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Castellano-Hinojosa A, Karlsen-Ayala E, Boyd NS, Strauss SL. Impact of repeated fumigant applications on soil properties, crop yield, and microbial communities in a plastic-mulched tomato production system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170659. [PMID: 38325480 DOI: 10.1016/j.scitotenv.2024.170659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
Pre-plant soil fumigation is widely applied to control nematodes, soil-borne fungal pathogens, and weeds in vegetable crops. However, most of the research evaluating the effect of fumigants on crop yield and soil microbial communities has been done on single compounds despite growers mainly applying fumigant combinations. We studied the effect of different fumigant combinations (chloropicrin, 1,3-dichloropropene, and metam potassium) on soil properties, crop yield, and the soil bacterial and fungal microbiome for two consecutive years in a plastic-mulched tomato production system in Florida (United States). While combinations of fumigants did not improve plant productivity more than the individual application of these products, application of fumigants with >60 % chloropicrin did significantly increase yield. Fumigant combinations had no significant effect on bacterial diversity, but fumigants with >35 % chloropicrin reduced soil fungal diversity and induced temporary changes in the soil bacterial and fungal community composition. These changes included short-term increases in the relative abundance of Firmicutes and Ascomycota, as well as decreases in other bacterial and fungal taxa. Repeated fumigation reduced network complexity and the relative abundance of several predicted bacterial functions and fungal guilds, particularly after fumigation and at end of harvest (3-months post fumigation). A structural equation model (SEM) showed fumigants not only directly impact crop yield, but they can also indirectly determine variations in plant productivity through effects on the soil microbiome. Overall, this study increases our understanding of the environmental and agricultural impacts of fumigants in a plastic-mulched tomato production system.
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Southwest Florida Research and Education Center, Department of Soil, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA
| | - Elena Karlsen-Ayala
- Southwest Florida Research and Education Center, Department of Soil, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA; Northern Research Station, United States Department of Agriculture, Forest Service, 51 Millpond Road, Hamden, CT 06517, 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, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA.
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Fang W, Huang B, Sun Y, Yan D, Li Y, Bruno T, Roncada P, Wang Q, Cao A. Soil amendments promoting nitrifying bacteria recovery faster than the denitrifying bacteria at post soil fumigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168041. [PMID: 37898206 DOI: 10.1016/j.scitotenv.2023.168041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/30/2023]
Abstract
Chloropicrin (CP) is a soil fumigant that not only reduces disease-causing pathogenic microbes but regrettably also those that benefit soil quality and crop health. However, we have few knowledge on rapidly restoring populations of beneficial microbes suppressed by CP fumigation. Here we used genetic sequencing technology to monitor changes in the recovery of soil bacteria in response to ammonium sulfate added to the soil following CP fumigation. The results showed that regardless of the N fertilizer addition rate, the accumulated NH4+-N in CP fumigated soil was rapidly consumed within 42 d. The rapid reduction in NH4+-N coincided with the observed recovery nitrogen-cycling microorganisms, especially the nitrification bacteria AOA and AOB that contributed to the formation of NH4+-N. Additionally, we further observed that the resilience index of nitrifying bacteria (AOB and AOA) was greater than the resilience index of denitrifying bacteria that contain the denitrification genes nirS, nirK and nosZ (0.12 to 0.55 vs. -0.27 to 0.073). These results revealed that N fertilizer stimulated the recovery of nitrifying bacteria more than denitrifying bacteria. Our research suggests that ammonium sulfate applied to CP fumigated soil could be used commercially to improve soil health as a result of an increase in beneficial microbes.
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Affiliation(s)
- Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Huang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China.
| | - Yang Sun
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, 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
| | - Tilocca Bruno
- Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Paola Roncada
- Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Qiuxia Wang
- 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.
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Azeem M, Arockiam Jeyasundar PGS, Ali A, Riaz L, Khan KS, Hussain Q, Kareem HA, Abbas F, Latif A, Majrashi A, Ali EF, Li R, Shaheen SM, Li G, Zhang Z, Zhu YG. Cow bone-derived biochar enhances microbial biomass and alters bacterial community composition and diversity in a smelter contaminated soil. ENVIRONMENTAL RESEARCH 2023; 216:114278. [PMID: 36115420 DOI: 10.1016/j.envres.2022.114278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Bone waste could be utilized as a potential amendment for remediation of smelter-contaminated soils. Nevertheless, the influences of cow bone-derived biochar (CB) on soil microbial biomass and microbial community composition in multi-metal contaminated mining soils are still not clearly documented. Hence, the cow bone was used as feedstock material for biochar preparation and pyrolyzed at two temperatures such as 500 °C (CB500) and 800 °C (CB800), and added to a smelter soil at the dosage of 0 (unamended control), 2.5, 5, and 10% (w/w); then, the soil treatments were cultivated by maize. The CB effect on soil biochemical attributes and response of soil microbial biomass, bacterial communities, and diversity indices were examined after harvesting maize. Addition of CB enhanced total nutrient contents (i.e., total nitrogen up to 26% and total phosphorus P up to 27%) and the nutrients availability (i.e., NH4 up to 50%; NO3 up to 31%; Olsen P up to 48%; extractable K up to 18%; dissolved organic carbon up to 74%) in the treated soil, as compared to the control. The CB500 application revealed higher microbial biomass C (up to 66%), P (up to 41%), and bacterial gene abundance (up to 76%) than the control. However, comparatively a lower microbial biomass nitrogen and diversity indices were observed in the biochar (both with CB500 and CB800) treated soils than in the unamended soils. At the phylum level, the highest dose (10% of CB500 and CB800 resulted in contrasting effects on the Proteobacteria diversity. The CB50010 favored the Pseudomonas abundance (up to 793%), Saccharibacteria (583%), Parcubacteria (138%), Actinobacteria (65%), and Firmicutes (48%) microbial communities, while CB80010 favored the Saccharibacteria (386%), Proteobacteria (12%) and Acidobacteria (11%), as compared to the control. These results imply that CB500 and CB800 have a remarkable impact on microbial biomass and bacterial diversity in smelter contaminated soils. Particularly, CB500 was found to be suitable for enhancing microbial biomass, bacterial growth of specific phylum, and diversity, which can be useful for bioremediation of mining soils.
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Affiliation(s)
- Muhammad Azeem
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Zhejiang Key Lab of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China; Institute of Soil and Environmental Sciences, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Punjab, 46300, Pakistan
| | | | - Amjad Ali
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Luqman Riaz
- Department of Environmental Sciences, University of Narowal, 51750, Punjab, Pakistan
| | - Khalid S Khan
- Institute of Soil and Environmental Sciences, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Punjab, 46300, Pakistan
| | - Qaiser Hussain
- Institute of Soil and Environmental Sciences, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Punjab, 46300, Pakistan
| | - Hafiz A Kareem
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fakhar Abbas
- College of Environmental Science and Engineering, Zhongkai Agriculture and Engineering University, Guangzhou, China
| | - Abdul Latif
- Barani Agricultural Research Institute, Chakwal, Punjab, 48800, Pakistan
| | - Ali Majrashi
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Esmat F Ali
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Ronghua Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Sabry M Shaheen
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water- and Waste-Management, Laboratory of Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285, Wuppertal, Germany; King Abdulaziz University, Faculty of Meteorology, Environment, and Arid Land Agriculture, Department of Arid Land Agriculture, 21589, Jeddah, Saudi Arabia; University of Kafrelsheikh, Faculty of Agriculture, Department of Soil and Water Sciences, 33516, Kafr El-Sheikh, Egypt.
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Zhejiang Key Lab of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, China
| | - Zenqqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Zhejiang Key Lab of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, China.
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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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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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Alleviating Soil Acidification Could Increase Disease Suppression of Bacterial Wilt by Recruiting Potentially Beneficial Rhizobacteria. Microbiol Spectr 2022; 10:e0233321. [PMID: 35254141 PMCID: PMC9045175 DOI: 10.1128/spectrum.02333-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Bacterial wilt is accompanied by microbial communities shift and soil acidification. However, the relationship between the changes of bacterial communities and bacterial wilt under the influence of different acidification levels has not been fully elucidated. Here, we analyzed the abundance of Ralstonia solanacearum, rhizosphere bacterial communities and carbon metabolism at differently acidic levels (pH 6.45, pH 5.60, pH 5.35, pH 4.90 and pH 4.45) and soil amendment treatment (CaO). The results indicated that both the abundance of R. solanacearum and the incidence of bacterial wilt showed a significant trend of first increasing and then decreasing with the increase of soil pH. The Firmicutes phylum and potentially beneficial genera Bacillus, Paenibacillus, Flavobacterium and Pseudomonas were significantly enriched at pH 6.45. The metabolic ability in response to the l-arginine and 4-hydroxybenzoic acid was significantly increased at pH 6.45. After using CaO to increase the pH of diseased soil from 5.45 to 6.05, the abundance of R. solanacearum and the incidence of bacterial wilt were significantly reduced, the Firmicutes and potentially beneficial genera Bacillus and Pseudomonas were significantly enriched. Overall, alleviating soil acidification to a slightly acidic level (pH 6.0–6.5) could suppress bacterial wilt by suppressing the growth of R. solanacearum and enriching the rhizosphere potentially beneficial bacteria, and further emphasized the importance of increasing soil pH in biological control of bacterial wilt. IMPORTANCE The rhizosphere microbiota and soil acidification have been shown to have impacts on bacterial wilt. However, the influence of different acidification levels on the rhizosphere communities and bacterial wilt has not been fully studied. In this study, the potentially beneficial bacteria (Bacillus and Pseudomonas) were significantly enriched in the slightly acidic soil (pH 6.45), leading to the increase of the metabolism of 4-hydroxybenzoic acid and the decrease of pathogenic R. solanacearum, thereby alleviating the occurrence of bacterial wilt. The changes of potentially beneficial bacteria and pathogenic R. solanacearum in strongly acidic soil (pH 5.35) with the highest incidence of bacterial wilt were just the opposite. These findings help clarify the mechanisms by which soil bacteria exert influence on bacterial wilt outbreak under different soil acidification levels.
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Pu R, Wang P, Guo L, Li M, Cui X, Wang C, Liu Y, Yang Y. The remediation effects of microbial organic fertilizer on soil microorganisms after chloropicrin fumigation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 231:113188. [PMID: 35051756 DOI: 10.1016/j.ecoenv.2022.113188] [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: 11/02/2021] [Revised: 01/05/2022] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
Soil fumigation with chloropicrin (CP) is an effective means of overcoming continuous cropping obstacles (CCO) in Panax notoginseng and improving its yield and quality. CP fumigation can change the microbial community of soil. Therefore, a key step after CP fumigation is the rapid restoration of soil microorganisms and the promotion of beneficial microorganism proliferation as the dominant flora. In this study, continuously cropped soil of P. notoginseng was fumigated with CP, and general organic fertilizer (GOF) or microbial organic fertilizer (MOF) was used to restore soil microorganisms after fumigation. Soil physical and chemical properties, soil microorganisms, and quality of P. notoginseng were investigated. The application of MOF and GOF after CP fumigation promoted increases in soil nitrogen (9.88% and 8.21%, respectively), phosphorus (21.39% and 11.57%, respectively), potassium (7.99% and 2.75%, respectively), and the quality of P. notoginseng; it also promoted the accumulation of saponins in the main roots (23.62% and 9.12%, respectively). Application of MOF and GOF can restore the diversity of microorganisms in the soil. MOF increased the relative abundance of the beneficial soil microorganisms Glomeromycota, Mortierellomycota, Humicola and Bacillus, thereby lowering the relative abundance of the harmful Ascomycota and Fusarium relative to GOF. In summary, CP fumigation reduces the diversity of microorganisms in the soil. The addition of organic fertilizer can promote microbial diversity and increase the relative abundance of beneficial species. Moreover, the promotion effect of MOF is better than that of GOF, thereby improving soil fertility and ultimately promoting the quality and yield of P. notoginseng.
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Affiliation(s)
- Rongfeng Pu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Panpan Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Lanping Guo
- China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Minghua Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan, China; Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming 650500, China; Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming 650500, China; Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming 650500, China; Sanqi Research Institute of Yunnan Province, Kunming 650500, Yunnan, China
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan, China; Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming 650500, China; Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming 650500, China; Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming 650500, China; Sanqi Research Institute of Yunnan Province, Kunming 650500, Yunnan, China
| | - Chengxiao Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan, China; Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming 650500, China; Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming 650500, China; Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming 650500, China; Sanqi Research Institute of Yunnan Province, Kunming 650500, Yunnan, China
| | - Yuan Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan, China; Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming 650500, China; Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming 650500, China; Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming 650500, China; Sanqi Research Institute of Yunnan Province, Kunming 650500, Yunnan, China.
| | - Ye Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan, China; Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming 650500, China; Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming 650500, China; Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming 650500, China; Sanqi Research Institute of Yunnan Province, Kunming 650500, Yunnan, China.
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Bhattacharyya C, Imchen M, Mukherjee T, Haldar S, Mondal S, Mukherji S, Haldar A, Kumavath R, Ghosh A. Rhizosphere impact bacterial community structure in the tea (Camellia sinensis (L.) O. Kuntze.) estates of Darjeeling, India. Environ Microbiol 2021; 24:2716-2731. [PMID: 34913573 DOI: 10.1111/1462-2920.15874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/09/2021] [Indexed: 11/28/2022]
Abstract
India contributes 28% of the world's tea production, and the Darjeeling tea of India is a world-famous tea variety known for its unique quality, flavor, and aroma. This study analyzed the spatial distribution of bacterial communities in the tea rhizosphere of six different tea estates at different altitudes. The organic carbon, total nitrogen, and available phosphate were higher in the rhizosphere soils than the bulk soils, irrespective of the sites. Alpha and beta diversities were significantly (p<0.05) higher in the bulk soil than in the rhizosphere. Among the identified phyla, the predominant ones were Proteobacteria, Actinobacteria, and Acidobacteria. At the genus level, only 4 out of 23 predominant genera (>1% relative abundance) could be classified viz. Candidatus Solibacter (5.36±0.36%), Rhodoplanes (4.87±0.3%), Candidatus Koribacter (2.3±0.67%), Prevotella (1.49±0.26%). The rhizosphere effect was prominent evident from the significant depletion of more ASVs (n=39) compared to enrichment (n=11). The functional genes also exhibit a similar trend with the enrichment of N2 fixation genes, disease suppression, and Acetoine synthesis. Our study reports that the rhizobiome of tea is highly selective by reducing the alpha and beta diversity while enriching the significant functional genes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Chandrima Bhattacharyya
- Department of Biochemistry, Bose Institute, P1/12 C.I.T, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya P.O, Kasaragod, Kerala, 671316, India
| | - Triparna Mukherjee
- Department of Biochemistry, Bose Institute, P1/12 C.I.T, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Shyamalina Haldar
- Department of Biochemistry, Asutosh College, University, of Calcutta, Kolkata, 700026, India
| | - Sangita Mondal
- Department of Biochemistry, Bose Institute, P1/12 C.I.T, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Shayantan Mukherji
- Department of Biochemistry, Bose Institute, P1/12 C.I.T, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Anwesha Haldar
- Department of Geography, East Calcutta Girls' College, under West Bengal State University, Lake Town, Kolkata, 700089, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya P.O, Kasaragod, Kerala, 671316, India
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute, P1/12 C.I.T, Scheme VIIM, Kolkata, 700054, West Bengal, India
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9
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Zhang D, Cheng H, Hao B, Li Q, Wu J, Zhang Y, Fang W, Yan D, Li Y, Wang Q, Jin X, He L, Cao A. Fresh chicken manure fumigation reduces the inhibition time of chloropicrin on soil bacteria and fungi and increases beneficial microorganisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117460. [PMID: 34438480 DOI: 10.1016/j.envpol.2021.117460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/22/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Chloropicrin (CP) controls soil-borne plant diseases caused by pathogenic microbes, increases crop yield, but has a long-term inhibitory effect on beneficial soil microorganisms. Therefore, we evaluated the effects of biofumigation material fresh chicken manure (FCM) on soil microorganisms, and the duration of those effects in this experiment. Our results showed that in the laboratory, FCM significantly increased substrate-induced respiration (SIR) of soil microorganisms by 2.2-3.2 times at 80 d compared to the control, however, CP significantly inhibited the SIR of soil microorganisms. FCM and CP increased NH4+-N concentration within 40 days which then returned to the control level. FCM increased NO3--N by 2.82-5.78 times by 80 days, compared with the control, while the concentration of NO3--N in the CP treatment was not significantly different from the control at the 80 day. Although in the laboratory FCM inhibited the relative abundance of 16 S rRNA and the nitrogen cycle functional genes AOA amoA, AOB amoA, nirK and nosZ over a 40-day period, the taxonomic diversity of soil bacteria and fungi in the FCM treatment were restored to unfumigated level within 90 days in the field. However, CP treatment has a strong inhibitory effect on soil microorganisms after 90 days. Importantly, the relative abundance of some beneficial microorganisms that control soil-borne pathogenic microbes or degrade pollutants increased significantly in FCM, including Bacillus, Pseudomonas and Streptomyces bacterial genera and Chaetomium and Mycothermus fungal genera. Noteworthy, like CP, FCM still had a strong inhibitory effect on Fusarium at 90 d. Our results indicated that FCM not only increased the content of inorganic nitrogen and improved the respiration rate of soil microorganisms, but it also shortened the recovery time of beneficial soil microorganisms and increased taxonomic diversity. Our previous reports showed that FCM and CP treatments had the same effect in disease control and crop growth. Combined with the results of this experiment, we believe that FCM has the potential to replace CP, which would eliminate CP's detrimental environmental impact, improve farmer safety and promote sustainable crop production.
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Affiliation(s)
- Daqi Zhang
- 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
| | - Baoqiang Hao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingjie Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jiajia Wu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yi Zhang
- 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
| | - 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
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xi Jin
- Hebei Technology Innovation Center for Green Management of Soil-borne Diseases Baoding University, Baoding, Hebei, 071000, China
| | - Lin He
- College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Hebei Technology Innovation Center for Green Management of Soil-borne Diseases Baoding University, Baoding, Hebei, 071000, China.
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10
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Zhu J, Cao A, Wu J, Fang W, Huang B, Yan D, Wang Q, Li Y. Effects of chloropicrin fumigation combined with biochar on soil bacterial and fungal communities and Fusarium oxysporum. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 220:112414. [PMID: 34126305 DOI: 10.1016/j.ecoenv.2021.112414] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
Chloropicrin (CP) can cause long-term damage to beneficial microbes which reduces soil health. Biochar (BC) can mitigate against the effects of CP by reducing the time for beneficial microbes to recover after CP fumigation. In this study, we used Real-Time Quantitative PCR to determine the effects of different rates of BC added to CP-fumigated soil on the speed of recovery of bacteria and fungi population and on changes to gene copy number of the target pathogen Fusarium oxysporum. And then we compared the structure and composition of the beneficial microbial community in the different treatments soil by using High throughput Illumina sequencing. As the results shown, adding 1 or 3% BC after CP fumigation accelerated the recovery of bacterial and fungal populations without increasing F. oxysporum abundance. BC also promoted the recovery of beneficial bacteria Rokubacteria and Latescibacteria damaged by CP. And these two bacteria may be related to the immunity of soil to F. oxysporum. In CP-fumigated soil, BC improved the disease resistance of the soil by increasing beneficial microbes, such as Steroidobacter, Sphingomonas, Purpureocillium and Mortierella. This combination of CP and BC is a new concept that could encourages the development of a healthy and sustainable soil ecosystems while controlling plant pathogens.
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Affiliation(s)
- Jiahong Zhu
- 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
| | - Jiajia Wu
- 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
| | - 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
| | - Qiuxia Wang
- 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.
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11
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Ramires PF, Tavella RA, Escarrone AL, Volcão LM, Honscha LC, de Lima Brum R, da Silva AB, da Silva Júnior FMR. Ecotoxicity of triclosan in soil: an approach using different species. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:41233-41241. [PMID: 33782822 DOI: 10.1007/s11356-021-13633-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Triclosan is an antimicrobial agent widely used in personal care products and an emerging contaminant with potential to have harmful effects to edaphic organisms. This study aimed to evaluate the impacts of exposure to triclosan on the microbiota, plants, and edaphic animals using isolated bioassays and a microcosm scale representation (multispecies system). Among the isolated bioassays, the phytotoxicity test with Lactuca sativa, avoidance test with Eisenia andrei, and acute toxicity with E. andrei and Armadillidium vulgare were used. The multispecies system used seeds of L. sativa and Sinapis alba, together with earthworms and terrestrial isopods. This system also evaluated microbial activity through alkaline phosphatase and the metabolic profile using Ecoplate™, BIOLOG microplates. Exposure to triclosan impacted seedling growth in the isolated bioassay and germination and root growth in the microcosm scale assay; it also caused mortality in terrestrial isopods, earthworm avoidance and alteration of alkaline phosphatase, and the consumption profile of carbohydrates and carboxylic acids in the microbiota. The ecotoxicological effects evaluated in the multispecies system were perceived even in low concentrations of triclosan, indicating that the interaction of this xenobiotic with the environment and organisms in a more realistic scenario can compromise ecosystem services.
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Affiliation(s)
- Paula Florêncio Ramires
- Programa de Pós-graduação em Ciências da Saúde, Rua Visconde de Paranaguá 102 Centro, Rio Grande, RS, 96203-900, Brazil
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália km 8 Bairro Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Ronan Adler Tavella
- Programa de Pós-graduação em Ciências da Saúde, Rua Visconde de Paranaguá 102 Centro, Rio Grande, RS, 96203-900, Brazil
| | - Ana Laura Escarrone
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália km 8 Bairro Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Lisiane Martins Volcão
- Programa de Pós-graduação em Ciências da Saúde, Rua Visconde de Paranaguá 102 Centro, Rio Grande, RS, 96203-900, Brazil
| | - Laiz Coutelle Honscha
- Programa de Pós-graduação em Ciências da Saúde, Rua Visconde de Paranaguá 102 Centro, Rio Grande, RS, 96203-900, Brazil
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália km 8 Bairro Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Rodrigo de Lima Brum
- Programa de Pós-graduação em Ciências da Saúde, Rua Visconde de Paranaguá 102 Centro, Rio Grande, RS, 96203-900, Brazil
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália km 8 Bairro Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Alícia Bonifácio da Silva
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália km 8 Bairro Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Flávio Manoel Rodrigues da Silva Júnior
- Programa de Pós-graduação em Ciências da Saúde, Rua Visconde de Paranaguá 102 Centro, Rio Grande, RS, 96203-900, Brazil.
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália km 8 Bairro Carreiros, Rio Grande, RS, 96203-900, Brazil.
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12
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Honscha LC, Campos AS, Tavella RA, Ramires PF, Volcão LM, Halicki PCB, Pech TM, Bernardi E, Ramos DF, Niemeyer JC, Baisch PRM, Baisch ALM, da Silva Júnior FMR. Bioassays for the evaluation of reclaimed opencast coal mining areas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:26664-26676. [PMID: 33495952 DOI: 10.1007/s11356-021-12424-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to use bioassays (single and multispecies) with organisms from different trophic levels to assess soil quality in reclaimed coal mining areas. Soil samples were collected from four sites: two sites with recent reclaim processes (one using topsoil and other using clayey soil), an natural attenuation site, and a control soil. The evaluated parameters were divided into (1) ecotoxicological tests (avoidance test with Eisenia andrei (earthworms) and Armadillidium vulgare (isopods); germination test with Sinapis alba seeds (mustard); reproduction tests with Folsomia candida (collembolans); bacterial toxicity test); (2) population and community assessments (a fungal count; microbial community analysis using Biolog EcoPlatesTM); (3) microcosms scale evaluation (the MS-3 multispecies system); and (4) chemical analysis (soil parameters, soil metal, and cations and anions in soil leachate). Results pointed to toxicity in the natural attenuation site that compromised of habitat function, probably due to low pH and low nutrient levels. The most recent reclaim process, using topsoil and clay soil, improved soil quality and fertility, with a further increase in habitat quality and heterogeneity. This study shows that some techniques used to reclaim degraded mining areas are effective in rebuilding habitats, sustaining soil biota, and reestablishing ecosystem services.
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Affiliation(s)
- Laiz Coutelle Honscha
- Laboratório de Ensaios Farmacológicos e Toxicológicos, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
- Programa de Pós graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
| | - Audrey Senandes Campos
- Laboratório de Ensaios Farmacológicos e Toxicológicos, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
| | - Ronan Adler Tavella
- Laboratório de Ensaios Farmacológicos e Toxicológicos, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
- Programa de Pós graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
| | - Paula Florencio Ramires
- Laboratório de Ensaios Farmacológicos e Toxicológicos, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
- Programa de Pós graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
| | - Lisiane Martins Volcão
- Laboratório de Ensaios Farmacológicos e Toxicológicos, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
- Programa de Pós graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
| | | | - Tatiani Maria Pech
- Universidade Federal de Santa Catarina - UFSC, Campus de Curitibanos, Curitibanos, SC, 89520-000, Brazil
| | | | - Daniela Fernandes Ramos
- Programa de Pós graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
| | - Júlia Carina Niemeyer
- Universidade Federal de Santa Catarina - UFSC, Campus de Curitibanos, Curitibanos, SC, 89520-000, Brazil
| | - Paulo Roberto Martins Baisch
- Laboratório de Oceanografia Geológica, Instituto de Oceanografia, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
| | - Ana Luíza Muccillo Baisch
- Laboratório de Ensaios Farmacológicos e Toxicológicos, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
- Programa de Pós graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
| | - Flávio Manoel Rodrigues da Silva Júnior
- Laboratório de Ensaios Farmacológicos e Toxicológicos, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil.
- Programa de Pós graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil.
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13
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Zhang S, Jiang Q, Liu X, Liu L, Ding W. Plant Growth Promoting Rhizobacteria Alleviate Aluminum Toxicity and Ginger Bacterial Wilt in Acidic Continuous Cropping Soil. Front Microbiol 2020; 11:569512. [PMID: 33424780 PMCID: PMC7793916 DOI: 10.3389/fmicb.2020.569512] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/02/2020] [Indexed: 11/20/2022] Open
Abstract
Long-term monoculture cropping is usually accompanied by soil acidification and microbial community shifts. Soil aluminum ions are dissolved under acidic condition (pH < 5.0), and the resulting aluminum bioavailability can cause toxic effects in plants. In this study, we investigated the bacterial community compositions and aluminum toxicity in fields monocultured with ginger for 35 years, 15 years, and 1 year. Within these fields are ginger plants without and with ginger bacterial wilt disease. The results confirmed that the degree of aluminum toxicity in the diseased soil was more severe than that in the healthy soil. Continuous cropping can significantly increase the bacterial diversity and change the bacterial community composition of ginger rhizosphere soil. The relative abundance of plant growth-promoting rhizobacteria (PGPRs) was increased in the soils used for the continuous cropping of ginger. Additionally, aluminum toxicity had a significant positive correlation with Bacillus, Pseudomonas, Arthrobacter, and Serratia in healthy soils. Based on these results, aluminum stress may stimulate the increase of PGPRs (Bacillus, Pseudomonas, Arthrobacter, and Serratia), thereby alleviating ginger aluminum toxicity and bacterial wilt in extremely acidic soil (pH < 4.5).
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Affiliation(s)
- Shuting Zhang
- College of Plant Protection, Southwest University, Chongqing, China
| | - Qipeng Jiang
- College of Plant Protection, Southwest University, Chongqing, China
| | - Xiaojiao Liu
- College of Plant Protection, Southwest University, Chongqing, China
| | - Liehua Liu
- College of Plant Protection, Southwest University, Chongqing, China
| | - Wei Ding
- College of Plant Protection, Southwest University, Chongqing, China
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14
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Mącik M, Gryta A, Sas-Paszt L, Frąc M. The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains. Int J Mol Sci 2020; 21:E8003. [PMID: 33121206 PMCID: PMC7663420 DOI: 10.3390/ijms21218003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Regarding the unfavourable changes in agroecosystems resulting from the excessive application of mineral fertilizers, biopreparations containing live microorganisms are gaining increasing attention. We assumed that the application of phosphorus mineral fertilizer enriched with strains of beneficial microorganisms contribute to favourable changes in enzymatic activity and in the genetic and functional diversity of microbial populations inhabiting degraded soils. Therefore, in field experiments conditions, the effects of phosphorus fertilizer enriched with bacterial strains on the status of soil microbiome in two chemically degraded soil types (Brunic Arenosol - BA and Abruptic Luvisol - AL) were investigated. The field experiments included treatments with an optimal dose of phosphorus fertilizer (without microorganisms - FC), optimal dose of phosphorus fertilizer enriched with microorganisms including Paenibacillus polymyxa strain CHT114AB, Bacillus amyloliquefaciens strain AF75BB and Bacillus sp. strain CZP4/4 (FA100) and a dose of phosphorus fertilizer reduced by 40% and enriched with the above-mentioned bacteria (FA60). The analyzes performed included: the determination of the activity of the soil enzymes (protease, urease, acid phosphomonoesterase, β-glucosidase), the assessment of the functional diversity of microorganisms with the application of BIOLOGTM plates and the characterization of the genetic diversity of bacteria, archaea and fungi with multiplex terminal restriction fragment length polymorphism and next generation sequencing. The obtained results indicated that the application of phosphorus fertilizer enriched with microorganisms improved enzymatic activity, and the genetic and functional diversity of the soil microbial communities, however these effects were dependent on the soil type.
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Affiliation(s)
- Mateusz Mącik
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
| | - Agata Gryta
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
| | - Lidia Sas-Paszt
- Institute of Horticulture in Skierniewice, Pomologiczna 18, 96-100 Skierniewice, Poland;
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
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15
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Ma X, Thakar SB, Zhang H, Yu Z, Meng L, Yue J. Bioinformatics Analysis of The Rhizosphere Microbiota of Dangshan Su Pear in Different Soil Types. Curr Bioinform 2020. [DOI: 10.2174/1574893615666200129104523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background:
The rhizosphere microbiota are of vital importance for plant growth and
health in terrestrial ecosystems. There have been extensive studies aiming to identify the microbial
communities as well as their relationship with host plants in different soil types.
Objective:
In the present study, we have employed the high-throughput sequencing technology to
investigate the composition and structure of rhizosphere microbiota prosperous at the root of
Dangshan Su pear growing in sandy soil and clay soil.
Methods:
A high-throughput amplicon sequencing survey of the bacterial 16S rRNA genes and
fungal ITS regions from rhizosphere microbiota was firstly performed. Subsequently, several
common bacterial and fungal communities were found to be essential to Dangshan Su pear by using
a series of bioinformatics and statistics tools. Finally, the soil-preferred microbiota were identified
through variance analysis and further characterized in the genus level.
Result:
Dangshan Su pears host rich and diverse microbial communities in thin layer of soil
adhering to their roots. The composition of dominant microbial phyla is similar across different soil
types, but the quantity of each microbial community varies significantly. Specially, the relative
abundance of Firmicutes increases from 9.69% to 61.66% as the soil ecosystem changes from clay
to sandy, which can be not only conducive to the degradation of complex plant materials, but also
responsible for the disinfestation of pathogens.
Conclusion:
Our results have a symbolic significance for the potential efforts of rhizosphere
microbiota on the soil bioavailability and plant health. Through selecting soil types and altering
microbial structures, the improvement of fruit quality of Dangshan Su pear is expected to be
achieved.
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Affiliation(s)
- Xiaojing Ma
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | | | - Huimin Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Zequan Yu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Li Meng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Junyang Yue
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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16
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Vischetti C, Casucci C, De Bernardi A, Monaci E, Tiano L, Marcheggiani F, Ciani M, Comitini F, Marini E, Taskin E, Puglisi E. Sub-Lethal Effects of Pesticides on the DNA of Soil Organisms as Early Ecotoxicological Biomarkers. Front Microbiol 2020; 11:1892. [PMID: 33013727 PMCID: PMC7461845 DOI: 10.3389/fmicb.2020.01892] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/20/2020] [Indexed: 01/13/2023] Open
Abstract
This review describes the researches performed in the last years to assess the impact of pesticide sub-lethal doses on soil microorganisms and non-target organisms in agricultural soil ecosystems. The overview was developed through the careful description and a critical analysis of three methodologies based on culture-independent approaches involving DNA extraction and sequencing (denaturing gradient gel electrophoresis, DGGE; next-generation sequencing, NGS) to characterize the microbial population and DNA damage assessment (comet assay) to determine the effect on soil invertebrates. The examination of the related published articles showed a continuous improvement of the possibility to detect the detrimental effect of the pesticides on soil microorganisms and non-target organisms at sub-lethal doses, i.e., doses which have no lethal effect on the organisms. Considering the overall critical discussion on microbial soil monitoring in the function of pesticide treatments, we can confirm the usefulness of PCR-DGGE as a screening technique to assess the genetic diversity of microbial communities. Nowadays, DGGE remains a preliminary technique to highlight rapidly the main differences in microbial community composition, which is able to give further information if coupled with culture-dependent microbiological approaches, while thorough assessments must be gained by high-throughput techniques such as NGS. The comet assay represents an elective technique for assessing genotoxicity in environmental biomonitoring, being mature after decades of implementation and widely used worldwide for its direct, simple, and affordable implementation. Nonetheless, in order to promote the consistency and reliability of results, regulatory bodies should provide guidelines on the optimal use of this tool, strongly indicating the most reliable indicators of DNA damage. This review may help the European Regulation Authority in deriving new ecotoxicological endpoints to be included in the Registration Procedure of new pesticides.
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Affiliation(s)
- Costantino Vischetti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Cristiano Casucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Arianna De Bernardi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Elga Monaci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Luca Tiano
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Fabio Marcheggiani
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Maurizio Ciani
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Francesca Comitini
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Enrica Marini
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Eren Taskin
- Department for Sustainable Food Process, Faculty of Agriculture, Food and Environmental Sciences, Catholic University of Sacred Heart, Piacenza, Italy
| | - Edoardo Puglisi
- Department for Sustainable Food Process, Faculty of Agriculture, Food and Environmental Sciences, Catholic University of Sacred Heart, Piacenza, Italy
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17
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Huang K, Jiang Q, Liu L, Zhang S, Liu C, Chen H, Ding W, Zhang Y. Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes. AMB Express 2020; 10:72. [PMID: 32297018 PMCID: PMC7158972 DOI: 10.1186/s13568-020-01006-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/07/2020] [Indexed: 12/31/2022] Open
Abstract
Root-knot nematode (RKN) disease is a soil-borne disease. However, most studies on RKN have focused on the screening of agents and the cultivation of resistant varieties, and reports on the interaction of RKNs with soil microorganisms are few. In this study, we performed Illumina high-throughput sequencing to analyze diseased and healthy soil and the microbial-community changes in rhizosphere soil after microbial treatment (Pseudomonas flurescens, Bacillus subtilis, Paecolomyces lilacinus). Results showed significant differences in the bacterial community richness and diversity between diseased and healthy soil and the presence of different microbial species. After treatment, the richness and diversity of microbial communities in soil, as well as the number and incidence of second-stage juvenile of RKNs, decreased. Through linear discriminant analysis effect size, Pearson correlation, and Venn diagram analysis, we screened five genera that were closely related to disease occurrence, among which Pseudomonas was most related to disease inhibition. Our results suggested that the occurrence of tobacco RKN was related to changes in soil microbial communities, and that the interactions among Pseudomonas, Bryobacter, Variibacter, Coniochaeta, and Metarhizium affected the health of rhizosphere soil.
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Zhang D, Yan D, Cheng H, Fang W, Huang B, Wang X, Wang X, Yan Y, Ouyang C, Li Y, Wang Q, Cao A. Effects of multi-year biofumigation on soil bacterial and fungal communities and strawberry yield. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 256:113415. [PMID: 31672346 DOI: 10.1016/j.envpol.2019.113415] [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] [Received: 07/01/2019] [Revised: 08/31/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Biofumigation is an effective, non-chemical method to control soil-borne pests and diseases and to maximize crop yield. We studied the responses of soil bacterial and fungal communities, the soil's nutritional state and strawberry yield, when the soil was biofumigated each year for five consecutive years using fresh chicken manure (BioFum). BioFum significantly increased the soil's NH4+-N, NO3--N, available P and K and organic matter. Fusarium spp. and Phytophthora spp. which are known to cause plant disease, were significantly decreased after BioFum. In addition, Biofum increased the soil's temperature, enhanced chlorophyll levels in the leaves of strawberry plants, and the soluble sugar and ascorbic acid content in strawberry fruit. We used high-throughput gene sequencing to monitor changes in the soil's bacterial and fungal communities. Although BioFum significantly decreased the diversity of these communities, it increased the relative abundance of some biological control agents in the phylum Actinobacteria and the genera Pseudomonas, Bacillus and Chaetomium. An increase in these biological control agents would reduce the incidence of soil-borne pathogens and plant disease. Although strawberry marketable yield using BioFum was higher in the first three years, the decline in the final two years could be due to the accumulation of P and K which may have delayed flowering and fruiting. Methods to overcome yield losses using BioFum need to be developed in the future. Our research, however, showed that BioFum enhanced soil fertility, reduced the presence of soil pathogens, increased the relative abundance of beneficial bacteria and fungi and improved strawberry quality. Unlike chemical soil treatments that can cause pest and disease resistance when used continuously over many years, our multi-year research program on BioFum showed that this treatment provided significant benefits to the soil, plant and strawberry fruit.
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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; Beijing Innovation Consortium of Agriculture Research System, Beijing, 100193, China
| | - Hongyan Cheng
- 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
| | - 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
| | - Yue Yan
- Agricultural Environmental Protection and Rural Energy Principal Station of Shandong Province, Shandong, 250014, 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
| | - 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
| | - 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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19
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Li P, Zhang Y, Meng Q, Liu Y, Tuyiringire D, Chen Z, Liang S. Effects of trichloroethylene stress on the microbiological characteristics of Mollisol. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 184:109595. [PMID: 31470249 DOI: 10.1016/j.ecoenv.2019.109595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 08/17/2019] [Accepted: 08/20/2019] [Indexed: 06/10/2023]
Abstract
Trichloroethylene (TCE), one of 129 kinds of priority pollutants, is the most common halogenated organic pollutant in the environment. To explore the changes in soil physicochemical properties and biological activities then clarify the effects of these factors on bacterial, fungal and actinomycetes communities in Mollisol under TCE stress is the significance of our research. The results indicated that when TCE concentration was greater than 10 mg kg-1, soil quality declined and soil decomposition of organic matter and cycling of mineral nutrients were inhibited through an effect on soil microbial biomass. Operational taxonomic units (OTUs) richness of the bacteria in Mollisol was altered by TCE contamination. The SChao1 and HShannon indices of bacterial communities in Mollisol decreased when 40 mg kg-1 TCE was applied. Meanwhile, the OTU richness of fungi in Mollisol was altered by TCE contamination. The HShannon indices of the fungal communities in Mollisol were inhibited by higher TCE concentrations (20 and 40 mg kg-1 TCE). TCE altered the content of some bacteria, fungi and actinomycetes involved in soil carbon and nitrogen cycling and metabolism, such as Acidobacteria, Proteobacteria, Planctomycetes, Chytridiomycota, Streptomycetales, Pseudonocardiales, Propionibacteriales and Rhizobiales, and thus influenced nutrient cycling and the process of energy metabolism in Mollisol. In addition, redundancy analysis (RDA) results indicated that physicochemical properties and biological activities under TCE contamination significantly affected soil microbial community composition thus confirming that TCE interfered with the carbon and nitrogen cycling and metabolism of soil microorganisms. The results of this study are of great importance for revealing the effects of TCE stress on the microbiological characteristics of Mollisol, and also provide more useful information for determining the potential ecological risk of organic pollutants in Mollisol.
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Affiliation(s)
- Pengfei Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| | - Ying Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| | - Qingjuan Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ying Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Diogene Tuyiringire
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian, 116600, China
| | - Shichao Liang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
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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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Shen G, Zhang S, Liu X, Jiang Q, Ding W. Soil acidification amendments change the rhizosphere bacterial community of tobacco in a bacterial wilt affected field. Appl Microbiol Biotechnol 2018; 102:9781-9791. [PMID: 30302520 PMCID: PMC6208964 DOI: 10.1007/s00253-018-9347-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/03/2018] [Accepted: 08/22/2018] [Indexed: 11/01/2022]
Abstract
Application of soil amendments has been wildly used to increase soil pH and control bacterial wilt. However, little is known about causal shifts in the rhizosphere microbial community of crops, especially when the field naturally harbors the disease of bacterial wilt to tobacco for many years due to long-term continuous cropping and soil acidification. In this study, biochar (CP), lime (LM), oyster shell powder (OS) and no soil amendment additions (Control; CK) were assessed for their abilities to improve the soil acidification, change the composition of rhizosphere soil bacterial communities and thus control tobacco bacterial wilt. The results showed that oyster shell powder significantly increased soil pH by 0.77 and reduced the incidence of tobacco bacterial wilt by 36.67% compared to the control. The Illumina sequencing -based community analysis showed that soil amendment applications affected the composition of rhizosphere bacterial community and increased the richness and diversity. In contrast, the richness and diversity correlated negatively to disease incidence. Using LEfSe analyses, 11 taxa were found to be closely related with disease suppression, in which Saccharibacteria, Aeromicrobium, and Pseudoxanthomonas could be potential indicators of disease suppression. Our results suggested that the suppression of bacterial wilt after the application of soil amendments (especially oyster shell powder) was attributed to the improved soil pH and increased bacterial richness and diversity.
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Affiliation(s)
- Guihua Shen
- Laboratory of Natural Products Pesticides, Plant Protection College of Southwest University, Chongqing, 400715, China
| | - Shuting Zhang
- Laboratory of Natural Products Pesticides, Plant Protection College of Southwest University, Chongqing, 400715, China
| | - Xiaojiao Liu
- Laboratory of Natural Products Pesticides, Plant Protection College of Southwest University, Chongqing, 400715, China
| | - Qipeng Jiang
- Laboratory of Natural Products Pesticides, Plant Protection College of Southwest University, Chongqing, 400715, China
| | - Wei Ding
- Laboratory of Natural Products Pesticides, Plant Protection College of Southwest University, Chongqing, 400715, China.
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Fang W, Yan D, Wang X, Huang B, Wang X, Liu J, Liu X, Li Y, Ouyang C, Wang Q, Cao A. Responses of Nitrogen-Cycling Microorganisms to Dazomet Fumigation. Front Microbiol 2018; 9:2529. [PMID: 30405582 PMCID: PMC6206233 DOI: 10.3389/fmicb.2018.02529] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/03/2018] [Indexed: 12/22/2022] Open
Abstract
The influence of soil fumigation on microorganisms involved in transforming nitrogen remains little understood, despite the use of fumigants for many decades to control soil-borne pathogens and plant-parasitic nematodes. We used real-time PCR (quantitative polymerase chain reaction) and 16S rRNA gene amplicon sequencing techniques to monitor changes in the diversity and community structure of microorganisms associated with nitrogen transfer after the soil was fumigated with dazomet (DZ). We also examined nitrous oxide (N2O) emissions from these microorganisms present in fumigated fluvo-aquic soil and lateritic red soil. Fumigation with DZ significantly reduced the abundance of 16S rRNA and nitrogen cycling functional genes (nifH, AOA amoA, AOB amoA, nxrB, narG, napA, nirK, nirS, cnorB, qnorB, and nosZ). At the same time, N2O production rates increased between 9.9 and 30 times after fumigation. N2O emissions were significantly correlated with NH 4 + , dissolved amino acids and microbial biomass nitrogen, but uncorrelated with functional gene abundance. Diversity indices showed that DZ temporarily stimulated bacterial diversity as well as caused a significant change in bacterial community composition. For example, DZ significantly decreased populations of N2-fixing bacteria Mesorhizobium and Paenibacillus, nitrifiers Nitrosomonas, and the denitrifiers Bacillus, Pseudomonas, and Paracoccus. The soil microbial community had the ability to recover to similar population levels recorded in unfumigated soils when the inhibitory effects of DZ fumigation were no longer evident. The microbial recovery rate, however, depended on the physicochemical properties of the soil. These results provided useful information for environmental safety assessments of DZ in China, for improving our understanding of the N-cycling pathways in fumigated soils, and for determining the potential responses of different N-cycling groups after fumigation.
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Affiliation(s)
- 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
| | - Xianli Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoning Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoman Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Canbin Ouyang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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