicate that the BD treatment could considerably alleviate the soil deterioration, improve soil microbial activity, and reassemble a non-pathogen unique microbiome that have more disease-suppressive agents and thus might be a promising disinfestation practice to control soil-borne disease in monoculture system.
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Huang B, Li J, Wang Q, Guo M, Yan D, Fang W, Ren Z, Wang Q, Ouyang C, Li Y, Cao A. Effect of soil fumigants on degradation of abamectin and their combination synergistic effect to root-knot nematode. PLoS One 2018; 13:e0188245. [PMID: 29889848 PMCID: PMC5995350 DOI: 10.1371/journal.pone.0188245] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/05/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Root-knot nematode (Meloidogyne spp., RKN) causes a disease that significantly reduces the yield of greenhouse cucumber crops year after year. Chemical control based on a single pesticide is now unreliable mainly due to pest resistance. Fumigant and non-fumigant pesticide combinations can potentially result in effective and economic RKN control. RESULTS Combining the insecticide abamectin (ABM) with fumigants dazomet (DZ) or chloropicrin (CP) significantly extended the half-life of ABM by an average of about 1.68 and 1.56 times respectively in laboratory trials, and by an average of about 2.02 and 1.69 times respectively in greenhouse trials. Laboratory experiments indicated that all the low rate ABM combination treatments controlled RKN through a synergistic effect. ABM diffused into the nematode epidermis more rapidly when ABM was combined with DZ and CP, giving effective nematode control and an increase cucumber total yield, compared to the use of these products alone. ABM combined with CP or DZ produced significantly higher total cucumber yield than when these products were used alone. CONCLUSIONS A low concentration of ABM combined with DZ in preference to CP would be an economic and practical way to control nematode and soilborne fungi in a greenhouse producing cucumbers.
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Affiliation(s)
- Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meixia Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Zongjie Ren
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Canbin Ouyang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
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Ueki A, Kaku N, Ueki K. Role of anaerobic bacteria in biological soil disinfestation for elimination of soil-borne plant pathogens in agriculture. Appl Microbiol Biotechnol 2018; 102:6309-6318. [DOI: 10.1007/s00253-018-9119-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/20/2018] [Accepted: 05/21/2018] [Indexed: 01/15/2023]
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Ren G, Ma Y, Guo D, Gentry TJ, Hu P, Pierson EA, Gu M. Soil Bacterial Community Was Changed after Brassicaceous Seed Meal Application for Suppression of Fusarium Wilt on Pepper. Front Microbiol 2018; 9:185. [PMID: 29487582 PMCID: PMC5816756 DOI: 10.3389/fmicb.2018.00185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
Application of Brassicaceous seed meal (BSM) is a promising biologically based disease-control practice but BSM could directly and indirectly also affect the non-target bacterial communities, including the beneficial populations. Understanding the bacterial response to BSM at the community level is of great significance for directing plant disease management through the manipulation of resident bacterial communities. Fusarium wilt is a devastating disease on pepper. However, little is known about the response of bacterial communities, especially the rhizosphere bacterial community, to BSM application to soil heavily infested with Fusarium wilt pathogen and cropped with peppers. In this study, a 25-day microcosm incubation of a natural Fusarium wilt pathogen-infested soil supplemented with three BSMs, i.e., Camelina sativa 'Crantz' (CAME), Brassica juncea 'Pacific Gold' (PG), and a mixture of PG and Sinapis alba cv. 'IdaGold' (IG) (PG+IG, 1:1 ratio), was performed. Then, a further 35-day pot experiment was established with pepper plants growing in the BSM treated soils. The changes in the bacterial community in the soil after 25 days of incubation and changes in the rhizosphere after an additional 35 days of pepper growth were investigated by 454 pyrosequencing technique. The results show that the application of PG and PG+IG reduced the disease index by 100% and 72.8%, respectively, after 35 days of pepper growth, while the application of CAME did not have an evident suppressive effect. All BSM treatments altered the bacterial community structure and decreased the bacterial richness and diversity after 25 days of incubation, although this effect was weakened after an additional 35 days of pepper growth. At the phylum/class and the genus levels, the changes in specific bacterial populations resulting from the PG and PG+IG treatments, especially the significant increase in Actinobacteria-affiliated Streptomyces and an unclassified genus and the significant decrease in Chloroflexi, were suspected to be one of the microbial mechanisms involved in PG-containing BSM-induced disease suppression. This study is helpful for our understanding of the mechanisms that lead to contrasting plant disease severity after the addition of different BSMs.
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Affiliation(s)
- Gaidi Ren
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Nanjing, China
- Key Lab of Food Quality and Safety of Jiangsu Province–State Key Laboratory Breeding Base, Nanjing, China
| | - Yan Ma
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Nanjing, China
- Key Lab of Food Quality and Safety of Jiangsu Province–State Key Laboratory Breeding Base, Nanjing, China
| | - Dejie Guo
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Nanjing, China
- Key Lab of Food Quality and Safety of Jiangsu Province–State Key Laboratory Breeding Base, Nanjing, China
| | - Terry J. Gentry
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Ping Hu
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Elizabeth A. Pierson
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Mengmeng Gu
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
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Li J, Huang B, Wang Q, Li Y, Fang W, Han D, Yan D, Guo M, Cao A. Effects of fumigation with metam-sodium on soil microbial biomass, respiration, nitrogen transformation, bacterial community diversity and genes encoding key enzymes involved in nitrogen cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 598:1027-1036. [PMID: 28476076 DOI: 10.1016/j.scitotenv.2017.02.058] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/05/2017] [Accepted: 02/07/2017] [Indexed: 06/07/2023]
Abstract
Metam-sodium (MS) is widely used as a soil pre-plant fumigant as methyl bromide is phased out of agriculture. However, the information about how fumigation with MS affects the soil microbial community is still limited. In this study, a 66-day-long experiment was conducted to ascertain the effects of MS on soil substrate-induced respiration (SIR), microbial biomass nitrogen (MBN), NH4+-N and NO3--N concentrations, as well as the abundance of the total bacteria and fungi and the expression of genes involved in nitrogen cycling. In addition, 16S rRNA amplicon sequencing was used to investigate the effect of MS on the soil bacterial community. The half-lives of high and low doses of methyl isothiocyanate (MITC) are 10.51h and 9.93h, respectively. MS caused a short-term inhibition of SIR, MBN; had an accumulation effect on NH4+-N concentration in the short term; reduced the abundance of the total bacteria and fungi; and suppressed the expression of the nifH, AOA-amoA, anammox bacteria, nosZ, nirS, and narG. In addition, under the influence of MS, soil bacterial diversity decreased significantly in the long term, bacterial community structure was affected, and there was a shift in the predominant population; for example, some genera, such as Paenibacillus and Luteimonas, significantly increased in number. These changes in bacterial flora may be closely related to the growth of crops. Our study provides useful information for environmental safety assessments of MS in China.
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Affiliation(s)
- Jun Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dawei Han
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Meixia Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China.
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Zhang S, Liu X, Jiang Q, Shen G, Ding W. Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity. AMB Express 2017; 7:178. [PMID: 28921475 PMCID: PMC5603465 DOI: 10.1186/s13568-017-0475-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/05/2017] [Indexed: 11/10/2022] Open
Abstract
Chloropicrin is widely used to control ginger wilt in China, which have an enormous impact on soil microbial diversity. However, little is known on the possible legacy effects on soil microbial community composition with continuous fumigation over different years. In this report, we used high throughput Illumina sequencing and Biolog ECO microplates to determine the bacterial community and microbial metabolic activity in ginger harvest fields of non-fumigation (NF), chloropicrin-fumigation for 1 year (F_1) and continuous chloropicrin-fumigation for 3 years (F_3). The results showed that microbial richness and diversity in F_3 were the lowest, while the metabolic activity had no significant difference. With the increase of fumigation years, the incidence of bacterial wilt was decreased, the relative abundance of Actinobacteria and Saccharibacteria were gradually increased. Using LEfSe analyses, we found that Saccharibacteria was the most prominent biomarker in F_3. Eight genera associated with antibiotic production in F_3 were screened out, of which seven belonged to Actinobacteria, and one belonged to Bacteroidetes. The study indicated that with the increase of fumigation years, soil antibacterial capacity may be increased (possible reason for reduced the incidence of bacterial wilt), and Saccharibacteria played a potential role in evaluating the biological effects of continuous fumigation.
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Affiliation(s)
- Shuting Zhang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715 China
| | - Xiaojiao Liu
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715 China
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, Netherlands
| | - Qipeng Jiang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715 China
| | - Guihua Shen
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715 China
| | - Wei Ding
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715 China
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Li J, Huang B, Wang Q, Li Y, Fang W, Yan D, Guo M, Cao A. Effect of fumigation with chloropicrin on soil bacterial communities and genes encoding key enzymes involved in nitrogen cycling. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 227:534-542. [PMID: 28499263 DOI: 10.1016/j.envpol.2017.03.076] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 01/18/2017] [Accepted: 03/31/2017] [Indexed: 06/07/2023]
Abstract
Chloropicrin (CP) is a potential alternative for methyl bromide as a soil fumigant given that the use of methyl bromide has become limited. However, little is known about how fumigation with CP affects the condition of the soil microbial community. In this study, 16S rRNA amplicon sequencing and quantitative PCR were combined to investigate the effect of CP on soil bacterial community. In total, 938,922 effective reads were obtained from 18 samples and clustered into 58,662 operational taxonomic units at a similarity cut-off of 97%. Both approaches showed that the primary structure of bacterial community in soil did not significantly change at the phylum level after fumigation, but CP had a significant impact on the abundance of the bacterial microbiome that was recovered and identified. Additionally, bacterial community diversity decreased significantly, and there was a shift in the predominant populations. Staphylococcus, Actinomadura, Acinetobacter and Streptomyces significantly decreased in number or disappeared, and Bacteroides, Lachnoclostridium, Pseudoalteromonas, Colwellia, Idiomarina and Cobetia became the new predominant populations. In addition, some species associated with biodegradation, such as Sphingomonas spp. and Rhodococcus spp., significantly increased in number. The abundance of ammonia-oxidizing archaea (AOA) were significantly inhibited, yet the abundance of ammonia-oxidizing bacteria (AOB) significantly increased, and denitrification was significantly promoted. These changes in bacterial flora can considerably impact soil function and health and lead to negative effects on the environment surrounding fumigated soils, indicating the need for proactive risk management. Our study provides useful information for environmental safety assessments of CP in China.
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Affiliation(s)
- Jun Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Meixia Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing, China.
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39
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40
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Effect of Long-Term Continuous Fumigation on Soil Microbial Communities. AGRONOMY-BASEL 2017. [DOI: 10.3390/agronomy7020037] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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41
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Seasonal and Interannual Fluctuation of the Microbial Soil Community in a Maize Field under Long-Term Conservation Agriculture Management. SUSTAINABILITY 2017. [DOI: 10.3390/su9050778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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42
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Chen WY, Li WH, Ju YR, Liao CM, Liao VHC. Life cycle toxicity assessment of earthworms exposed to cadmium-contaminated soils. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:360-369. [PMID: 28130694 DOI: 10.1007/s10646-017-1769-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
Cadmium (Cd) is of great concern in the soil environment and it can damage terrestrial organisms. The purpose of this study was to employ a toxicokinetic/toxicodynamic (TK/TD) approach to investigate the effects of toxicologically relevant Cd accumulation on the life cycle growth of earthworms (Lumbricus rubellus and Eisenia fetida) and to assess potential terrestrial ecosystem risk. We reanalyzed growth toxicity and whole body and pellet accumulation data linked with TK/TD and life cycle growth models to estimate key rate constants. The growth risk of earthworms exposed to Cd was also assessed. This study found that the estimated whole body killing rate constant (0.114 g d μg-1) was much lower than that of pellet (0.248 g d μg-1). The recovery rate constant for whole body (6.02 d-1) was much higher than that of pellet (2.91 d-1). We also employed a life cycle-based probabilistic risk assessment model to estimate the growth inhibition risk for earthworms in response to environmentally relevant concentrations of Cd in Taiwan. Results showed that earthworms had a 90% growth inhibition probability risk of body weight, which was lower than 872.33 mg based on assessment of toxicologically relevant Cd accumulation. This study suggests that toxicologically relevant Cd accumulation could accurately reflect the capacity of Cd toxicity to earthworms. The integrated life cycle toxicity of earthworms exposed to Cd in this study provides a robust and applicable tool for the management of ecological risk assessment of Cd-contaminated soil.
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Affiliation(s)
- Wei-Yu Chen
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1 Roosevelt Road, Sec. 4, Taipei, 10617, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, No. 100, Shih-Chuan 1st Road, Kaohsiung, 80708, Taiwan
| | - Wen-Hsuan Li
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1 Roosevelt Road, Sec. 4, Taipei, 10617, Taiwan
| | - Yun-Ru Ju
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1 Roosevelt Road, Sec. 4, Taipei, 10617, Taiwan
| | - Chung-Min Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1 Roosevelt Road, Sec. 4, Taipei, 10617, Taiwan
| | - Vivian Hsiu-Chuan Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1 Roosevelt Road, Sec. 4, Taipei, 10617, Taiwan.
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Sobek EA, Zak JC. The Soil FungiLog procedure: method and analytical approaches toward understanding fungal functional diversity. Mycologia 2017; 95:590-602. [DOI: 10.1080/15572536.2004.11833063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - J. C. Zak
- Department of Biological Sciences, P.O. Box 43131, Texas Tech University, Lubbock, Texas 79409
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Huang B, Li J, Fang W, Liu P, Guo M, Yan D, Wang Q, Cao A. Effect of Soil Fumigation on Degradation of Pendimethalin and Oxyfluorfen in Laboratory and Ginger Field Studies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:8710-8721. [PMID: 27787973 DOI: 10.1021/acs.jafc.6b01437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Herbicides are usually applied to agricultural fields following soil fumigation to provide effective weed control in high-value cash crops. However, phytotoxicity has been observed in ginger seedlings following the application of herbicides in fumigated fields. This study tested a mixture of herbicides (pendimethalin and oxyfluorfen) and several fumigant treatments in laboratory and field studies to determine their effect on the growth of ginger. The results showed that soil fumigation significantly (P < 0.05) extended the degradation period of these herbicides in the field and in laboratory studies. The half-life of pendimethalin was extended by an average of approximately 1.29 times in the field and 1.74 times in the laboratory. The half-life of oxyfluorfen was extended by an average of about 1.19 times in the field and 1.32 times in the laboratory. Moreover, the extended period of herbicide degradation in the fumigant and nonfumigant treatments significantly reduced ginger plant height, leaf number, stem diameter, and the chlorophyll content. The study concluded that applying a dose below the recommended rate of these herbicides in chloropicrin (CP) or CP + 1,3-dichloropropene fumigated ginger fields is appropriate, as application of the recommended herbicide dose in fumigated soil may be phytotoxic to ginger.
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Affiliation(s)
- Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100193, China
| | - Jun Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100193, China
| | - Pengfei Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100193, China
| | - Meixia Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100193, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests , Beijing 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100193, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests , Beijing 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100193, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests , Beijing 100193, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100193, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests , Beijing 100193, China
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45
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Ma J, Ibekwe AM, Yang CH, Crowley DE. Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 563-564:199-209. [PMID: 27135583 DOI: 10.1016/j.scitotenv.2016.04.122] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 05/21/2023]
Abstract
Microbial diversity of agricultural soils has been well documented, but information on leafy green producing soils is limited. In this study, we investigated microbial diversity and community structures in 32 (16 organic, 16 conventionally managed soils) from California (CA) and Arizona (AZ) using pyrosequencing, and identified factors affecting bacterial composition. Results of detrended correspondence analysis (DCA) and dissimilarity analysis showed that bacterial community structures of conventionally managed soils were similar to that of organically managed soils; while the bacterial community structures in soils from Salinas, California were different (P<0.05) from those in soils from Yuma, Arizona and Imperial Valley, California. Canonical correspondence analysis (CCA) and artificial neural network (ANN) analysis of bacterial community structures and soil variables showed that electrical conductivity (EC), clay content, water-holding capacity (WHC), pH, total nitrogen (TN), and organic carbon (OC) significantly (P<0.05) correlated with microbial communities. CCA based variation partitioning analysis (VPA) showed that soil physical properties (clay, EC, and WHC), soil chemical variables (pH, TN, and OC) and sampling location explained 16.3%, 12.5%, and 50.9%, respectively, of total variations in bacterial community structure, leaving 13% of the total variation unexplained. Our current study showed that bacterial community composition and diversity in major fresh produce growing soils from California and Arizona is a function of soil physiochemical characteristics and geographic distances of sampling sites.
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Affiliation(s)
- Jincai Ma
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; USDA-ARS U. S. Salinity Laboratory, Riverside, CA 92507, United States
| | - A Mark Ibekwe
- USDA-ARS U. S. Salinity Laboratory, Riverside, CA 92507, United States.
| | - Ching-Hong Yang
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI 53211, United States
| | - David E Crowley
- Department of Environmental Sciences, University of California, Riverside, CA 92521, United States
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Kang Y, Hao Y, Shen M, Zhao Q, Li Q, Hu J. Impacts of supplementing chemical fertilizers with organic fertilizers manufactured using pig manure as a substrate on the spread of tetracycline resistance genes in soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 130:279-288. [PMID: 27152658 DOI: 10.1016/j.ecoenv.2016.04.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 04/15/2016] [Accepted: 04/23/2016] [Indexed: 06/05/2023]
Abstract
Using pig manure (PM) compost as a partial substitute for the conventional chemical fertilizers (CFs) is considered an effective approach in sustainable agricultural systems. This study aimed to analyze the impacts of supplementing CF with organic fertilizers (OFs) manufactured using pig manure as a substrate on the spread of tetracycline resistance genes (TRGs) as well as the community structures and diversities of tetracycline-resistant bacteria (TRB) in bulk and cucumber rhizosphere soils. In this study, three organic fertilizers manufactured using the PM as a substrate, namely fresh PM, common OF, and bio-organic fertilizer (BF), were supplemented with a CF. Composted manures combined with a CF did not significantly increase TRB compared with the CF alone, but PM treatment resulted in the long-term survival of TRB in soil. The use of CF+PM also increased the risk of spreading TRGs in soil. As beneficial microorganisms in BF may function as reservoirs for the spread of antibiotic resistance genes, care should be taken when adding them to the OF matrix. The PM treatment significantly altered the community structures and increased the species diversity of TRB, especially in the rhizosphere soil. BF treatment caused insignificant changes in the community structure of TRB compared with CF treatment, yet it reduced the species diversities of TRB in soil. Thus, the partial use of fresh PM as a substitute for CF could increase the risk of spread of TRGs. Apart from plant growth promotion, BF was a promising fertilizer owing to its potential ability to control TRGs.
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Affiliation(s)
- Yijun Kang
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China; College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Yangyang Hao
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Min Shen
- College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Qingxin Zhao
- College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Qing Li
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Jian Hu
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China.
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47
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Xiao L, Liu GB, Zhang JY, Xue S. Long-term effects of vegetational restoration on soil microbial communities on the Loess Plateau of China. Restor Ecol 2016. [DOI: 10.1111/rec.12374] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Lie Xiao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation; Northwest A&F University; Yangling 712100 P. R. China
- State Key Laboratory Base of Eco-hydraulic Engineering in Arid Area; Xi'an University of Technology; Xi'an 710048 P. R. China
| | - Guo-bin Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation; Northwest A&F University; Yangling 712100 P. R. China
| | - Jiao-yang Zhang
- School of Resource and Environment; Northwest A&F University; Yangling 712100 P. R. China
| | - Sha Xue
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation; Northwest A&F University; Yangling 712100 P. R. China
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Peng Z, Zeng D, Wang Q, Niu L, Ni X, Zou F, Yang M, Sun H, Zhou Y, Liu Q, Yin Z, Pan K, Jing B. Decreased microbial diversity and Lactobacillus group in the intestine of geriatric giant pandas (Ailuropoda melanoleuca). World J Microbiol Biotechnol 2016; 32:79. [PMID: 27038949 DOI: 10.1007/s11274-016-2034-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 02/14/2016] [Indexed: 01/19/2023]
Abstract
It has been established beyond doubt that giant panda genome lacks lignin-degrading related enzyme, gastrointestinal microbes may play a vital role in digestion of highly fibrous bamboo diet. However, there is not much information available about the intestinal bacteria composition in captive giant pandas with different ages. In this study, we compared the intestinal bacterial community of 12 captive giant pandas from three different age groups (subadults, adults, and geriatrics) through PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR analysis. Results indicated that microbial diversity in the intestine of adults was significantly higher than that of the geriatrics (p < 0.05), but not significant compared to the subadults (p > 0.05). The predominant bands in DGGE patterns shared by the twelve pandas were related to Firmicutes and Proteobacteria. Additionally, in comparison to healthy individuals, antibiotic-treated animals showed partial microbial dysbiosis. Real-time PCR analyses confirmed a significantly higher abundance of the Lactobacillus in the fecal microbiota of adults (p < 0.05), while other bacterial groups and species detected did not significantly differ among the three age groups (p > 0.05). This study revealed that captive giant pandas with different ages showed different intestinal bacteria composition.
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Affiliation(s)
- Zhirong Peng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dong Zeng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
| | - Qiang Wang
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, 610081, China
| | - Lili Niu
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, 610081, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Fuqin Zou
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingyue Yang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
| | - Hao Sun
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
| | - Yi Zhou
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qian Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
| | - Zhongqiong Yin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bo Jing
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
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Liu X, Cheng X, Wang H, Wang K, Qiao K. Effect of fumigation with 1,3-dichloropropene on soil bacterial communities. CHEMOSPHERE 2015; 139:379-385. [PMID: 26210186 DOI: 10.1016/j.chemosphere.2015.07.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/10/2015] [Accepted: 07/13/2015] [Indexed: 05/20/2023]
Abstract
1,3-Dichloropropene (1,3-D) is a potential candidate as a soil fumigant because of the restriction of methyl bromide (MB) in soil fumigation. So far, little is known about the bacteria diversity in 1,3-D fumigated soil. Therefore, the impact of 1,3-D on soil bacterial community was determined by the 16S rRNA gene amplicon 454 sequencing. A total of 230,617 valid reads and 19,366 OTUs were obtained from the thirteen samples. 454 sequencing results revealed that Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria and Firmicutes were predominant phylum in soils. Bacterial diversity was affected initially, while recovered in the later treatments and soils from 1,3-D treatment plots had a higher bacterial diversity. The results of this study demonstrated that 1,3-D had only a short-term and transitory impact on the indigenous soil microbial community. Our study would provide useful information for evaluating ecological safety of 1,3-D in China.
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Affiliation(s)
- Xiumei Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
| | - Xingkai Cheng
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
| | - Hongyan Wang
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, People's Republic of China.
| | - Kaiyun Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
| | - Kang Qiao
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
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Feld L, Hjelmsø MH, Nielsen MS, Jacobsen AD, Rønn R, Ekelund F, Krogh PH, Strobel BW, Jacobsen CS. Pesticide Side Effects in an Agricultural Soil Ecosystem as Measured by amoA Expression Quantification and Bacterial Diversity Changes. PLoS One 2015; 10:e0126080. [PMID: 25938467 PMCID: PMC4418756 DOI: 10.1371/journal.pone.0126080] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 03/29/2015] [Indexed: 11/26/2022] Open
Abstract
Background and Methods Assessing the effects of pesticide hazards on microbiological processes in the soil is currently based on analyses that provide limited insight into the ongoing processes. This study proposes a more comprehensive approach. The side effects of pesticides may appear as changes in the expression of specific microbial genes or as changes in diversity. To assess the impact of pesticides on gene expression, we focused on the amoA gene, which is involved in ammonia oxidation. We prepared soil microcosms and exposed them to dazomet, mancozeb or no pesticide. We hypothesized that the amount of amoA transcript decreases upon pesticide application, and to test this hypothesis, we used reverse-transcription qPCR. We also hypothesized that bacterial diversity is affected by pesticides. This hypothesis was investigated via 454 sequencing and diversity analysis of the 16S ribosomal RNA and RNA genes, representing the active and total soil bacterial communities, respectively. Results and Conclusion Treatment with dazomet reduced both the bacterial and archaeal amoA transcript numbers by more than two log units and produced long-term effects for more than 28 days. Mancozeb also inhibited the numbers of amoA transcripts, but only transiently. The bacterial and archaeal amoA transcripts were both sensitive bioindicators of pesticide side effects. Additionally, the numbers of bacterial amoA transcripts correlated with nitrate production in N-amended microcosms. Dazomet reduced the total bacterial numbers by one log unit, but the population size was restored after twelve days. The diversity of the active soil bacteria also seemed to be re-established after twelve days. However, the total bacterial diversity as reflected in the 16S ribosomal RNA gene sequences was largely dominated by Firmicutes and Proteobacteria at day twelve, likely reflecting a halt in the growth of early opportunists and the re-establishment of a more diverse population. We observed no effects of mancozeb on diversity.
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Affiliation(s)
- Louise Feld
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
- * E-mail:
| | - Mathis Hjort Hjelmsø
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
| | - Morten Schostag Nielsen
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
| | - Anne Dorthe Jacobsen
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
| | - Regin Rønn
- University of Copenhagen, Department of Biology, Section of Terrestrial Ecology, Copenhagen, Denmark
| | - Flemming Ekelund
- University of Copenhagen, Department of Biology, Section of Terrestrial Ecology, Copenhagen, Denmark
| | - Paul Henning Krogh
- University of Aarhus, Department of Bioscience, Section of Soil Fauna Ecology and Ecotoxicology, Silkeborg, Denmark
| | - Bjarne Westergaard Strobel
- University of Copenhagen, Department of Plant and Environmental Sciences, Section of Environmental Chemistry and Physics, Frederiksberg, Denmark
| | - Carsten Suhr Jacobsen
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
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