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Song Y, Yao S, Li X, Wang T, Jiang X, Bolan N, Warren CR, Northen TR, Chang SX. Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems. ECO-ENVIRONMENT & HEALTH 2024; 3:227-237. [PMID: 38680731 PMCID: PMC11047296 DOI: 10.1016/j.eehl.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/05/2024] [Accepted: 03/04/2024] [Indexed: 05/01/2024]
Abstract
Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.
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Affiliation(s)
- Yang Song
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi Yao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaona Li
- School of Environment and Ecology, Jiangnan University, Wuxi 225127, China
| | - Tao Wang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610299, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nanthi Bolan
- School of Agriculture and Environment, The University of Western Australia, Nedland, WA-6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Nedland, WA-6009, Australia
- Healthy Environments and Lives (HEAL) National Research Network, Australia
| | - Charles R. Warren
- School of Life and Environmental Sciences, University of Sydney, Heydon-Laurence Building A08, NSW 2006, Australia
| | - Trent R. Northen
- Environmental Genomics and System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Scott X. Chang
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
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Lu T, Lei C, Gao M, Lv L, Zhang C, Qian H, Tang T. A risk entropy approach for linking pesticides and soil bacterial communities. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133970. [PMID: 38457974 DOI: 10.1016/j.jhazmat.2024.133970] [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: 12/29/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Pesticides play a vital role in ensuring modern agricultural production, but also adversely affecting soil health. Microorganisms are the cornerstone of soil ecology, however, to date, there are few unified standards to measure the risk of soil pesticide residues to soil microbial community. To compensate for this gap, we collected soil samples from 55 orchards and monitored and risk-assessed 165 pesticides to microbial community in the soil. Results showed that a total of 137 pesticides were detected in all samples. Pesticide residues significantly influenced the microbial diversity and community structure in orchard soils, particularly fungicides and herbicides. The risk entropy of each pesticide was calculated in all samples and it was found that 60% of the samples had a "pesticide risk" (Risk quotient > 0.01), where the relative abundance significantly increased in 43 genera and significantly decreased in 111 genera (p < 0.05). Through multiple screens, we finally identified Bacillus and Sphingomonas as the most abundant sensitive genera under pesticide perturbation. The results showed that despite the complexity of the effects of pesticide residues on soils health, we could reveal them by identifying changes in soil bacterial, especially by the differences of microbial biomarkers abundance. The present study could provide new insights into the research strategy for pesticide pollution on soil microbial communities. ENVIRONMENTAL IMPLICATION: The risk of pesticide residues in soil needs to be quantified and standardized. We believe that microorganisms can be used as a marker to indicate soil pesticide residue risk. For this end, we investigated the residues of 165 pesticides in 55 orchard soil samples, calculated pesticide risk entropy and their effects on the soil microbial community. Through multiple analyzing and screening, we ultimately identified that, out of the 154 detected biomarkers, Bacillus and Sphingomonas were the most abundant sensitive genera under pesticide perturbation, which have the potential to be used as key biomarkers of soil microbiomes induced by pesticide perturbation.
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Affiliation(s)
- Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Mingyu Gao
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Lu Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory for Pesticide Residue Detection of Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chunrong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory for Pesticide Residue Detection of Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory for Pesticide Residue Detection of Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Kim N, Jo J, Lee J, Lee GH, Yu BY, Pyo H, Lee J, Choi J. Environmental forensics using stable and radioactive isotopes in naturally attenuated soil after phenol-leakage accidents. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132007. [PMID: 37527592 DOI: 10.1016/j.jhazmat.2023.132007] [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: 02/21/2023] [Revised: 06/02/2023] [Accepted: 07/04/2023] [Indexed: 08/03/2023]
Abstract
Phenol is a carcinogenic and hazardous chemical used in multiple industries and poses a high risk of chemical spills into the environment. To date, environmental forensic research has not focused on chemically remediated soils. In this study, an advanced environmental forensic analysis was performed on microbial communities and breakdown products of phenol, carbon stable isotopes, and radioactive isotopes in phenol-contaminated soil. As indicators of phenol-spill accidents after natural attenuation, higher δ13C levels and lower 14C/12C ratios were observed in phenol-contaminated soil compared with uncontaminated soil. In addition, 16s rRNA gene analysis revealed that phenol-breakdown products identified by gas chromatography-mass spectrometry and the presence of soil bacteria, such as Nocardioides, Faecalibacterium, and Bacteroides, were indicators of phenol-leakage accidents. Therefore, the proposed environmental forensic strategy is a valuable tool for identifying the location of previously occurring chemical accidents and estimating the ecological impact after the natural attenuation of contaminated soils.
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Affiliation(s)
- Naeun Kim
- Center for Sustainable Environment Research, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Graduate School of Energy and Environment, Korea University, Seoul 02841, Republic of Korea
| | - Jungman Jo
- Center for Sustainable Environment Research, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Civil & Environmental Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jinkyung Lee
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Gwan-Ho Lee
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Byung-Yong Yu
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Heesoo Pyo
- International Advanced Analysis Institute, B-339, 140 Tongil-ro, Deogyang-gu, Goyang-si, Gyeonggi-do 10594, Republic of Korea
| | - Jeongae Lee
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.
| | - Jaeyoung Choi
- Center for Sustainable Environment Research, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Graduate School of Energy and Environment, Korea University, Seoul 02841, Republic of Korea.
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Muthu Prabhu S, Yusuf M, Ahn Y, Park HB, Choi J, Amin MA, Yadav KK, Jeon BH. Fluoride occurrence in environment, regulations, and remediation methods for soil: A comprehensive review. CHEMOSPHERE 2023; 324:138334. [PMID: 36893864 DOI: 10.1016/j.chemosphere.2023.138334] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Fluoride, a naturally occurring chemical element, is largely insoluble in soils. More than 90% of the fluoride in soil is bound to soil particles and is unable to be dissolved. As part of the soil, fluoride is predominantly located in the colloid or clay fraction of the soil, and the movement of fluoride is strongly affected by the sorption capacity of the soil, which is affected by pH, the type of soil sorbent present, and the salinity. The Canadian Council of Ministers of the Environment soil quality guideline for fluoride in soils under a residential/parkland land use scenario is 400 mg/kg. In this review, we focus on fluoride contamination in soil and subsurface environments, and the various sources of fluorides are discussed in detail. The average fluoride concentration in soil in different countries and their regulations for soil and water are comprehensively reviewed. In this article, the latest advances in defluoridation methods are highlighted and the importance of further research addressing efficient and cost-effective methods to remediate fluoride contamination in soil is critically discussed. Methods used to mitigate fluoride risks by removing fluoride from the soil are presented. We strongly recommend that regulators and soil chemists in all countries explore opportunities to improve defluoridation methods and consider adopting more stringent regulations for fluoride in soil depending on geologic conditions.
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Affiliation(s)
- Subbaiah Muthu Prabhu
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, 04763, Republic of Korea; Department of Chemistry, School of Advanced Sciences, VIT-AP University, Vijayawada, 522 237, Andhra Pradesh, India
| | - Mohammed Yusuf
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Yongtae Ahn
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Ho Bum Park
- Department of Energy Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jaeyoung Choi
- Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology, Hwarang-ro 14, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Mohammed A Amin
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Tatibad, Bhopal, 462044, India
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
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Jeong H, Jung BJ, Kim JH, Choi SH, Lee YJ, Kim KS. Instant pH sensor based on the functionalized cellulose for detecting strong acid leaks. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211660. [PMID: 35308630 PMCID: PMC8924762 DOI: 10.1098/rsos.211660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/10/2022] [Indexed: 05/03/2023]
Abstract
Acid spills cause large-scale environmental damage and casualties. To respond to such incidents, a sensor capable of detecting acid leaks is required. Cellulose is a useful substrate material for the fast detection of acid leaks because it has high hydrophilicity and porosity. On the other hand, methods of manufacturing cellulose-based sensors are still complicated or time-consuming. Thus, in this study, a simple and rapid synthesis method for a cellulose-based pH sensor was proposed. The functionalization of α-cellulose was achieved via chloroacetyl chloride, and Congo red was covalently immobilized to the functionalized cellulose for detecting strong acids. The manufacturing process was composed of two steps as above and finished within 8 h. The developed sensor exhibited absorbance changes in the pH range of 0.2 to 3.0, and response time was shorter than 1 s. A prototype system using this sensor was manufactured and tested, and it detected acid leaks easily and quickly.
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Affiliation(s)
- Hoseong Jeong
- Department of Architectural Engineering and Smart City Interdisciplinary Major Program, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Byung Jun Jung
- Department of Materials Science and Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Jae Hyun Kim
- Department of Architectural Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Seung-Ho Choi
- Department of Architectural Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Yoon Jung Lee
- Department of Architectural Engineering and Smart City Interdisciplinary Major Program, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Kang Su Kim
- Department of Architectural Engineering and Smart City Interdisciplinary Major Program, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
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Lavado GJ, Baderna D, Carnesecchi E, Toropova AP, Toropov AA, Dorne JLCM, Benfenati E. QSAR models for soil ecotoxicity: Development and validation of models to predict reproductive toxicity of organic chemicals in the collembola Folsomia candida. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127236. [PMID: 34844354 DOI: 10.1016/j.jhazmat.2021.127236] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Soil pollution is a critical environmental challenge: the substances released in the soil can adversely affect humans and the ecosystem. Several bioassays were developed to investigate the soil ecotoxicity of chemicals with soil microbes, plants, invertebrates and vertebrates. The 28-day collembolan reproduction test with the springtail Folsomia candida is a recently introduced bioassay described by OECD guideline 232. Although the importance of springtails for maintaining soil quality, toxicity data for Collembola are still limited. We have developed two QSAR models for the prediction of reproductive toxicity induced by organic compounds in Folsomia candida using 28 days NOEC data. We assembled a dataset with the highest number of compounds available so far: 54 compounds were collected from publicly available sources, including plant protection products, reactive intermediates and industrial chemicals, household and cosmetic ingredients, drugs, environmental transformation products and polycyclic aromatic hydrocarbons. The models were developed using partial least squares regression (PLS) and the Monte Carlo technique with respectively the open source tools Small Dataset Modeler and CORAL software. Both QSAR models gave good predictive performance even though based on a small dataset, so they could serve for the ecological risk assessment of chemicals for terrestrial organisms.
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Affiliation(s)
- Giovanna J Lavado
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Sciences Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, Milano, Italy
| | - Diego Baderna
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Sciences Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, Milano, Italy.
| | - Edoardo Carnesecchi
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80177, 3508 TD Utrecht, the Netherlands
| | - Alla P Toropova
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Sciences Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, Milano, Italy
| | - Andrey A Toropov
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Sciences Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, Milano, Italy
| | - Jean Lou C M Dorne
- Scientific Committee and Emerging Risks Unit, European Food Safety Authority, Via Carlo Magno 1A, Parma, Italy
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Sciences Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, Milano, Italy
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Recent Developments in Plasmonic Sensors of Phenol and Its Derivatives. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112210519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many scientists are increasingly interested in on-site detection methods of phenol and its derivatives because these substances have been universally used as a significant raw material in the industrial manufacturing of various chemicals of antimicrobials, anti-inflammatory drugs, antioxidants, and so on. The contamination of phenolic compounds in the natural environment is a toxic response that induces harsh impacts on plants, animals, and human health. This mini-review updates recent developments and trends of novel plasmonic resonance nanomaterials, which are assisted by various optical sensors, including colorimetric, fluorescence, localized surface plasmon resonance (LSPR), and plasmon-enhanced Raman spectroscopy. These advanced and powerful analytical tools exhibit potential application for ultrahigh sensitivity, selectivity, and rapid detection of phenol and its derivatives. In this report, we mainly emphasize the recent progress and novel trends in the optical sensors of phenolic compounds. The applications of Raman technologies based on pure noble metals, hybrid nanomaterials, and metal–organic frameworks (MOFs) are presented, in which the remaining establishments and challenges are discussed and summarized to inspire the future improvement of scientific optical sensors into easy-to-operate effective platforms for the rapid and trace detection of phenol and its derivatives.
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Assessment of Soil Contamination by Gas Cloud Generated from Chemical Fire Using Metabolic Profiling and Associated Bacterial Communities. MINERALS 2021. [DOI: 10.3390/min11040372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chemical accidents have frequently occurred in South Korea as a result of the huge amount of chemicals being used in various industries. Even though fire accidents accounted for 71.9% of chemical accidents during 2008–2018 in South Korea, most ecological research and investigation has focused on leakage accidents since most fire or explosion gases are diffused out and disappear into the atmosphere. In this study, the possibility of soil contamination by toluene combustion is proposed. A fire simulation batch test was performed and identified the combustion by-products such as methylbenzene, ethylbenzene, ethynylbenzene, benzaldehyde, 1-phenyl-1-propyne, naphthalene, 2-methylindene using gas chromatography coupled with mass spectrometry (GC–MS). Naphthyl-2-methyl-succinic acid, a metabolic intermediate of naphthalene metabolism derived from the combustion product of toluene, was also discovered in field soil and the secondary metabolites such as streptomycin 6-phosphate, 3-Nitroacrylate, oxaloacetate using LC–MS. Moreover, Streptomyces scabiei, participating in naphthalene metabolism, was also discovered in filed soil (contaminated soil) using 16s rRNA sequencing. As a result, bacterial stress responses in field soil (contaminated soil) affected by gas cloud were identified by discovering metabolites relating to bacterial self-defense action such as fatty biosynthesis. This study draws a conclusion that soil can be polluted enough to affect bacteria by gas cloud and soil bacteria and can encounter stress for a long term even though toluene and its combustion products had already decomposed in soil.
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