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Awad A, Pena R. An improved method for extraction of soil fungal mycelium. MethodsX 2023; 11:102477. [PMID: 38023315 PMCID: PMC10679939 DOI: 10.1016/j.mex.2023.102477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
Fungal mycelium is a major component of the soil microbiome. The soil hyphosphere represents a complex and dynamic niche for specific microorganisms, where multitrophic interactions occur, affecting ecosystem processes. However, extracting fungal mycelium from the soil to enable its taxonomical, chemical, and structural characterisation is challenging in the absence of a fast, efficient, and low-cost procedure. In this study, an old method (Bingle and Paul 1985), based on successive soil wet filtrations and density gradient centrifugation, was improved and tested in three different soil types (silty clay, silty clay loam, and loamy sand). The improved method reduced the number of filtrations by about five times and the centrifugation time from 40 min to 1 min. It avoided using any chemical substance which may impair further chemical analyses or DNA isolation and amplification. The method efficiency was about 50 % in the clay and 23 % in the sandy soils. However, a pre-step consisting of removing the fine-root fragments and other debris under the stereomicroscope may increase the method efficiency to more than 65 %, independent of the soil type.•A simple, efficient, and low-cost method suitable for extracting soil mycelium from a large number of samples.•The protocol includes successive soil wet filtrations and sucrose gradient centrifugation.•The method efficiency increases if the fine-root fragments and other debris are previously removed from the soil.
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2
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Niu B, Chen Q, Jiao H, Yang X, Shao M, Wang J, Si G, Lei T, Yang Y, Zhang G, Guggenberger G. Networks of mineral-associated organic matter fractions in forest ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165555. [PMID: 37454842 DOI: 10.1016/j.scitotenv.2023.165555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/23/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Mineral-associated organic matter (MAOM), the largest soil carbon pool, is formed through a series of organo-mineral interaction mechanisms. However, different organo-mineral fractions relevant to specific stabilization mechanisms and their response to environmental variables are poorly understood, which hinders accurate prediction of MAOM preservation under climate change. We applied sequential chemical extraction to separate MAOM into different organo-mineral fractions. To assess of response of different organo-mineral fractions to climate change, alpine forest soils with high environmental sensitivity along a controlled environmental gradient were selected. Residual OM and weakly adsorbed OM were the primary organo-mineral fractions, accounting for approximately 45.1-67.7 % and 16.4-30.6 %, respectively, of the total organic carbon (TOC). Climate exerted considerable indirect effects on the preservation of organo-mineral fractions through weathering and edaphic and biotic variables. Moreover, organo-mineral fractions were closely associated with metal cations (mainly Fe3+/Al3+) and secondary minerals, forming complex networks. Water-soluble OM (WSOM), weakly adsorbed OM and Fe/Al oxyhydroxides-stabilized OM were tightly linked, occupying the central position of the networks, and were closely related to soil pH, moisture and prokaryotic composition, indicating that edaphic and biotic factors might play important roles in maintaining the network structure and topology. In addition, Fe/Al-OM complexes, oxyhydroxides-stabilized OM and residual OM in the network were greatly impacted by climate and weathering factors, including precipitation, temperature and the plagioclase index of alteration (PIA). The complex network among organo-mineral fractions sheds light on MAOM dynamic stabilization for better predicting MAOM preservation under climate change.
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Affiliation(s)
- Bin Niu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Qiuyu Chen
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Manchester, Manchester M139PL, UK
| | - Hongzhe Jiao
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoqin Yang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Shao
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Jian Wang
- Land and Resource College, China West Normal University, Nanchong 637009, China
| | - Guicai Si
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tianzhu Lei
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yibo Yang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Gengxin Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Georg Guggenberger
- Institute of Soil Science, Leibniz Universität Hannover, Hanover 30419, Germany
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3
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Vemulapalli SPB, Griesinger C, Dittmar T. Expanding the Limits of Structural Characterization of Marine Dissolved Organic Matter Using Nonuniform Sampling Frequency-Reversed Edited HSQC NMR. Anal Chem 2023; 95:14770-14776. [PMID: 37725656 PMCID: PMC10551856 DOI: 10.1021/acs.analchem.3c02923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023]
Abstract
The multiplicity-edited heteronuclear single quantum correlation (ME-HSQC) NMR method is widely used for the structural characterization of marine dissolved organic matter (DOM), which is a complex molecular mixture comprising millions of individual compounds. However, the standard ME-HSQC suffers from significant signal cancellation and subsequent loss of crucial structural information due to the overlap between CH3/CH (positive) and CH2 (negative) cross-peaks in overcrowded regions. This study introduces nonuniform sampling in frequency-reversed ME-HSQC (NUS FR-ME-HSQC), highlighting its remarkable potential for the comprehensive structural characterization of marine DOM. By reversing the frequency of CH2 cross-peaks into an empty region, the FR-ME-HSQC method effectively simplifies the spectra and eliminates signal cancellation. We demonstrate that nonuniform sampling enables the acquisition of comparable spectra in half the time or significantly enhances the sensitivity in time-equivalent spectra. Comparative analysis also identifies vulnerable CH2 cross-peaks in the standard ME-HSQC that coincide with CH3 and CH cross-peaks, resulting in the loss of critical structural details. In contrast, the NUS FR-ME-HSQC retains these missing correlations, enabling in-depth characterization of marine DOM. These findings highlight the potential of NUS FR-ME-HSQC as an advanced NMR technique that effectively addresses challenges such as signal overcrowding and prolonged experimental times, enabling the thorough investigation of complex mixtures with implications in several fields, including chemistry, metabolomics, and environmental sciences. The advantages of NUS FR-ME-HSQC are experimentally demonstrated on two solid-phase-extracted DOM (SPE-DOM) samples from the surface and deep ocean. With this new technology, differences in the composition of DOM from various aquatic environments can be assigned to individual molecules.
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Affiliation(s)
- Sahithya Phani Babu Vemulapalli
- Research
Group for Marine Geochemistry, Institute for Chemistry and Biology
of the Marine Environment (ICBM), University
of Oldenburg, 26129 Oldenburg, Germany
| | - Christian Griesinger
- Department
of NMR Based Structural Biology, Max Planck
Institute (MPI) for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Thorsten Dittmar
- Research
Group for Marine Geochemistry, Institute for Chemistry and Biology
of the Marine Environment (ICBM), University
of Oldenburg, 26129 Oldenburg, Germany
- Helmholtz
Institute for Functional Marine Biodiversity at the University of
Oldenburg (HIFMB), 26129 Oldenburg, Germany
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4
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Song G, Simpson AJ, Hayes MHB. Compositional changes in the humin fraction resulting from the long-term cultivation of an Irish grassland soil: Evidence from FTIR and multi-NMR spectroscopies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163280. [PMID: 37028664 DOI: 10.1016/j.scitotenv.2023.163280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/27/2023]
Abstract
Soil humin (HN), a major long-term sink for carbon in the pedosphere, plays a key role in the global carbon cycle, and has been less extensively studied than the humic and fulvic acids components. There are increasing concerns about the depletions of soil organic matter (SOM) arising from modern soil cultivation practices but there has been little focus on how HN can be altered as the result. This study has compared the HN components in a soil under cultivation for wheat for >30 years with those from an adjacent contiguous soil that had been under long-term grass for all that time. A urea-fortified basic solution isolated additional humic fractions from soils that had been exhaustively extracted in basic media. Then further exhaustive extractions of the residual soil material with dimethyl sulfoxide, amended with sulphuric acid isolated what may be called the "true" HN fraction. The long-term cultivation resulted in a loss of 53 % soil organic carbon in the surface soil. Infrared and multi-NMR spectroscopies showed the "true" HN to be dominated by aliphatic hydrocarbons and carboxylated structures, but with clear evidence for lesser amounts of carbohydrate and peptide materials, and with weaker evidence for lignin-derived substances. These lesser-amount structures can be sorbed on the soil mineral colloid surfaces and/or covered by the hydrophobic HN component or entrained within these which have strong affinities for the mineral colloids. HN from the cultivated site contained less carbohydrate and more carboxyl groups suggesting slow transformations took place resulting from the cultivation, but these were much slower than for the other components of SOM. It is recommended that a study be made of the HN in a soil under long-term cultivation for which the SOM content has reached a steady state and where HN will be expected to dominate the components of SOM.
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Affiliation(s)
- Guixue Song
- Institute of Marine Science & Technology, Shandong Univeristy, Qingdao campus, Qingdao, Shandong 266237, China
| | - Andre J Simpson
- Department of Chemistry, University of Toronto, Scarborough Campus, Toronto, Ontario M1C 1A4, Canada
| | - Michael H B Hayes
- Department of Chemical Sciences, University of Limerick, Castletroy, Limerick, Ireland.
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5
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Serk H, Nilsson MB, Figueira J, Krüger JP, Leifeld J, Alewell C, Schleucher J. Organochemical Characterization of Peat Reveals Decomposition of Specific Hemicellulose Structures as the Main Cause of Organic Matter Loss in the Acrotelm. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17410-17419. [PMID: 36399683 PMCID: PMC9730845 DOI: 10.1021/acs.est.2c03513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Peatlands store carbon in the form of dead organic residues. Climate change and human impact impose risks on the sustainability of the peatlands carbon balance due to increased peat decomposition. Here, we investigated molecular changes in the upper peat layers (0-40 cm), inferred from high-resolution vertical depth profiles, from a boreal peatland using two-dimensional 1H-13C nuclear magnetic resonance (NMR) spectroscopy, and comparison to δ13C, δ15N, and carbon and nitrogen content. Effects of hydrological conditions were investigated at respective sites: natural moist, drainage ditch, and natural dry. The molecular characterization revealed preferential degradation of specific side-chain linkages of xylan-type hemicelluloses within 0-14 cm at all sites, indicating organic matter losses up to 25%. In contrast, the xylan backbone, galactomannan-type hemicelluloses, and cellulose were more resistant to degradation and accumulated at the natural moist and drainage site. δ13C, δ15N, and carbon and nitrogen content did not correlate with specific hemicellulose structures but reflected changes in total carbohydrates. Our analysis provides novel insights into peat carbohydrate decomposition and indicates substantial organic matter losses in the acrotelm due to the degradation of specific hemicellulose structures. This suggests that variations in hemicellulose content and structure influence peat stability, which may have important implications with respect to climate change.
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Affiliation(s)
- Henrik Serk
- Department
of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
- Department
of Forest Ecology and Management, Swedish
University of Agricultural Sciences, SE-90183 Umeå, Sweden
| | - Mats B. Nilsson
- Department
of Forest Ecology and Management, Swedish
University of Agricultural Sciences, SE-90183 Umeå, Sweden
| | - João Figueira
- Department
of Chemistry, SciLife Lab, Umeå University, SE-90187 Umeå, Sweden
| | - Jan Paul Krüger
- UDATA
GmbH − Umwelt und Bildung, Hindenburgstrasse 1, 67433 Neustadt an der Weinstraße, Germany
- Departement
Umweltgeowissenschaften, Universität
Basel, Bernoullistrasse
30, CH-4056 Basel, Switzerland
| | - Jens Leifeld
- Departement
Umweltgeowissenschaften, Universität
Basel, Bernoullistrasse
30, CH-4056 Basel, Switzerland
- Agroscope,
Climate and Agriculture Group, Reckenholzstrasse 191, CH-8046 Zurich, Switzerland
| | - Christine Alewell
- Departement
Umweltgeowissenschaften, Universität
Basel, Bernoullistrasse
30, CH-4056 Basel, Switzerland
| | - Jürgen Schleucher
- Department
of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
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6
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Tadini AM, Goranov AI, Martin-Neto L, Bernardi ACC, Oliveira PPA, Pezzopane JRM, Hatcher PG. Structural characterization using 2D NMR spectroscopy and TMAH-GC × GC-MS: Application to humic acids from soils of an integrated agricultural system and an Atlantic native forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152605. [PMID: 34971684 DOI: 10.1016/j.scitotenv.2021.152605] [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: 09/21/2021] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Understanding the chemical make-up of soils and their structure is critical for constraining the role of soil organic matter (SOM) into the global biogeochemical cycles, as well as to understand the capability of SOM to sequester carbon and mitigate greenhouse gas emissions. Here, we use two-dimensional 1H-13C heteronuclear single quantum coherence nuclear magnetic resonance (2D 1H-13C HSQC NMR) spectroscopy to structurally characterize the most refractory component of SOM, the humic acid (HA). The observations from 2D 1H-13C HSQC NMR were coupled with lignin phenol and fatty acid measurements using tetramethylammonium hydroxide (TMAH) thermochemolysis - two-dimensional gas chromatography - mass spectrometry (TMAH-GC × GC-MS). We studied humic acids extracted from an integrated Crop - Livestock - Forest System (CLFS) agricultural area and an undisturbed Atlantic Native Forest (NF) area. We evaluated soils from two different depths: the topsoil (0-20 cm) and subsoil (60-100 cm) layers, and reveal the presence of oxidized ligninaceous phenols as we had previously hypothesized. Collectively, our results indicate that there are significant oxidative processes with increasing soil depth which are more pronounced in the CLFS relative to the NF area. Degradation of stearic acid with increasing depth in the CLFS soils indicated that the CLFS is more microbiologically active than NF. Therefore, CLFS is less biochemically stable than we originally perceived. The enhanced bio-reactivity of CLFS is likely driving the enhanced carbon sequestration in the CLFS soils. This is perhaps due to the diversity of biomass remnants available at the CLFS soil rhizosphere which allows for more different types of biomass to be sequestered as oxidized ligninaceous phenols. Our results employing structural characterization with 2D 1H-13C HSQC NMR and TMAH-GC × GC-MS provide a new layer of knowledge about the practice of integrated agricultural systems and allow us to understand the structure and fate of sequestered carbon in soils from different soil environments.
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Affiliation(s)
- Amanda M Tadini
- Embrapa Instrumentação, São Carlos, SP, Brazil; Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA.
| | - Aleksandar I Goranov
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | | | | | | | | | - Patrick G Hatcher
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
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7
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Weber J, Jamroz E, Kocowicz A, Debicka M, Bekier J, Ćwieląg-Piasecka I, Ukalska-Jaruga A, Mielnik L, Bejger R, Jerzykiewicz M. Optimized isolation method of humin fraction from mineral soil material. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2022; 44:1289-1298. [PMID: 34272620 PMCID: PMC8960568 DOI: 10.1007/s10653-021-01037-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/08/2021] [Indexed: 05/12/2023]
Abstract
Humic substances, including humin fraction, play a key role in the fate of organic and inorganic xenobiotics contaminating the environment. Humin is an important fraction of humic substances, which has been the least studied to date. This is due to the difficulties connected with its isolation that pose a number of methodological problems. Methods of humin fraction isolation can be divided into following main groups: (1) digestion of mineral soil components with HF/HCl followed by alkali extraction of HA and FA; (2) alkali extraction of HA and FA followed by extraction of humin by different organic solvents; and (3) alkali extraction of HA and FA followed by HF/HCl digestion of mineral soil components. Nevertheless, each of these methods has different limitations. We described in detail a useful procedure of humin isolation, in which this fraction was not extracted, but isolated from the soil by removing its soluble organic and mineral components. A modified method of HA and FA extraction with 0.1 M NaOH, according to the International Humic Substances Society, was used in the first step. Then, the mineral components in the residue were digested with the 10% HF/HCl. Unlike the procedures oriented to increase the concentration of organic matter, samples were treated several times with the HF/HCl mixture until the mineral fraction was almost completely digested. The main assumption of the method modification was to obtain the highest yield with the lowest possible ash content, but without affecting humin chemical structure. The results showed that the proposed procedure is characterized by a high efficiency and recovery and, therefore, it can be used to isolate high amounts of humin from soil.
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Affiliation(s)
- Jerzy Weber
- Institute of Soil Science and Environmental Protection, Wroclaw University of Environmental and Life Sciences, ul. Grunwaldzka 53, 50-357 Wrocław, Poland
| | - Elżbieta Jamroz
- Institute of Soil Science and Environmental Protection, Wroclaw University of Environmental and Life Sciences, ul. Grunwaldzka 53, 50-357 Wrocław, Poland
| | - Andrzej Kocowicz
- Institute of Soil Science and Environmental Protection, Wroclaw University of Environmental and Life Sciences, ul. Grunwaldzka 53, 50-357 Wrocław, Poland
| | - Magdalena Debicka
- Institute of Soil Science and Environmental Protection, Wroclaw University of Environmental and Life Sciences, ul. Grunwaldzka 53, 50-357 Wrocław, Poland
| | - Jakub Bekier
- Institute of Soil Science and Environmental Protection, Wroclaw University of Environmental and Life Sciences, ul. Grunwaldzka 53, 50-357 Wrocław, Poland
| | - Irmina Ćwieląg-Piasecka
- Institute of Soil Science and Environmental Protection, Wroclaw University of Environmental and Life Sciences, ul. Grunwaldzka 53, 50-357 Wrocław, Poland
| | - Aleksandra Ukalska-Jaruga
- Institute of Soil Science and Plant Cultivation, Department of Soil Science, Erosion and Land Conservation, State Research Institute, ul. Czartoryskich 8, 24-100 Puławy, Poland
| | - Lilla Mielnik
- Department of Bioengineering, Lab of Physics and Agrophysics, West Pomeranian University of Technology, ul. Papieża Pawła VI 3, 71-459 Szczecin, Poland
| | - Romualda Bejger
- Department of Bioengineering, Lab of Physics and Agrophysics, West Pomeranian University of Technology, ul. Papieża Pawła VI 3, 71-459 Szczecin, Poland
| | - Maria Jerzykiewicz
- Faculty of Chemistry, Biomaterials Chemistry Group, University of Wroclaw, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
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Wang Y, Tian L, Wang L, Yan X, Shan J, Ji R. Degradation, transformation, and non-extractable residue formation of nitrated nonylphenol isomers in an oxic soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 289:117880. [PMID: 34352632 DOI: 10.1016/j.envpol.2021.117880] [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: 04/16/2021] [Revised: 07/19/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Nitrated nonylphenols (NNPs) are main metabolites of the endocrine-disrupting nonylphenols in soil, yet their fate is unknown. Here, using four NNP isomers (NNP111, NNP112, NNP65, and NNP38), the degradation pattern of NNPs was investigated in an oxic soil for 266 days. Specifically, NNP111 was 14C-labeled to facilitate investigating its degradation, transformation, and non-extractable residue (NER) formation. NNPs degradation was isomer-specific with the decreasing order of half-life: NNP111 (126 days) > NNP112 (76 days) > NNP65 (14 days) > NNP38 (8.4 days), providing direct evidence of the greater persistence of NNPs in soil than their parent NPs. At the end of the incubation, 8.5 %, 7.3 %, and 39.9 % of 14C-NNP111 was mineralized, transformed to 2-amino-NP111, and formed NERs in active soil, respectively. In contrast, NERs in sterilized soils were significantly lower, amounting to 15.1 % and 17.3 % in autoclaved and γ-irradiated soil, respectively. The majority of the NERs (>70 %) were in humin fraction, in which type I NER was the predominant (>90 %) mode for NER formation. Our results provide comprehensive knowledge on the fate of NNPs in soil, demonstrating that isomer-specific behavior, transformation products of NNPs, and NER formation should be considered when evaluating environmental fate and risks of NNPs.
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Affiliation(s)
- Yongfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, China; Quanzhou Institute for Environment Protection Industry, Nanjing University, Beifeng Road, 362000, Quanzhou, China
| | - Lili Tian
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, China
| | - Lianhong Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, China
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-ecological Experimental Station, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-ecological Experimental Station, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China.
| | - Rong Ji
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, China; Quanzhou Institute for Environment Protection Industry, Nanjing University, Beifeng Road, 362000, Quanzhou, China
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9
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Kikuchi J, Yamada S. The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science. RSC Adv 2021; 11:30426-30447. [PMID: 35480260 PMCID: PMC9041152 DOI: 10.1039/d1ra03008f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 08/31/2021] [Indexed: 12/22/2022] Open
Abstract
The environment, from microbial ecosystems to recycled resources, fluctuates dynamically due to many physical, chemical and biological factors, the profile of which reflects changes in overall state, such as environmental illness caused by a collapse of homeostasis. To evaluate and predict environmental health in terms of systemic homeostasis and resource balance, a comprehensive understanding of these factors requires an approach based on the "exposome paradigm", namely the totality of exposure to all substances. Furthermore, in considering sustainable development to meet global population growth, it is important to gain an understanding of both the circulation of biological resources and waste recycling in human society. From this perspective, natural environment, agriculture, aquaculture, wastewater treatment in industry, biomass degradation and biodegradable materials design are at the forefront of current research. In this respect, nuclear magnetic resonance (NMR) offers tremendous advantages in the analysis of samples of molecular complexity, such as crude bio-extracts, intact cells and tissues, fibres, foods, feeds, fertilizers and environmental samples. Here we outline examples to promote an understanding of recent applications of solution-state, solid-state, time-domain NMR and magnetic resonance imaging (MRI) to the complex evaluation of organisms, materials and the environment. We also describe useful databases and informatics tools, as well as machine learning techniques for NMR analysis, demonstrating that NMR data science can be used to evaluate the exposome in both the natural environment and human society towards a sustainable future.
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Affiliation(s)
- Jun Kikuchi
- Environmental Metabolic Analysis Research Team, RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
- Graduate School of Bioagricultural Sciences, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8601 Japan
- Graduate School of Medical Life Science, Yokohama City University 1-7-29 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
| | - Shunji Yamada
- Environmental Metabolic Analysis Research Team, RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
- Prediction Science Laboratory, RIKEN Cluster for Pioneering Research 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe 650-0047 Japan
- Data Assimilation Research Team, RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe 650-0047 Japan
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10
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Ning P, Lane D, Ghosh Biswas R, Soong R, Schmidig D, Frei T, De Castro P, Kovacevic I, Graf S, Wegner S, Busse F, Kuehn T, Struppe J, Fey M, Stronks HJ, Monette M, Simpson MJ, Simpson AJ. Comprehensive Multiphase NMR Probehead with Reduced Radiofrequency Heating Improves the Analysis of Living Organisms and Heat-Sensitive Samples. Anal Chem 2021; 93:10326-10333. [PMID: 34259008 DOI: 10.1021/acs.analchem.1c01932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Comprehensive multiphase (CMP) NMR, first described in 2012, combines all of the hardware components necessary to analyze all phases (solid, gel, and solution) in samples in their natural state. In combination with spectral editing experiments, it can fully differentiate phases and study the transfer of chemical species across and between phases, providing unprecedented molecular-level information in unaltered natural systems. However, many natural samples, such as swollen soils, plants, and small organisms, contain water, salts, and ionic compounds, making them electrically lossy and susceptible to RF heating, especially when using high-strength RF fields required to select the solid domains. While dedicated reduced-heating probes have been developed for solid-state NMR, to date, all CMP-NMR probes have been based on solenoid designs, which can lead to problematic sample heating. Here, a new prototype CMP probe was developed, incorporating a loop gap resonator (LGR) for decoupling. Temperature increases are monitored in salt solutions analogous to those in small aquatic organisms and then tested in vivo on Hyalella azteca (freshwater shrimp). In the standard CMP probe (solenoid), 80% of organisms died within 4 h under high-power decoupling, while in the LGR design, all organisms survived the entire test period of 12 h. The LGR design reduced heating by a factor of ∼3, which allowed 100 kHz decoupling to be applied to salty samples with generally ≤10 °C sample heating. In addition to expanding the potential for in vivo research, the ability to apply uncompromised high-power decoupling could be beneficial for multiphase samples containing true crystalline solids that require the strongest possible decoupling fields for optimal detection.
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Affiliation(s)
- Paris Ning
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Daniel Lane
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | | | - Ronald Soong
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Daniel Schmidig
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Thomas Frei
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Peter De Castro
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Ivan Kovacevic
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Stephan Graf
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Sebastian Wegner
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Falko Busse
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Till Kuehn
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Jochem Struppe
- Bruker BioSpin Corp., 15 Fortune Drive, Billerica, Massachusetts 01821-3991, United States
| | - Michael Fey
- Bruker BioSpin Corp., 15 Fortune Drive, Billerica, Massachusetts 01821-3991, United States
| | - Henry J Stronks
- Bruker Ltd., 2800 High Point Drive, Milton, Ontario L9T 6P4, Canada
| | - Martine Monette
- Bruker Ltd., 2800 High Point Drive, Milton, Ontario L9T 6P4, Canada
| | - Myrna J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - André J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
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11
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Rehman ZU, Vrouwenvelder JS, Saikaly PE. Physicochemical Properties of Extracellular Polymeric Substances Produced by Three Bacterial Isolates From Biofouled Reverse Osmosis Membranes. Front Microbiol 2021; 12:668761. [PMID: 34349735 PMCID: PMC8328090 DOI: 10.3389/fmicb.2021.668761] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
This work describes the chemical composition of extracellular polymeric substances (EPS) produced by three bacteria (RO1, RO2, and RO3) isolated from a biofouled reverse osmosis (RO) membrane. We isolated pure cultures of three bacterial strains from a 7-year-old biofouled RO module that was used in a full-scale seawater treatment plant. All the bacterial strains showed similar growth rates, biofilm formation, and produced similar quantities of proteins and polysaccharides. The gel permeation chromatography showed that the EPS produced by all the strains has a high molecular weight; however, the EPS produced by strains RO1 and RO3 showed the highest molecular weight. Fourier Transform Infrared Spectroscopy (FTIR), Proton Nuclear Magnetic Resonance (1H NMR), and Carbon NMR (13C NMR) were used for a detailed characterization of the EPS. These physicochemical analyses allowed us to identify features of EPS that are important for biofilm formation. FTIR analysis indicated the presence of α-1,4 glycosidic linkages (920 cm-1) and amide II (1,550 cm-1) in the EPS, the presence of which has been correlated with the fouling potential of bacteria. The presence of α-glycoside linkages was further confirmed by 13C NMR analysis. The 13C NMR analysis also showed that the EPS produced by these bacteria is chemically similar to foulants obtained from biofouled RO membranes in previous studies. Therefore, our results support the hypothesis that the majority of substances that cause fouling on RO membranes originate from bacteria. Investigation using 1H NMR showed that the EPS contained a high abundance of hydrophobic compounds, and these compounds can lead to flux decline in the membrane processes. Genome sequencing of the isolates showed that they represent novel species of bacteria belonging to the genus Bacillus. Examination of genomes showed that these bacteria carry carbohydrates-active enzymes that play a role in the production of polysaccharides. Further genomic studies allowed us to identify proteins involved in the biosynthesis of EPS and flagella involved in biofilm formation. These analyses provide a glimpse into the physicochemical properties of EPS found on the RO membrane. This knowledge can be useful in the rational design of biofilm control treatments for the RO membrane.
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Affiliation(s)
- Zahid Ur Rehman
- Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Johannes S Vrouwenvelder
- Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Pascal E Saikaly
- Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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12
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López-Martínez VG, Guerrero-Álvarez JA, Ronderos-Lara JG, Murillo-Tovar MA, Solá-Pérez JE, León-Rivera I, Saldarriaga-Noreña H. Spectral Characteristics Related to Chemical Substructures and Structures Indicative of Organic Precursors from Fulvic Acids in Sediments by NMR and HPLC-ESI-MS. Molecules 2021; 26:molecules26134051. [PMID: 34279390 PMCID: PMC8272027 DOI: 10.3390/molecules26134051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this work was to determine Fulvic Acids (FAs) in sediments to better know their composition at the molecular level and to propose substructures and structures of organic precursors. The sediment samples were obtained from a priority area for the conservation of ecosystems and biodiversity in Mexico. FAs were extracted and purified using modifications to the International Humic Substances Society method. The characterization was carried out by 1D and 2D nuclear magnetic resonance (NMR) and high-performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) in positive (ESI+) and negative (ESI−) modes. Twelve substructures were proposed by the COSY and HSQC experiments, correlating with compounds likely belonging to lignin derivatives obtained from soils as previously reported. The analysis of spectra obtained by HPLC-ESI-MS indicated likely presence of compounds chemically similar to that of the substructures elucidated by NMR. FAs studied are mainly constituted by carboxylic acids, hydroxyl, esters, vinyls, aliphatics, substituted aromatic rings, and amines, presenting structures related to organic precursors, such as lignin derivatives and polysaccharides.
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Affiliation(s)
- Verónica Gisela López-Martínez
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - Jorge A. Guerrero-Álvarez
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - José Gustavo Ronderos-Lara
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - Mario Alfonso Murillo-Tovar
- CONACYT-Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62290, Morelos, Mexico;
| | - Jorge Ernesto Solá-Pérez
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburna de Hidalgo Inn, Merida C.P. 97203, Yucatán, Mexico;
| | - Ismael León-Rivera
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - Hugo Saldarriaga-Noreña
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
- Correspondence:
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13
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Hansen PE. NMR of Natural Products as Potential Drugs. Molecules 2021; 26:3763. [PMID: 34205539 PMCID: PMC8235798 DOI: 10.3390/molecules26123763] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 01/21/2023] Open
Abstract
This review outlines methods to investigate the structure of natural products with emphasis on intramolecular hydrogen bonding, tautomerism and ionic structures using NMR techniques. The focus is on 1H chemical shifts, isotope effects on chemical shifts and diffusion ordered spectroscopy. In addition, density functional theory calculations are performed to support NMR results. The review demonstrates how hydrogen bonding may lead to specific structures and how chemical equilibria, as well as tautomeric equilibria and ionic structures, can be detected. All these features are important for biological activity and a prerequisite for correct docking experiments and future use as drugs.
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Affiliation(s)
- Poul Erik Hansen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
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14
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Pham DM, Kasai T, Yamaura M, Katayama A. Humin: No longer inactive natural organic matter. CHEMOSPHERE 2021; 269:128697. [PMID: 33139048 DOI: 10.1016/j.chemosphere.2020.128697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
The discovery of the function of humin (HM), an insoluble fraction of humic substances (HSs), as an extracellular electron mediator (EEM) in 2012 has provided insight into the role of HM in nature and its potential for in situ bioremediation of pollutants. The EEM function is thought to enable the energy network of various microorganisms using HM. Recently, a number of studies on the application of HM as EEM in anaerobic microbial cultures have been conducted. Even so, there is a need for developing a holistic view of HM EEM function. In this paper, we summarize all the available information on the properties of HM EEM function, its applications, possible redox-active structures, and the interaction between HM and microbial cells. We also suggest scopes for future HM research.
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Affiliation(s)
- Duyen Minh Pham
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya, 464-8603, Japan
| | - Takuya Kasai
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya, 464-8603, Japan; Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Mirai Yamaura
- Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Arata Katayama
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya, 464-8603, Japan; Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.
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15
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Song G, Hayes MHB, Novotny EH. A two-year incubation study of transformations of crop residues into soil organic matter (SOM) and a procedure for the sequential isolation and the fractionation of components of SOM. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:143034. [PMID: 33139004 DOI: 10.1016/j.scitotenv.2020.143034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
Maize (Zea mays) stover, with its natural 13C abundance, was incubated for two years in a gravelly brown earth sandy loam soil that had been under long term cultivation to wheat (Triticum aestivum) for more than 30 years. The relative abundances of 13C in the maize amendment allowed the contributions of the stover to be traced in the components of soil organic matter (SOM) isolated and fractionated using a sequential exhaustive extraction (SEE) process that gave 16 distinct fractions. These were caracterised using elemental, δ13C, FTIR, and 13C NMR analyses. Emphasis is placed on results for two years of incubation but to some extent data are compared with those for similar fractions taken after one year of incubation. Amounts of maize-derived organic carbon in the humic (HA) and fulvic (FA) isolates were more than twice those in the fractions after one year of incubation. The NMR results highlighted compositional differences between the fractions and showed increased contributions of lignin to the HAs and FAs (and especially in the cases of the HAs) as pH increased, and it was evident that humification was taking place after two years of incubation. The most recalcitrant humin fraction, isolated in the final solvent in the sequence, dimethylsulphoxide (DMSO) and sulfuric acid, is composed predominantly of methylene moieties, is compositionally and structurally very different from the humic and hydrophilic isolates, but identical to that which did not dissolve in the solvent. That suggests that exhaustively pre-extracting soil with the NaOH/urea solvent system used will allow a truly representative humin to be obtained using the DMSO/acid solvent system.
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Affiliation(s)
- Guixue Song
- Institute of Marine Science & Technology, Shandong University, Qingdao 266237, China.
| | - Michael H B Hayes
- Department of Chemical Sciences, University of Limerick, Limerick, Ireland.
| | - Etelvino H Novotny
- Embrapa Soils, Rua Jardim Botânico, 1024 CEP 22460-000 Rio de Janeiro, RJ, Brazil
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16
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Chaubey B, Singh P, Pal S. Solution-state NMR evaluation of molecular interaction between monoaromatic carboxylic acids and dissolved humic acid. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:17775-17788. [PMID: 33400107 DOI: 10.1007/s11356-020-12092-1] [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: 09/16/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Understanding the nature of interactions between the aromatic organic pollutants with dissolved humic acid (HA) is fundamental for the prediction of their environmental fate and subsequent development of efficient remediation methods. The present study employs solution-state 1H/19F NMR methods to investigate the non-covalent interaction between aqueous peat humic acid (Aldrich HA) and monoaromatic carboxylic acids (CA), viz., 2, 6 diflourobenzoic acid (DFBA) and its non-fluorinated analog, benzoic acid (BA). NMR self-diffusion measurement of HA protons confirmed micellar nature indicating possibility of encapsulation of small molecules through host-guest interaction. 19F-1H and 1H-1H saturation transfer difference (STD) experiments reveal the mode of insertion of CA into HA superstructure. The strength of interaction has been evaluated by analyzing T1/T2 relaxation times and self-diffusion coefficients of CA as a function of HA concentration. Association constants extracted for CA-HA complexes from NMR diffusion experiments reflected that the association between DFBA-HA (2.34 mM-1) is significantly higher than that of BA-HA (0.97 mM-1). The experimental outcome reiterated that substitution of -H with halogen atoms (-F in specific) to aromatic ring plays a dominant role in modulating the strength of association and mode of insertion of organic pollutants into HA superstructure. The present study emphasizes that AHA can be a potential remediating agent for organic contaminants due to its superior binding affinity compared to less humified extracted HA (EHA) from Karwar, Rajasthan, India.
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Affiliation(s)
- Bhawna Chaubey
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, 342037, India
| | - Pooja Singh
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, 342037, India
| | - Samanwita Pal
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, 342037, India.
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17
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Effect of Organic and Conventional Systems Used to Grow Pecan Trees on Diversity of Soil Microbiota. DIVERSITY 2020. [DOI: 10.3390/d12110436] [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
Agronomic management modifies the soil bacterial communities and may alter the carbon fractions. Here, we identify differences in several chemical and biological soil variables, as well as bacterial composition between organic (Org) and conventional (Conv) agronomic management in pecan (Carya illinoinensis) orchards located in Coahuila, Mexico. The analyzed variables were pH, N, P, K, soil organic matter, organic matter quality, soil organic carbon, C/N ratio, carbon fractions, microbial biomass carbon, easily extractable Glomalin, colony-forming units, CO2 emissions, and the enzyme activity. The DNA of soil bacteria was extracted, amplified (V3-V4 16S rRNA), and sequenced using Illumina. To compare variables between agronomic managements, t tests were used. Sequences were analyzed in QIIME (Quantitative Insights Into Microbial Ecology). A canonical correspondence analysis (CCA) was used to observe associations between the ten most abundant phyla and soil variables in both types of agronomic managements. In Org management, variables related to the capture of recalcitrant carbon compounds were significant, and there was a greater diversity of bacterial communities capable of promoting organic carbon sequestration. In Conv management, variables related to the increase in carbon mineralization, as well as the enzymatic activity related to the metabolism of labile compounds, were significant. The CCA suggested a separation between phyla associated with some variables. Agronomic management impacted soil chemical and biological parameters related to carbon dynamics, including bacterial communities associated with carbon sequestration. Further research is still necessary to understand the plasticity of some bacterial communities, as well as the soil–plant dynamics.
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18
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Schwichtenberg T, Bogdan D, Carignan CC, Reardon P, Rewerts J, Wanzek T, Field JA. PFAS and Dissolved Organic Carbon Enrichment in Surface Water Foams on a Northern U.S. Freshwater Lake. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14455-14464. [PMID: 33164508 DOI: 10.1021/acs.est.0c05697] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Information is needed on the concentration of per- and polyfluoroalkyl substances (PFAS) in foams on surface waters impacted by aqueous film-forming foam (AFFF). Nine pairs of foam and underlying bulk water were collected from a single freshwater lake impacted by PFAS and analyzed for PFAS by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF) and for dissolved organic carbon (DOC). The DOC of two foam:bulk water pairs was characterized by 1H NMR. Foams were comprised of 16 PFAS with concentrations as high as 97 000 ng/L (PFOS) along with longer-chain, more hydrophobic PFAS. Only five PFAS (PFOS and shorter chain lengths) were quantified in underlying bulk waters. Enrichment factors (foam:bulk water) ranged from 10 (PFHxA) up to 2830 (PFOS). Foams impacted by AFFF gave the greatest concentrations and number of PFAS classes with PFOS concentrations exceeding the EPA health advisory level (70 ng/L). PFAS concentrations were significantly below published critical micelle concentrations and constituted <0.1% of overall DOC concentrations in foam, indicating that PFAS are a minor fraction of DOC and that DOC likely plays a central role in foam formation. Estimates indicate that foam ingestion is a potentially important route of exposure for children and adults when they are in surface waters where foam is present.
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Affiliation(s)
- Trever Schwichtenberg
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Dorin Bogdan
- AECOM, Grand Rapids, Michigan 49546, United States
| | - Courtney C Carignan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Patrick Reardon
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Justin Rewerts
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Thomas Wanzek
- Crop and Soil Science, Oregon State University, Corvallis, Oregon 97331, United States
| | - Jennifer A Field
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon 97331, United States
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19
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Devarajan D, Liang L, Gu B, Brooks SC, Parks JM, Smith JC. Molecular Dynamics Simulation of the Structures, Dynamics, and Aggregation of Dissolved Organic Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:13527-13537. [PMID: 32985864 DOI: 10.1021/acs.est.0c01176] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dissolved organic matter (DOM) plays a significant role in the transport and transformation of pollutants in the aquatic environment. However, the experimental characterization of DOM has been limited mainly to bulk properties, and the molecular-level interactions among various components of DOM remain to be fully characterized. Here, we use molecular dynamics (MD) simulations to probe the structural properties of model DOM systems at atomic detail. The 200 ns simulations, validated by available experimental data, reveal processes and mechanisms by which chemical species (cations, peptides, lipids, lignin, carbohydrates, and some low-molecular-weight aliphatic and aromatic compounds) aggregate to form complex DOM. The DOM aggregates are dynamic, consisting of a hydrophobic core and amphiphilic exterior. The lipid tails and other hydrophobic fragments form the core, with hydrophilic and amphiphilic groups exposed to water, making DOM accessible to both polar and nonpolar species. Thus, the lipid component acts as a nucleator, whereas cations (especially Ca2+) connect the molecular fragments on the surface by coordinating with the O-containing functional groups of DOM. The structural details revealed here provide new insights including surface accessible atoms, overall assemblage, and interactions among the molecules of DOM for understanding the kinetics and mechanisms through which DOM interacts with metal and other contaminants.
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Affiliation(s)
- Deepa Devarajan
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Liyuan Liang
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
| | - Scott C Brooks
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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20
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Structural Characterization of Dissolved Organic Matter in Permafrost Peatland Lakes. WATER 2020. [DOI: 10.3390/w12113059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Thermokarst lakes result from the thawing of ice-rich permafrost and are widespread across northern landscapes. These waters are strong emitters of methane, especially in permafrost peatland regions, where they are stained black by high concentrations of dissolved organic matter (DOM). In the present study, we aimed to structurally characterize the DOM from a set of peatland thermokarst lakes that are known to be intense sites of microbial decomposition and methane emission. Samples were collected at different depths from three thermokarst lakes in the Sasapimakwananisikw (SAS) River valley near the eastern Hudson Bay community of Kuujjuarapik–Whapmagoostui (Nunavik, Canada). Samples were analyzed by spectrofluorometry, Fourier-transform infrared spectroscopy (FTIR), nuclear magnetic resonance spectroscopy (NMR), and elemental analysis. Fluorescence analyses indicated considerable amounts of autochthonous DOM in the surface waters of one of SAS 1A, indicating a strong bioavailability of labile DOM, and consequently a greater methanogenic potential. The three lakes differed in their chemical composition and diversity, suggesting various DOM transformations phenomena. The usefulness of complementary analytical approaches to characterize the complex mixture of DOM in permafrost peatland waters cannot be overlooked, representing a first step towards greater comprehension of the organic geochemical properties of these permafrost-derived systems.
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21
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Xu J, Dai Y, Shi Y, Zhao S, Tian H, Zhu K, Jia H. Mechanism of Cr(VI) reduction by humin: Role of environmentally persistent free radicals and reactive oxygen species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 725:138413. [PMID: 32298894 DOI: 10.1016/j.scitotenv.2020.138413] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/25/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Humic substances, especially humin (HM) in its solid phase, is considered to be the main electron donor during the reduction of Cr(VI) in the environment. This work explores the reaction mechanism between Cr(VI) and the functional groups contained in HM, environmentally persistent free radicals (EPFRs), and reactive oxygen species (ROS). We examine the changes in the functional groups, EPFRs, and ROS on HM during the reaction, and inhibit the production of ROS to verify their effect. Our results demonstrate that the carboxyl and phenolic hydroxyl groups contained in HM are consumed during the reaction. The phenolic hydroxyl group can directly react with Cr(VI) as an electron donor, and can also transfer electrons to molecular oxygen to generate superoxide radicals to reduce Cr(VI). EPFRs also exhibit the same reaction pathway. The molecular oxygen in the solution gains electrons to generate O2·-, which further reacts with Cr(VI) to reduce it to Cr(III). The production and effect of active oxygen are verified by removing oxygen from the solution. In this study, the contribution of active oxygen to the reduction of Cr(VI) is approximately 30%. This study provides theoretical support for revealing the effects of humic substances on the conversion of Cr(VI).
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Affiliation(s)
- Jun Xu
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Yunchao Dai
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Yafang Shi
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Song Zhao
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Haixia Tian
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Kecheng Zhu
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Hanzhong Jia
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
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22
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Structural characterization of the lignin from Saxifraga (Saxifraga oppositifolia L.) stems. Int J Biol Macromol 2020; 155:656-665. [DOI: 10.1016/j.ijbiomac.2020.03.258] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 11/15/2022]
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23
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Distinct Assembly Processes and Microbial Communities Constrain Soil Organic Carbon Formation. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.oneear.2020.03.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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24
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Pavitt AS, Tratnyek PG. Electrochemical characterization of natural organic matter by direct voltammetry in an aprotic solvent. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019; 21:1664-1683. [PMID: 31576393 DOI: 10.1039/c9em00313d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The complex and indeterminant composition of NOM makes characterization of its redox properties challenging. Approaches that have been taken to address this challenge include chemical probe reactions, potentiometric titrations, chronocoulometry, and voltammetry. In this study, we revisit the use of direct voltammetric methods in aprotic solvents by applying an expanded and refined suite of methods to a large set of NOM samples and model compounds (54 NOM samples from 10 different sources, 7 NOM model compounds, and 2 fresh extracts of plant materials that are high in redox-active quinonoid model compounds dissolved in DMSO). Refinements in the methods of fitting the data obtained by staircase cyclic voltammetry (SCV) provided improved definition of peaks, and square wave voltammetry (SWV), performed under the same conditions as SCV, provided even more reliable identification and quantitation of peaks. Further evidence is provided that DMSO improves the electrode response by unfolding some of the tertiary structure of NOM polymers, thereby allowing greater contact between redox active functional groups and the electrode surface. We averaged experimental peak potentials for all NOM compounds and calculated potentials in water. Average values for Epa1, Epc1, and Ep1 in DMSO were -0.866 ± 0.069, -1.35 ± 0.071, and -0.831 ± 0.051 V vs. Ag/Ag+, and -0.128, -0.613, and -0.0930 V vs. SHE in water. In addition to peak potentials, the breadth of SCV peaks was quantified as a way to characterize the degree to which the redox activity of NOM is due to a continuum of contributing functional groups. The average breadth values were 1.63 ± 0.24, 1.28 ± 0.34, and 0.648 ± 0.15 V for Epa1, Epc1, and Ep1 respectively. Comparative analysis of the overall dataset-from SCV and SWV on all NOMs and model compounds-revealed that NOM redox properties vary over a narrower range than expected based on model compound properties. This lack of diversity in redox properties of NOM is similar to conclusions from other recent work on the molecular structure of NOM, all of which could be the result of selectivity in the common extraction methods used to obtain the materials.
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Affiliation(s)
- Ania S Pavitt
- OHSU-PSU School of Public Health, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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25
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Shakeri Yekta S, Hedenström M, Svensson BH, Sundgren I, Dario M, Enrich-Prast A, Hertkorn N, Björn A. Molecular characterization of particulate organic matter in full scale anaerobic digesters: An NMR spectroscopy study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 685:1107-1115. [PMID: 31390701 DOI: 10.1016/j.scitotenv.2019.06.264] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/04/2019] [Accepted: 06/17/2019] [Indexed: 05/24/2023]
Abstract
This study assesses the molecular characteristics of particulate organic matter (POM) in agricultural and food waste digesters and elucidates the molecular properties of the recalcitrant POM fraction, which remains in the digestate after AD process. Molecular properties of POM in influent (substrate) and effluent (digestate) of seven full-scale AD plants (three agricultural waste and four food waste digesters) were characterized and compared using solid-state 13C cross-polarization magic angle spinning (CP-MAS) and solution-state 1H,13C heteronuclear single-quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy. Comparison of the POM structural compositions of substrate and digestate from each AD plant revealed an enrichment of protein structures relative to the carbohydrates in most cases, implying a preferential degradation of the carbohydrates over proteins and/or increase of microbial biomass upon AD of agricultural and food wastes. Distinctive molecular structures of labile and recalcitrant fractions of POM, subjected to AD, were identified by comparing the NMR spectra of all substrate and digestate POM. Accordingly, the labile POM fraction in food and agricultural solid wastes is characterized by structural entities of lipids and starch-like carbohydrates, whereas recalcitrant POM structures resemble alkyl and aromatic subunits of amino acids, lignin, and polysaccharides with β-glycosidic linkages. This information serves as a basis to further explore optimization approaches for improving AD of the underutilized POM and the fate of organic matter in digestate-amended arable lands.
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Affiliation(s)
- Sepehr Shakeri Yekta
- Department of Thematic Studies-Environmental Change and Biogas Research Center, Linköping University, 581 83 Linköping, Sweden.
| | | | - Bo H Svensson
- Department of Thematic Studies-Environmental Change and Biogas Research Center, Linköping University, 581 83 Linköping, Sweden
| | - Ingrid Sundgren
- Department of Thematic Studies-Environmental Change and Biogas Research Center, Linköping University, 581 83 Linköping, Sweden
| | - Mårten Dario
- Department of Thematic Studies-Environmental Change and Biogas Research Center, Linköping University, 581 83 Linköping, Sweden
| | - Alex Enrich-Prast
- Department of Thematic Studies-Environmental Change and Biogas Research Center, Linköping University, 581 83 Linköping, Sweden
| | - Norbert Hertkorn
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry, 85764 Neuherberg, Germany
| | - Annika Björn
- Department of Thematic Studies-Environmental Change and Biogas Research Center, Linköping University, 581 83 Linköping, Sweden
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26
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Gao X, Tan W, Zhao Y, Wu J, Sun Q, Qi H, Xie X, Wei Z. Diversity in the Mechanisms of Humin Formation during Composting with Different Materials. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3653-3662. [PMID: 30821974 DOI: 10.1021/acs.est.8b06401] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Humins (HMs) play a very important role in various environmental processes and are crucial for regulating global carbon and nitrogen cycles in various ecosystems. Composting is a controlled decomposition process accompanied by the stabilization of organic solid waste materials. During composting, active fractions of organic substances can be transformed into HMs containing stable and complex macromolecules. However, the structural heterogeneity and formation mechanisms of HMs during composting with various substrates have not been clarified. Here, the structure and composition of HMs extracted from livestock manure (LM) and straw (SW) during composting were investigated by excitation-emission matrices spectroscopy and Fourier transform infrared spectroscopy. The results showed that the stability and humification of LM-HM were lower than that of SW-HM. The parallel factor analysis components of the HM in LM composting contained the same fluorescent unit, and the intermediate of cellulose degradation affected the structure of the HM from SW composting. Structural equation modeling demonstrated that low-molecular-weight compounds were key factors in humification. On the basis of the structure and key factors impacting HM, we constructed two mechanisms for the formation of HM from different composting processes. The LM-HMs from different humification processes have multiple identical fluorescent structural units, and the high humification of SW is affected by its polysaccharide constituents, which contains a fluorescent component in their skeleton, providing a basis for studying HM in composting.
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Affiliation(s)
- Xintong Gao
- College of Life Science , Northeast Agricultural University , Harbin 150030 , China
| | - Wenbing Tan
- State Key Laboratory of Environment Criteria and Risk Assessment , Chinese Research Academy of Environmental Sciences , Beijing 100012 , China
| | - Yue Zhao
- College of Life Science , Northeast Agricultural University , Harbin 150030 , China
| | - Junqiu Wu
- College of Life Science , Northeast Agricultural University , Harbin 150030 , China
| | - Qinghong Sun
- College of Life Science , Northeast Agricultural University , Harbin 150030 , China
| | - Haishi Qi
- College of Life Science , Northeast Agricultural University , Harbin 150030 , China
| | - Xinyu Xie
- College of Life Science , Northeast Agricultural University , Harbin 150030 , China
| | - Zimin Wei
- College of Life Science , Northeast Agricultural University , Harbin 150030 , China
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27
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Zhu Q, Wu Y, Zeng J, Wang X, Zhang T, Lin X. Influence of bacterial community composition and soil factors on the fate of phenanthrene and benzo[a]pyrene in three contrasting farmland soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:229-237. [PMID: 30677667 DOI: 10.1016/j.envpol.2018.12.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/24/2018] [Accepted: 12/25/2018] [Indexed: 06/09/2023]
Abstract
The fate of polycyclic aromatic hydrocarbons (PAHs) determines their potential risk in soil, which may be directly affected by abiotic conditions and indirectly through the changes in decomposer communities. In comparison, the indirect effects on the fate remain largely elusive. In this study, the fate of phenanthrene and benzo[a]pyrene and the corresponding bacterial changes were investigated in three contaminated farmland soils using a 14C tracer method and Miseq sequencing. The results showed that most benzo[a]pyrene was consistently extractable with dichloromethane (DCM) after the 60-day incubation (60.4%-78.2%), while phenanthrene was mainly mineralized to CO2 during the 30-day incubation (40.4%-58.7%). Soils from Guangzhou (GZ) showed a different distribution pattern of 14C-PAHs exemplified by low mineralization and disparate bound residue formation. The PAH fate in the Shenyang (SY) and Nanjing (NJ) soils were similar to each other than to that in the GZ soil. The fate in the GZ soil seemed to be linked to the distinct edaphic properties, such as organic matter content, however soil microbial community could have influenced the distribution pattern of PAHs. This potential role of microorganisms was reflected by the unique changes in the copy numbers of Gram positive RHDα gene, and by the distinct shifts in bacterial community composition during the incubation. A quite different shift in bacterial communities was found in the GZ microcosms which may influence PAH mineralization and non-extractable residue (NER) formation.
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Affiliation(s)
- Qinghe Zhu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xingxiang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Taolin Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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28
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Hayden HL, Rochfort SJ, Ezernieks V, Savin KW, Mele PM. Metabolomics approaches for the discrimination of disease suppressive soils for Rhizoctonia solani AG8 in cereal crops using 1H NMR and LC-MS. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:1627-1638. [PMID: 30360288 DOI: 10.1016/j.scitotenv.2018.09.249] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
The suppression of soilborne crop pathogens such as Rhizoctonia solani AG8 may offer a sustainable and enduring method for disease control, though soils with these properties are difficult to identify. In this study, we analysed the soil metabolic profiles of suppressive and non-suppressive soils over 2 years of cereal production. We collected bulk and rhizosphere soil at different cropping stages and subjected soil extracts to liquid chromatography-mass spectrometry (LC-MS) and proton nuclear magnetic resonance spectroscopy (1H NMR) analyses. Community analyses of suppressive and non-suppressive soils using principal component analyses and predictive modelling of LC-MS and NMR datasets respectively, revealed distinct biochemical profiles for the two soil types with clustering based on suppressiveness and cropping stage. NMR spectra revealed the suppressive soils to be more abundant in sugar molecules than non-suppressive soils, which were more abundant in lipids and terpenes. LC-MS features that were significantly more abundant in the suppressive soil were identified and assessed as potential biomarkers for disease suppression. The structures of a potential class of LC-MS biomarkers were elucidated using accurate mass data and MS fragmentation spectrum information. The most abundant compound found in association with suppressive soils was confirmed to be a macrocarpal, which is an antimicrobial secondary metabolite. Our study has demonstrated the utility of environmental metabolomics for the study of disease suppressive soils, resulting in the discovery of a macrocarpal biomarker for R. solani AG8 suppressive soil which can be further studied functionally in association with suppression pot trials and microbial isolation studies.
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Affiliation(s)
- Helen L Hayden
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia.
| | - Simone J Rochfort
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Vilnis Ezernieks
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia
| | - Keith W Savin
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia
| | - Pauline M Mele
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
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29
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Yang L, Li Y, Su F, Li H. A study of the microbial metabolomics analysis of subsurface wastewater infiltration system. RSC Adv 2019; 9:39674-39683. [PMID: 35541424 PMCID: PMC9076178 DOI: 10.1039/c9ra05290a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/21/2019] [Indexed: 11/21/2022] Open
Abstract
Microbial action in SWIS is one of the main ways to remove contaminants. Studying the metabolic processes and pathways of microorganisms is helpful to reveal the mechanism of pollutant removal in the “black box” process of SWIS. In this study, based on metabolomics and UPLC-MS, partial least squares (PLS-DA), principal component analysis (PCA) pattern recognition and cluster analysis were used to classify the microbial samples. According to the model's variable importance factor (VIP value) being greater than 1.5, a total of 53 potential biomarkers were screened out. There was a significant correlation between the microbial metabolites and soil profile. Most microbial metabolites were concentrated in the H2 layer (subsurface layer of SWIS), while there were relatively few in the H4 and H6 layers (middle and lower layers of SWIS); organic acids and alcohol metabolites mainly existed in the anoxic environment (H4 layer); antibiotics, growth hormones and pigments and other small molecule metabolites mainly existed under anaerobic conditions (H6 layer). The results of RDA analysis indicated that environmental factors had an effect on the microbial metabolites. With the variation of different height profiles, the metabolites were significantly affected by ORP and NO3−, which were negatively correlated. The above conclusions indicated that metabolomics is a reliable, accurate and effective method to quantitatively characterize the stability of SWIS. Microbial action in SWIS is one of the main ways to remove contaminants.![]()
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Affiliation(s)
- Lei Yang
- School of Resources and Civil Engineering
- Northeastern University
- Shenyang 110819
- China
| | - Yinghua Li
- School of Resources and Civil Engineering
- Northeastern University
- Shenyang 110819
- China
| | - Fei Su
- School of Resources and Civil Engineering
- Northeastern University
- Shenyang 110819
- China
| | - Haibo Li
- School of Resources and Civil Engineering
- Northeastern University
- Shenyang 110819
- China
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30
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The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen. ISME JOURNAL 2018; 13:977-988. [PMID: 30538275 PMCID: PMC6461840 DOI: 10.1038/s41396-018-0331-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/27/2018] [Accepted: 11/28/2018] [Indexed: 02/08/2023]
Abstract
Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.
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31
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Pham DM, Katayama A. Humin as an External Electron Mediator for Microbial Pentachlorophenol Dechlorination: Exploration of Redox Active Structures Influenced by Isolation Methods. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15122753. [PMID: 30563164 PMCID: PMC6313380 DOI: 10.3390/ijerph15122753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/13/2018] [Accepted: 12/02/2018] [Indexed: 01/26/2023]
Abstract
Humin (HM) has been reported to function as an external electron mediator (EEM) in various microbial reducing reactions. In this study, the effect of isolation methods on EEM functionality and the chemical/electrochemical structures of HM were examined based on the correlation between dechlorination rates in the anaerobic HM-dependent pentachlorophenol (PCP)-dechlorinating consortium and the chemical/electrochemical structures of HM. A lack of PCP dechlorination activity suggested no EEM function in the HM samples prepared as a soluble fraction in dimethyl sulfoxide and sulfuric acid (which did not contain any electric capacitance). Other HM samples exhibited EEM functionality as shown by the dechlorination activity ranging from 0.55 to 3.48 (µmol Cl−) L−1d−1. The comparison of dechlorination activity with chemical structural characteristics suggested that HM with EEM functionalities had predominantly aliphatic and carbohydrate carbons with the partial structures C=O, O=C–N, and O=C–O. EEM functionality positively correlated with the proportion of O=C–N and O=C–O, suggesting an association between peptidoglycan structure and EEM functionality. The lack of detection of a quinone structure in one HM sample with EEM functionality and a negative correlation with aromatic or C=C carbon suggested that the mechanism containing quinone structures is a minor component for the functionality of EEM.
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Affiliation(s)
- Duyen Minh Pham
- Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan.
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya 464-8603, Japan.
| | - Arata Katayama
- Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan.
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya 464-8603, Japan.
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32
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Gentile L, Wang T, Tunlid A, Olsson U, Persson P. Ferrihydrite Nanoparticle Aggregation Induced by Dissolved Organic Matter. J Phys Chem A 2018; 122:7730-7738. [PMID: 30165023 DOI: 10.1021/acs.jpca.8b05622] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ferrihydrite (Fh) nanoparticles are omnipresent in nature and often highly mobile because of their colloidal stability. Thus, Fh serves as a vector for iron as well as associated nutrients and contaminants. Here, we demonstrate, using small-angle X-ray scattering combined with cryo-transmission electron microscopy (cryo-TEM), that dissolved organic matter (DOM), extracted from a boreal forest soil, induce aggregation of Fh nanoparticles, of radius 3 nm, into fractal aggregates, having a fractal dimension D = 1.7. The DOM consists of both fractal-like colloids (>100 nm) and small molecular DOM, but the attractive Fh interparticle interaction was mediated by molecular DOM alone as shown by cryo-TEM. This highlights the importance of using soil extracts, including all size fractions, in studies of the colloidal behavior of DOM-mineral aggregates. The Fh nanoparticles also self-assemble during synthesis into aggregates with the same fractal dimension as the DOM-Fh aggregates. We propose that, in both the absence and presence of DOM, the aggregation is controlled by the Fh particle charge, and the process can be viewed as a linear polymerization into a self-avoiding random walk structure. The theoretical D value for this is 5/3, which is in close agreement with our Fh and DOM-Fh results.
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Affiliation(s)
- Luigi Gentile
- Department of Biology, MEMEG Unit , Lund University , Sölvegatan 35 , Lund 223 62 , Sweden
| | - Tao Wang
- Department of Biology, MEMEG Unit , Lund University , Sölvegatan 35 , Lund 223 62 , Sweden
| | - Anders Tunlid
- Department of Biology, MEMEG Unit , Lund University , Sölvegatan 35 , Lund 223 62 , Sweden
| | - Ulf Olsson
- Department of Chemistry, Physical Chemistry Division , Lund University , Naturvetarvägen 14 , Lund 223 62 , Sweden
| | - Per Persson
- Department of Biology, MEMEG Unit , Lund University , Sölvegatan 35 , Lund 223 62 , Sweden.,Centre for Environmental and Climate Research (CEC) , Lund University , Sölvegatan 35 , Lund 223 62 , Sweden
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33
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Zhang J, Yin H, Wang H, Xu L, Samuel B, Liu F, Chen H. Reduction mechanism of hexavalent chromium by functional groups of undissolved humic acid and humin fractions of typical black soil from Northeast China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:16913-16921. [PMID: 29623643 DOI: 10.1007/s11356-018-1878-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Soil organic matters (SOM) have a great retention effect on Cr(VI) migration in subsurface environment, which act as the main electron donors for Cr(VI) reduction; however, Cr(VI) reduction mechanism by different SOM fractions is still unclear, such as undissolved humic acid (HA) and humin (HM). In this study, HA and HM fractions extracted from typical black soil from Northeast China were used to investigate the reaction mechanism between humus functional groups and Cr(VI). According to the results, phenol and hydroxyl were determined as the main electron donors for Cr(VI) reduction by HA and HM instead of carboxyl and carbonyl, which were more likely involved in Cr complexation. Furthermore, Cr(VI) reduction was more dependent on aromatic carbon, rather than aliphatic carbon, and functional groups on the particle surfaces of HA and HM were much more active for Cr(VI) reduction than their interior part. Additionally, HM was found to have a relatively low Cr(VI) reduction capability compared with HA resulting from its high content of cellulose structures that are quite resistant to Cr(VI) oxidation. These results suggest that in the soil environment, undissolved HA tends to play a much more important role than HM in Cr(VI) reduction and retention in the condition that their mass contents are comparable.
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Affiliation(s)
- Jia Zhang
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing, 100083, People's Republic of China
| | - Huilin Yin
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing, 100083, People's Republic of China
| | - Hui Wang
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing, 100083, People's Republic of China
| | - Lin Xu
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing, 100083, People's Republic of China
| | - Barnie Samuel
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing, 100083, People's Republic of China
| | - Fei Liu
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing, 100083, People's Republic of China.
| | - Honghan Chen
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing, 100083, People's Republic of China
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Shakeri Yekta S, Hedenström M, Stehr JE, Dario M, Hertkorn N, Björn A. Pretreatment of anaerobic digester samples by hydrochloric acid for solution-state 1H and 13C NMR spectroscopic characterization of organic matter. CHEMOSPHERE 2018; 199:201-209. [PMID: 29438947 DOI: 10.1016/j.chemosphere.2018.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/02/2018] [Accepted: 02/04/2018] [Indexed: 06/08/2023]
Abstract
Pretreatment of anaerobic digester samples by hydrochloric acid (HCl) resulted in removal of Fe-based mineral and coordination compounds, attenuating their interferences with solution-state nuclear magnetic resonance (NMR) spectroscopic characterization of the solid phase organic matter. Substrate (influent) and digestate (effluent) samples from two full-scale anaerobic digesters, designated CD (co-digester) and SSD (sewage sludge digester), were investigated. Pretreatment of CD samples with 0.2-2.0 mol l-1 HCl and pretreatment of SSD samples with 1.0-3.0 mol l-1 HCl removed 96-100% and 76-80% of total Fe, respectively. Pretreatment declined overall paramagnetic characteristics of digestate samples, manifested by 50% (CD) and 70% (SSD) decrease in electron paramagnetic resonance signal intensities. As a result, meaningful solution-state 1H,13C heteronuclear single quantum coherence and 1H NMR spectra of DMSO-d6 soluble organic matter could be acquired. Sample pretreatment with the lowest concentration of HCl resulted in alteration of C:N ratios in solid phase, likely due to removal of labile organic and inorganic C- and N-containing compounds, while elevating the HCl concentration did not further change the C:N ratios. Furthermore, sample pretreatment increased the solubility of carbohydrates and proteins in DMSO-d6, enabling the detection of NMR resonances from certain structural units of carbohydrates (e.g. anomeric O2CH) and proteins (e.g. CHα in amino acids). Both attenuation of the paramagnetic matrix as well as an enhanced solubility of carbohydrate and protein fractions of the samples in DMSO-d6 solvent contributed to an improved molecular characterization of anaerobic digester samples by solution-state NMR analysis.
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Affiliation(s)
- Sepehr Shakeri Yekta
- Department of Thematic Studies-Environmental Change and Biogas Research Center, Linköping University, 581 83 Linköping, Sweden.
| | | | - Jan Eric Stehr
- Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Mårten Dario
- Department of Thematic Studies-Environmental Change and Biogas Research Center, Linköping University, 581 83 Linköping, Sweden
| | - Norbert Hertkorn
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry (BGC), 85764 Neuherberg, Germany
| | - Annika Björn
- Department of Thematic Studies-Environmental Change and Biogas Research Center, Linköping University, 581 83 Linköping, Sweden
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Nuclear Magnetic Resonance Analysis of Changes in Dissolved Organic Matter Composition with Successive Layering on Clay Mineral Surfaces. SOIL SYSTEMS 2018. [DOI: 10.3390/soils2010008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Wang JJ, Lafrenière MJ, Lamoureux SF, Simpson AJ, Gélinas Y, Simpson MJ. Differences in Riverine and Pond Water Dissolved Organic Matter Composition and Sources in Canadian High Arctic Watersheds Affected by Active Layer Detachments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1062-1071. [PMID: 29301070 DOI: 10.1021/acs.est.7b05506] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Regional warming has caused permafrost thermokarst and disturbances, such as active layer detachments (ALDs), which may alter carbon feedback in Arctic ecosystems. However, it is currently unclear how these disturbances alter DOM biogeochemistry in rivers and ponds in Arctic ecosystems. Water samples from the main river channel, ALD-disturbed/undisturbed tributaries, and disturbed/undisturbed ponds within a catchment in the Canadian High Arctic were collected and analyzed using carbon isotopes and spectroscopic methods. Both river and pond samples had large variations in dissolved organic carbon (DOC) concentrations. Ponds, particularly ALD-disturbed ponds, had much older 14C DOC ages than rivers. Results from δ13C and absorption and fluorescence analyses indicate higher autochthonous contributions in ponds than rivers and increasing autochthonous contributions from upper to lower reaches of the main channel. The disturbed samples had less carbohydrates but more carboxyl-rich alicyclic molecules in 1H nuclear magnetic resonance spectra than undisturbed samples. These ALD-impacted samples also contained less terrestrial-humic-like but more oxidized-quinone-like components in the fluorescence spectra. Interestingly, the disturbed pond DOM displayed the greatest DOM oxidation with ALDs compared to undisturbed areas. Compared to Arctic rivers, small Arctic ponds have DOM predominantly from permafrost and microbial sources and may have a disproportionally stronger positive feedback on climate warming.
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Affiliation(s)
- Jun-Jian Wang
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough , 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Melissa J Lafrenière
- Department of Geography and Planning, Queen's University , 68 University Ave., Kingston, Ontario K7L 3N6, Canada
| | - Scott F Lamoureux
- Department of Geography and Planning, Queen's University , 68 University Ave., Kingston, Ontario K7L 3N6, Canada
| | - André J Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough , 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Yves Gélinas
- GEOTOP and the Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke West, Montréal, Quebec H4B 1R6, Canada
| | - Myrna J Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough , 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
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Kikuchi J, Ito K, Date Y. Environmental metabolomics with data science for investigating ecosystem homeostasis. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 104:56-88. [PMID: 29405981 DOI: 10.1016/j.pnmrs.2017.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/19/2017] [Accepted: 11/19/2017] [Indexed: 05/08/2023]
Abstract
A natural ecosystem can be viewed as the interconnections between complex metabolic reactions and environments. Humans, a part of these ecosystems, and their activities strongly affect the environments. To account for human effects within ecosystems, understanding what benefits humans receive by facilitating the maintenance of environmental homeostasis is important. This review describes recent applications of several NMR approaches to the evaluation of environmental homeostasis by metabolic profiling and data science. The basic NMR strategy used to evaluate homeostasis using big data collection is similar to that used in human health studies. Sophisticated metabolomic approaches (metabolic profiling) are widely reported in the literature. Further challenges include the analysis of complex macromolecular structures, and of the compositions and interactions of plant biomass, soil humic substances, and aqueous particulate organic matter. To support the study of these topics, we also discuss sample preparation techniques and solid-state NMR approaches. Because NMR approaches can produce a number of data with high reproducibility and inter-institution compatibility, further analysis of such data using machine learning approaches is often worthwhile. We also describe methods for data pretreatment in solid-state NMR and for environmental feature extraction from heterogeneously-measured spectroscopic data by machine learning approaches.
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Affiliation(s)
- Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan.
| | - Kengo Ito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Wang JJ, Pisani O, Lin LH, Lun OOY, Bowden RD, Lajtha K, Simpson AJ, Simpson MJ. Long-term litter manipulation alters soil organic matter turnover in a temperate deciduous forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:865-875. [PMID: 28711848 DOI: 10.1016/j.scitotenv.2017.07.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/09/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Understanding soil organic matter (OM) biogeochemistry at the molecular-level is essential for assessing potential impacts from management practices and climate change on shifts in soil carbon storage. Biomarker analyses and nuclear magnetic resonance (NMR) spectroscopy were used in an ongoing detrital input and removal treatment experiment in a temperate deciduous forest in Pennsylvania, USA, to examine how above- and below-ground plant inputs control soil OM quantity and quality at the molecular-level. From plant material to surface soils, the free acyclic lipids and cutin, suberin, and lignin biomarkers were preferentially retained over free sugars and free cyclic lipids. After 20years of above-ground litter addition (Double Litter) or exclusion (No Litter) treatments, soil OM composition was relatively more degraded, as revealed by solid-state 13C NMR spectroscopy. Under Doubled Litter inputs, soil carbon and phospholipid fatty acid (PLFA) concentrations were unchanged, suggesting that the current OM degradation status is a reflection of microbial-mediated degradation that occurred prior to the 20-year sampling campaign. Soil OM degradation was higher in the No Litter treatments, likely due to the decline in fresh, above-ground litter inputs over time. Furthermore, root and root and litter exclusion treatments (No Roots and No Inputs, respectively) both significantly reduced free sugars and PLFAs and increased preservation of suberin-derived compounds. PLFA stress ratios and the low N-acetyl resonances from diffusion edited 1H NMR also indicate substrate limitations and reduced microbial biomass with these treatments. Overall, we highlight that storage of soil carbon and its biochemical composition do not linearly increase with plant inputs because the microbial processing of soil OM is also likely altered in the studied forest.
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Affiliation(s)
- Jun-Jian Wang
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Oliva Pisani
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Lisa H Lin
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Olivia O Y Lun
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Richard D Bowden
- Department of Environmental Science, Allegheny College, Meadville, PA 16335, USA
| | - Kate Lajtha
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
| | - André J Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Myrna J Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada.
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Dutta Majumdar R, Bliumkin L, Lane D, Soong R, Simpson M, Simpson AJ. Analysis of DOM phototransformation using a looped NMR system integrated with a sunlight simulator. WATER RESEARCH 2017; 120:64-76. [PMID: 28478296 DOI: 10.1016/j.watres.2017.04.067] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
Photochemical transformation plays an important role in functionalizing and degrading dissolved organic matter (DOM), producing one of the most complex mixtures known. In this study, using a flow-based design, nuclear magnetic resonance (NMR) spectroscopy is directly interfaced with a sunlight simulator enabling the study of DOM photodegradation in situ with high temporal resolution over 5 days. Samples from Suwannee River (Florida), Nordic Reservoir (Norway), and Pony Lake (Antarctic) are studied. Phototransformation of DOM is dominated by the degradation of aromatics and unsaturated structures (many arising from lignin) into carboxylated and hydroxylated products. To assess longer term changes, the samples were continuously irradiated for 17.5 days, followed by the identification a wide range of compounds and assessment of their fate using off-line 2D-NMR. This study demonstrates the applicability of the looped system to follow degradation in a non-targeted fashion (the mixture as a whole) and target analysis (tracing specific metabolites), which holds great potential to study the fate and transformation of contaminants and nutrients in the presence of DOM. It also demonstrates that components that remain unresolved in 1D NMR can be identified using 2D methods.
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Affiliation(s)
- Rudraksha Dutta Majumdar
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Liora Bliumkin
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Daniel Lane
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Ronald Soong
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Myrna Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - André J Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada.
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Large perturbations in CO 2 flux and subsequent chemosynthesis are induced in agricultural soil by the addition of elemental sulfur. Sci Rep 2017; 7:4732. [PMID: 28680102 PMCID: PMC5498539 DOI: 10.1038/s41598-017-04934-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/22/2017] [Indexed: 11/08/2022] Open
Abstract
The microbial contribution to soil organic matter has been shown to be much larger than previously thought and thus it plays a major role in carbon cycling. Among soil microorganisms, chemoautotrophs can fix CO2 without sunlight and can glean energy through the oxidation of reduced elements such as sulfur. Here we show that the addition of sulfur to soil results in an initial surge in production of CO2 through microbial respiration, followed by an order of magnitude increase in the capture of carbon from the atmosphere as elemental sulfur is oxidised to sulfate. Thiobacillus spp., take advantage of specific conditions to become the dominant chemoautotrophic group that consumes CO2. We discern the direct incorporation of atmospheric carbon into soil carbohydrate, protein and aliphatic compounds and differentiate these from existing biomass. These results suggest that chemoautotrophs can play a large role in carbon cycling and that this carbon is heavily influenced by land management practises.
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Deary ME, Ekumankama CC, Cummings SP. Development of a novel kinetic model for the analysis of PAH biodegradation in the presence of lead and cadmium co-contaminants. JOURNAL OF HAZARDOUS MATERIALS 2016; 307:240-252. [PMID: 26785214 DOI: 10.1016/j.jhazmat.2015.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/16/2015] [Accepted: 12/09/2015] [Indexed: 06/05/2023]
Abstract
We report on the results of a 40 week study in which the biodegradation of 16 US EPA polycyclic aromatic hydrocarbons (PAHs) was followed in microcosms containing soil of high organic carbon content (11%) in the presence and absence of lead and cadmium co-contaminants. The total spiked PAH concentration was 2166mg/kg. Mercury amendment was also made to give an abiotic control. A novel kinetic model has been developed to explain the observed biphasic nature of PAH degradation. The model assumes that PAHs are distributed across soil phases of varying degrees of bioaccessibility. The results of the analysis suggest that overall percentage PAH loss is dependent on the respective rates at which the PAHs (a) are biodegraded by soil microorganisms in pore water and bioaccessible soil phases and (b) migrate from bioaccessible to non-bioaccessible soil phases. In addition, migration of PAHs to non-bioaccessible and non-Soxhlet-extractable soil phases associated with the humin pores gives rise to an apparent removal process. The presence of metal co-contaminants shows a concentration dependent inhibition of the biological degradation processes that results in a reduction in overall degradation. Lead appears to have a marginally greater inhibitory effect than cadmium.
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Affiliation(s)
- Michael E Deary
- Department of Geography,Faculty of Engineering and Environment, Northumbria University, Ellison Building, Newcastle upon Tyne NE1 8ST, United Kingdom.
| | - Chinedu C Ekumankama
- Department of Geography,Faculty of Engineering and Environment, Northumbria University, Ellison Building, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Stephen P Cummings
- Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle upon Tyne NE1 8ST, United Kingdom
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Shah F, Nicolás C, Bentzer J, Ellström M, Smits M, Rineau F, Canbäck B, Floudas D, Carleer R, Lackner G, Braesel J, Hoffmeister D, Henrissat B, Ahrén D, Johansson T, Hibbett DS, Martin F, Persson P, Tunlid A. Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors. THE NEW PHYTOLOGIST 2016; 209:1705-19. [PMID: 26527297 PMCID: PMC5061094 DOI: 10.1111/nph.13722] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/22/2015] [Indexed: 05/21/2023]
Abstract
Ectomycorrhizal fungi are thought to have a key role in mobilizing organic nitrogen that is trapped in soil organic matter (SOM). However, the extent to which ectomycorrhizal fungi decompose SOM and the mechanism by which they do so remain unclear, considering that they have lost many genes encoding lignocellulose-degrading enzymes that are present in their saprotrophic ancestors. Spectroscopic analyses and transcriptome profiling were used to examine the mechanisms by which five species of ectomycorrhizal fungi, representing at least four origins of symbiosis, decompose SOM extracted from forest soils. In the presence of glucose and when acquiring nitrogen, all species converted the organic matter in the SOM extract using oxidative mechanisms. The transcriptome expressed during oxidative decomposition has diverged over evolutionary time. Each species expressed a different set of transcripts encoding proteins associated with oxidation of lignocellulose by saprotrophic fungi. The decomposition 'toolbox' has diverged through differences in the regulation of orthologous genes, the formation of new genes by gene duplications, and the recruitment of genes from diverse but functionally similar enzyme families. The capacity to oxidize SOM appears to be common among ectomycorrhizal fungi. We propose that the ancestral decay mechanisms used primarily to obtain carbon have been adapted in symbiosis to scavenge nutrients instead.
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Affiliation(s)
- Firoz Shah
- Department of BiologyMicrobial Ecology GroupLund UniversityEcology BuildingSE‐223 62LundSweden
| | - César Nicolás
- Department of BiologyMicrobial Ecology GroupLund UniversityEcology BuildingSE‐223 62LundSweden
| | - Johan Bentzer
- Department of BiologyMicrobial Ecology GroupLund UniversityEcology BuildingSE‐223 62LundSweden
| | - Magnus Ellström
- Department of BiologyMicrobial Ecology GroupLund UniversityEcology BuildingSE‐223 62LundSweden
| | - Mark Smits
- Centre for Environmental SciencesHasselt UniversityBuilding DAgoralaan3590DiepenbeekLimburgBelgium
| | - Francois Rineau
- Centre for Environmental SciencesHasselt UniversityBuilding DAgoralaan3590DiepenbeekLimburgBelgium
| | - Björn Canbäck
- Department of BiologyMicrobial Ecology GroupLund UniversityEcology BuildingSE‐223 62LundSweden
| | - Dimitrios Floudas
- Department of BiologyMicrobial Ecology GroupLund UniversityEcology BuildingSE‐223 62LundSweden
- Biology DepartmentLasry Center for BioscienceClark University950 Main StreetWorcesterMA01610‐1477USA
| | - Robert Carleer
- Centre for Environmental SciencesHasselt UniversityBuilding DAgoralaan3590DiepenbeekLimburgBelgium
| | - Gerald Lackner
- Department of Pharmaceutical Microbiology at the Hans Knöll InstituteFriedrich‐Schiller‐UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Jana Braesel
- Department of Pharmaceutical Microbiology at the Hans Knöll InstituteFriedrich‐Schiller‐UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans Knöll InstituteFriedrich‐Schiller‐UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS)UMR7257Université Aix‐MarseilleMarseille13288France
- Department of Biological SciencesKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Dag Ahrén
- Department of BiologyMicrobial Ecology GroupLund UniversityEcology BuildingSE‐223 62LundSweden
- Bioinformatics Infrastructures for Life Sciences (BILS)Department of BiologyLund UniversityEcology BuildingSE‐223 62LundSweden
| | - Tomas Johansson
- Department of BiologyMicrobial Ecology GroupLund UniversityEcology BuildingSE‐223 62LundSweden
| | - David S. Hibbett
- Biology DepartmentLasry Center for BioscienceClark University950 Main StreetWorcesterMA01610‐1477USA
| | - Francis Martin
- Institut de la Recherche Agronomique (INRA)Laboratory of Excellence ARBREUMR INRA‐Université de Lorraine ‘Interactions Arbres/Micro‐organismes’INRA‐Nancy54280ChampenouxFrance
| | - Per Persson
- Department of BiologyMicrobial Ecology GroupLund UniversityEcology BuildingSE‐223 62LundSweden
- Centre for Environmental and Climate Research (CEC)Lund UniversityEcology BuildingSE‐223 62LundSweden
| | - Anders Tunlid
- Department of BiologyMicrobial Ecology GroupLund UniversityEcology BuildingSE‐223 62LundSweden
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Masoom H, Courtier-Murias D, Farooq H, Soong R, Kelleher BP, Zhang C, Maas WE, Fey M, Kumar R, Monette M, Stronks HJ, Simpson MJ, Simpson AJ. Soil Organic Matter in Its Native State: Unravelling the Most Complex Biomaterial on Earth. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:1670-1680. [PMID: 26783947 DOI: 10.1021/acs.est.5b03410] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Since the isolation of soil organic matter in 1786, tens of thousands of publications have searched for its structure. Nuclear magnetic resonance (NMR) spectroscopy has played a critical role in defining soil organic matter but traditional approaches remove key information such as the distribution of components at the soil-water interface and conformational information. Here a novel form of NMR with capabilities to study all physical phases termed Comprehensive Multiphase NMR, is applied to analyze soil in its natural swollen-state. The key structural components in soil organic matter are identified to be largely composed of macromolecular inputs from degrading biomass. Polar lipid heads and carbohydrates dominate the soil-water interface while lignin and microbes are arranged in a more hydrophobic interior. Lignin domains cannot be penetrated by aqueous solvents even at extreme pH indicating they are the most hydrophobic environment in soil and are ideal for sequestering hydrophobic contaminants. Here, for the first time, a complete range of physical states of a whole soil can be studied. This provides a more detailed understanding of soil organic matter at the molecular level itself key to develop the most efficient soil remediation and agricultural techniques, and better predict carbon sequestration and climate change.
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Affiliation(s)
- Hussain Masoom
- Department of Chemistry, University of Toronto , Toronto, Ontario Canada , M1C 1A4
| | | | - Hashim Farooq
- Department of Chemistry, University of Toronto , Toronto, Ontario Canada , M1C 1A4
| | - Ronald Soong
- Department of Chemistry, University of Toronto , Toronto, Ontario Canada , M1C 1A4
| | - Brian P Kelleher
- School of Chemical Sciences, Dublin City University , Dublin, Ireland
| | - Chao Zhang
- Department of Chemistry, University of Toronto , Toronto, Ontario Canada , M1C 1A4
| | - Werner E Maas
- Bruker BioSpin Corp., Billerica, Massachusetts 01821-3991, United States
| | - Michael Fey
- Bruker BioSpin Corp., Billerica, Massachusetts 01821-3991, United States
| | - Rajeev Kumar
- Bruker BioSpin Canada, Milton, Ontario Canada , L9T 1Y6
| | | | | | - Myrna J Simpson
- Department of Chemistry, University of Toronto , Toronto, Ontario Canada , M1C 1A4
| | - André J Simpson
- Department of Chemistry, University of Toronto , Toronto, Ontario Canada , M1C 1A4
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Zhang Y, Wang F, Zhu X, Zeng J, Zhao Q, Jiang X. Extracellular polymeric substances govern the development of biofilm and mass transfer of polycyclic aromatic hydrocarbons for improved biodegradation. BIORESOURCE TECHNOLOGY 2015; 193:274-80. [PMID: 26141288 DOI: 10.1016/j.biortech.2015.06.110] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/21/2015] [Accepted: 06/22/2015] [Indexed: 05/15/2023]
Abstract
The hypothesis that extracellular polymeric substances (EPS) affect the formation of biofilms for subsequent enhanced biodegradation of polycyclic aromatic hydrocarbons was tested. Controlled formation of biofilms on humin particles and biodegradation of phenanthrene and pyrene were performed with bacteria and EPS-extracted bacteria of Micrococcus sp. PHE9 and Mycobacterium sp. NJS-P. Bacteria without EPS extraction developed biofilms on humin, in contrast the EPS-extracted bacteria could not attach to humin particles. In the subsequent biodegradation of phenanthrene and pyrene, the biodegradation rates by biofilms were significantly higher than those of EPS-extracted bacteria. Although, both the biofilms and EPS-extracted bacteria showed increases in EPS contents, only the EPS contents in biofilms displayed significant correlations with the biodegradation efficiencies of phenanthrene and pyrene. It is proposed that the bacterial-produced EPS was a key factor to mediate bacterial attachment to other surfaces and develop biofilms, thereby increasing the bioavailability of poorly soluble PAH for enhanced biodegradation.
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Affiliation(s)
- Yinping Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Nanjing Normal University Center for Analysis and Testing, Nanjing 210046, China
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiaoshu Zhu
- Nanjing Normal University Center for Analysis and Testing, Nanjing 210046, China
| | - Jun Zeng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qiguo Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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45
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Zhang C, Zhang D, Xiao Z, Li Z, Suzuki D, Katayama A. Characterization of humins from different natural sources and the effect on microbial reductive dechlorination of pentachlorophenol. CHEMOSPHERE 2015; 131:110-6. [PMID: 25819981 DOI: 10.1016/j.chemosphere.2015.02.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 05/26/2023]
Abstract
Humins have been reported to function as an electron mediator for microbial reducing reactions. However, the physicochemical properties and the functional moieties of humins from different natural sources have been poorly characterized. In this study, humins extracted from seven types of soil and from a river sediment were examined on the effect on microbial reductive dechlorination of pentachlorophenol (PCP) and characterized polyphasically. All humins facilitated microbial reductive dechlorination of PCP as electron mediators using formate as carbon source, with different dechlorination rates ranging from 0.99 to 7.63 (μmol Cl-) L(-1) d(-1). The highest rates were observed in humins with high carbon contents, extracted from Andisols containing allophone as major clay. Yields of the humins and the elemental compositions varied among sources. Fourier transform infrared analysis showed that all the humins exhibited similar spectra with different absorbance intensity; these data are indicative of their similar structures and identical classes of functional groups. The electron spin resonance spectra of humins prepared at different pH showed typical changes for the semiquinone-type radicals, suggestive of quinone moieties for the redox activity of the humins. Cyclic voltammetry analysis confirmed the presence of redox-active moieties in all the humins, with the estimated redox potentials in the range of -0.30 to -0.13 V (versus a standard hydrogen electrode), falling into the range of standard redox potential between the oxidation of formate as electron donor and the initial dechlorination of PCP as electron acceptor.
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Affiliation(s)
- Chunfang Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Hangzhou 310058, China; EcoTopia Science Institute, Nagoya University, Nagoya 464-8603, Japan
| | - Dongdong Zhang
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Zhixing Xiao
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Zhiling Li
- EcoTopia Science Institute, Nagoya University, Nagoya 464-8603, Japan
| | - Daisuke Suzuki
- EcoTopia Science Institute, Nagoya University, Nagoya 464-8603, Japan
| | - Arata Katayama
- EcoTopia Science Institute, Nagoya University, Nagoya 464-8603, Japan; Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan.
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Liang C, Gutknecht JLM, Balser TC. Microbial lipid and amino sugar responses to long-term simulated global environmental changes in a California annual grassland. Front Microbiol 2015; 6:385. [PMID: 25999926 PMCID: PMC4419726 DOI: 10.3389/fmicb.2015.00385] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 04/14/2015] [Indexed: 11/13/2022] Open
Abstract
Global environmental change is predicted to have major consequences for carbon cycling and the functioning of soil ecosystems. However, we have limited knowledge about its impacts on the microorganisms, which act as a "valve" between carbon sequestered in soils versus released into the atmosphere. In this study we examined microbial response to continuous 9-years manipulation of three global change factors (elevated CO2, warming, and nitrogen deposition), singly and in combination using two methods: lipid and amino sugar biomarkers at the Jasper Ridge Global Change Experiment (JRGCE). The two methods yielded important distinctions. There were limited microbial lipid differences, but many significant effects for microbial amino sugars. We found that CO2 was not a direct factor influencing soil carbon and major amino sugar pools, but had a positive impact on bacterial-derived muramic acid. Likewise, warming and nitrogen deposition appeared to enrich residues specific to bacteria despite an overall depletion in total amino sugars. The results indicate that elevated CO2, warming, and nitrogen deposition all appeared to increase bacterial-derived residues, but this accumulation effect was far offset by a corresponding decline in fungal residues. The sensitivity of microbial residue biomarker amino sugars to warming and nitrogen deposition may have implications for our predictions of global change impacts on soil stored carbon.
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Affiliation(s)
- Chao Liang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China ; Department of Soil Science, University of Wisconsin-Madison Madison, WI, USA
| | | | - Teri C Balser
- Department of Soil Science, University of Wisconsin-Madison Madison, WI, USA ; Department of Soil and Water Science, University of Florida, Gainesville FL, USA
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Olshansky Y, Polubesova T, Chefetz B. Degradation of plant cuticles in soils: impact on formation and sorptive ability of humin-mineral matrices. JOURNAL OF ENVIRONMENTAL QUALITY 2015; 44:849-858. [PMID: 26024265 DOI: 10.2134/jeq2014.10.0452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Plant cuticles are important precursors for soil organic matter, in particular for soil humin, which is considered an efficient sorbent for organic pollutants. In this study, we examined degradation and transformation of cuticles isolated from fruit and leaves in loamy sand and sandy clay loessial arid brown soils. We then studied sorption of phenanthrene and carbamazepine to humin-mineral matrices isolated from the incubated soils. Low degradation (22%) was observed for agave cuticle in a sandy clay soil system, whereas high degradation (68-78%) was obtained for agave cuticle in a loamy sand soil system and for loamy sand and sandy clay soils amended with tomato cuticle. During incubation, most of the residual organic matter was accumulated in the humin fraction. Sorption of phenanthrene was significantly higher for humin-mineral matrices obtained from soils incubated with plant cuticles as compared with soils without cuticle application. Sorption of carbamazepine to humin-mineral matrices was not affected by cuticle residues. Cooperative sorption of carbamazepine on humin-mineral matrices isolated from sandy clay soil is suggested. Sorption-desorption hysteresis of both phenanthrene and carbamazepine was lower for humin-mineral matrices obtained from soils incubated with plant cuticles as compared with nonamended soils. Our results show that cuticle composition significantly affects the rate and extent of cuticle degradation in soils and that plant cuticle application influences sorption and desorption of polar and nonpolar pollutants by humin-mineral matrices.
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48
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C/N ratio drives soil actinobacterial cellobiohydrolase gene diversity. Appl Environ Microbiol 2015; 81:3016-28. [PMID: 25710367 DOI: 10.1128/aem.00067-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/15/2015] [Indexed: 11/20/2022] Open
Abstract
Cellulose accounts for approximately half of photosynthesis-fixed carbon; however, the ecology of its degradation in soil is still relatively poorly understood. The role of actinobacteria in cellulose degradation has not been extensively investigated despite their abundance in soil and known cellulose degradation capability. Here, the diversity and abundance of the actinobacterial glycoside hydrolase family 48 (cellobiohydrolase) gene in soils from three paired pasture-woodland sites were determined by using terminal restriction fragment length polymorphism (T-RFLP) analysis and clone libraries with gene-specific primers. For comparison, the diversity and abundance of general bacteria and fungi were also assessed. Phylogenetic analysis of the nucleotide sequences of 80 clones revealed significant new diversity of actinobacterial GH48 genes, and analysis of translated protein sequences showed that these enzymes are likely to represent functional cellobiohydrolases. The soil C/N ratio was the primary environmental driver of GH48 community compositions across sites and land uses, demonstrating the importance of substrate quality in their ecology. Furthermore, mid-infrared (MIR) spectrometry-predicted humic organic carbon was distinctly more important to GH48 diversity than to total bacterial and fungal diversity. This suggests a link between the actinobacterial GH48 community and soil organic carbon dynamics and highlights the potential importance of actinobacteria in the terrestrial carbon cycle.
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49
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Zhang H, Ding W, He X, Yu H, Fan J, Liu D. Influence of 20-year organic and inorganic fertilization on organic carbon accumulation and microbial community structure of aggregates in an intensively cultivated sandy loam soil. PLoS One 2014; 9:e92733. [PMID: 24667543 PMCID: PMC3965464 DOI: 10.1371/journal.pone.0092733] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 02/24/2014] [Indexed: 11/18/2022] Open
Abstract
To evaluate the long-term effect of compost (CM) and inorganic fertilizer (NPK) application on microbial community structure and organic carbon (OC) accumulation at aggregate scale, soils from plots amended with CM, NPK and no fertilizer (control) for 20 years (1989-2009) were collected. Soil was separated into large macroaggregate (>2,000 μm), small macroaggregate (250-2,000 μm), microaggregate (53-250 μm), silt (2-53 μm) and clay fraction (<2 μm) by wet-sieving, and their OC concentration and phospholipid fatty acids (PLFA) were measured. The 20-year application of compost significantly (P<0.05) increased OC by 123-134% and accelerated the formation of macroaggregates, but decreased soil oxygen diffusion coefficient. NPK mainly increased OC in macroaggregates and displayed weaker influence on aggregation. Bacteria distributed in all aggregates, while fungi and actinobacteria were mainly in macroaggregates and microaggregates. The ratio of monounsaturated to branched (M/B) PLFAs, as an indicator for the ratio of aerobic to anaerobic microorganisms, increased inversely with aggregate size. Both NPK and especially CM significantly (P<0.05) decreased M/B ratios in all aggregates except the silt fraction compared with the control. The increased organic C in aggregates significantly (P<0.05) negatively correlated with M/B ratios under CM and NPK. Our study suggested that more efficient OC accumulations in aggregates under CM-treated than under NPK-treated soil was not only due to a more effective decrease of actinobacteria, but also a decrease of monounsaturated PLFAs and an increase of branched PLFAs. Aggregations under CM appear to alter micro-habitats to those more suitable for anaerobes, which in turn boosts OC accumulation.
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Affiliation(s)
- Huanjun Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- * E-mail:
| | - Xinhua He
- Forests NSW, NSW Department of Primary Industries, West Pennant Hills, New South Wales, Australia
- School of Plant Biology, University of Western Australia, Crawley, Western Australia, Australia
| | - Hongyan Yu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jianling Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Deyan Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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50
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Chang RR, Mylotte R, Hayes MHB, Mclnerney R, Tzou YM. A comparison of the compositional differences between humic fractions isolated by the IHSS and exhaustive extraction procedures. Naturwissenschaften 2014; 101:197-209. [DOI: 10.1007/s00114-013-1140-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/27/2013] [Accepted: 12/29/2013] [Indexed: 11/28/2022]
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