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Shen Z, Han T, Huang J, Li J, Daba NA, Gilbert N, Khan MN, Shah A, Zhang H. Soil organic carbon regulation by pH in acidic red soil subjected to long-term liming and straw incorporation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 367:122063. [PMID: 39098074 DOI: 10.1016/j.jenvman.2024.122063] [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: 11/01/2023] [Revised: 04/24/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
The manipulation of soil pH through liming and straw incorporation plays a pivotal role in influencing soil organic carbon (SOC) dynamics in acidic red soil. This study aimed to assess the impact of these practices on SOC and elucidate the relationship between SOC and pH. Over a 31-year field experiment, seven different fertilization treatments were implemented: unfertilized (CK), nitrogen and potassium fertilizers (NK), NK with lime (NKCa), nitrogen, phosphorous, and potassium fertilizers (NPK), NPK with lime (NPKCa), NPK with straw (NPKS), and NPKS with lime (NPKSCa). Results revealed that liming and straw incorporation significantly elevated soil pH by 0.13-0.73 units. Lime application boosted SOC and mineral-associated organic carbon (MAOC) by 20.2% and 28.7%, respectively, in NK treatment, whereas its impact on SOC in NPK and NPKS treatments were negligible. SOC witnessed a 17.1% increase with NPKS and a 15.2% increase with NPKSCa compared to NPK alone. Notably, NPKS and NPKSCa led to a significant surge in particulate organic carbon (POC) by 19.7% and 37.7%, respectively, albeit NPKSCa reduced MAOC by 14.9% relative to NPK. Linear regression analysis unveiled a positive correlation between POC and soil pH, while SOC and MAOC exhibited an initial rise at lower pH levels followed by stabilization as pH continuously increasing. A partial least squares path model showed two pathways through which pH influenced SOC: firstly, by positively affecting SOC through increasing Fe and Al oxides contents and enhanced aggregate stability, and secondly, by negatively influencing SOC through altered ratios of fungi/bacteria and Gram-positive bacteria/Gram-negative bacteria. In conclusion, the long-term effects of lime and straw application on SOC and MAOC were contingent upon soil pH, with more pronounced positive effects observed at lower pH levels. These findings underscore the importance of considering soil pH when implementing lime and straw strategies to mitigate acidification and regulate SOC in acidic red soil.
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Affiliation(s)
- Zhe Shen
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tianfu Han
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Jing Huang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; Qiyang Farmland Ecosystem National Observation and Research Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Qiyang, Hunan, 426182, China
| | - Jiwen Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Nano Alemu Daba
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ntagisanimana Gilbert
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Muhammad Numan Khan
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Asad Shah
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huimin Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; Qiyang Farmland Ecosystem National Observation and Research Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Qiyang, Hunan, 426182, China.
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2
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Hwang JH, Choi TR, Kim S, Lee Y, Shin Y, Choi S, Oh J, Kim SH, Park JH, Bhatia SK, Yang YH. Evaluation of simplified ester-linked fatty acid analysis (ELFA) for phospholipid fatty acid (PLFA) analysis of bacterial population. Anal Biochem 2024; 695:115638. [PMID: 39127328 DOI: 10.1016/j.ab.2024.115638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Phospholipid fatty acid (PLFA) analysis is used for characterizing microbial communities based on their lipid profiles. This method avoids biases from PCR or culture, allowing data collection in a natural state. However, PLFA is labor-intensive due to lipid fractionation. Simplified ester-linked fatty acid analysis (ELFA), which skips lipid fractionation, offers an alternative. It utilizes base-catalyzed methylation to derivatize only lipids, not free fatty acids, and found glycolipid and neutral lipid fractions are scarcely present in most bacteria, allowing lipid fractionation to be skipped. ELFA method showed a high correlation to PLFA data (r = 0.99) and higher sensitivity than the PLFA method by 1.5-2.57-fold, mainly due to the higher recovery of lipids, which was 1.5-1.9 times higher than with PLFA. The theoretical limit of detection (LOD) and limit of quantification (LOQ) for the ELFA method indicated that 1.54-fold less sample was needed for analysis than with the PLFA method. Our analysis of three bacterial cultures and a simulated consortium revealed the effectiveness of the ELFA method by its simple procedure and enhanced sensitivity for detecting strain-specific markers, which were not detected in PLFA analysis. Overall, this method could be easily used for the population analysis of synthetic consortia.
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Affiliation(s)
- Jeong Hyeon Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Tae-Rim Choi
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Suwon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Yeda Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Yuni Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Suhye Choi
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Jinok Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Sang-Hyoun Kim
- Department of Civil and Environmental Engineering, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jeong-Hoon Park
- Sustainable Technology and Wellness R&D Group, Korea Institute of Industrial Technology (KITECH), Jeju-si, 63243, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul, 05029, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul, 05029, Republic of Korea.
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3
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Cenčič Predikaka T, Mastnak T, Svoljšak Jerman M, Finšgar M. Ex situ bioremediation of diesel fuel-contaminated soil in two different climates. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2023; 25:1881-1889. [PMID: 37125609 DOI: 10.1080/15226514.2023.2204165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The petroleum industry is often faced with accidental spills and discharges that pollute valuable natural resources such as soil. The purpose of this study was to assess bioremediation potential of an on-site landfarming unit (LU), a highly economical solution that complies with the zero-waste policy, for bioremediation of the contaminated soil after an actual diesel fuel leakage in a fuel depot. The first aim was to evaluate the effects of different climates on hydrocarbon bioremediation. For this reason, a part of the contaminated soil was moved from the initial location with a sub-Mediterranean climate to an LU at another location with a temperate continental climate. Our results demonstrated that remediation in sub-Mediterranean climate is less effective than the remediation in a temperate continental climate. The second aim of this study was to evaluate the effect of different plant species on the microbial population during bioremediation. For that purpose, 365-day monitoring of phospholipid fatty acids (PLFA) was performed. Our results support the hypothesis that plant-assisted bioremediation can diminish toxic effects of diesel-polluted soil and that the changes in plant species during bioremediation cause changes in the microbial population.
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Affiliation(s)
- Tjaša Cenčič Predikaka
- Institute for Chemistry, Ecology, Measurements and Analytics, IKEMA d.o.o, Lovrenc na Dravskem polju, Slovenia
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Tinkara Mastnak
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | | | - Matjaž Finšgar
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
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4
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Caro TA, McFarlin J, Jech S, Fierer N, Kopf S. Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil. Proc Natl Acad Sci U S A 2023; 120:e2211625120. [PMID: 37036980 PMCID: PMC10120080 DOI: 10.1073/pnas.2211625120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/06/2023] [Indexed: 04/12/2023] Open
Abstract
The rate at which microorganisms grow and reproduce is fundamental to our understanding of microbial physiology and ecology. While soil microbiologists routinely quantify soil microbial biomass levels and the growth rates of individual taxa in culture, there is a limited understanding of how quickly microbes actually grow in soil. For this work, we posed the simple question: what are the growth rates of soil microorganisms? In this study, we measure these rates in three distinct soil environments using hydrogen-stable isotope probing of lipids with 2H-enriched water. This technique provides a taxa-agnostic quantification of in situ microbial growth from the degree of 2H enrichment of intact polar lipid compounds ascribed to bacteria and fungi. We find that growth rates in soil are quite slow and correspond to average generation times of 14 to 45 d but are also highly variable at the compound-specific level (4 to 402 d), suggesting differential growth rates among community subsets. We observe that low-biomass microbial communities exhibit more rapid growth rates than high-biomass communities, highlighting that biomass quantity alone does not predict microbial productivity in soil. Furthermore, within a given soil, the rates at which specific lipids are being synthesized do not relate to their quantity, suggesting a general decoupling of microbial abundance and growth in soil microbiomes. More generally, we demonstrate the utility of lipid-stable isotope probing for measuring microbial growth rates in soil and highlight the importance of measuring growth rates to complement more standard analyses of soil microbial communities.
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Affiliation(s)
- Tristan A. Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO80309
| | - Jamie McFarlin
- Department of Geology and Geophysics, University of Wyoming, Laramie, WY82071
| | - Sierra Jech
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO80309
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO80309
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
| | - Sebastian Kopf
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO80309
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5
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Finkel PL, Carrizo D, Parro V, Sánchez-García L. An Overview of Lipid Biomarkers in Terrestrial Extreme Environments with Relevance for Mars Exploration. ASTROBIOLOGY 2023; 23:563-604. [PMID: 36880883 PMCID: PMC10150655 DOI: 10.1089/ast.2022.0083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Lipid molecules are organic compounds, insoluble in water, and based on carbon-carbon chains that form an integral part of biological cell membranes. As such, lipids are ubiquitous in life on Earth, which is why they are considered useful biomarkers for life detection in terrestrial environments. These molecules display effective membrane-forming properties even under geochemically hostile conditions that challenge most of microbial life, which grants lipids a universal biomarker character suitable for life detection beyond Earth, where a putative biological membrane would also be required. What discriminates lipids from nucleic acids or proteins is their capacity to retain diagnostic information about their biological source in their recalcitrant hydrocarbon skeletons for thousands of millions of years, which is indispensable in the field of astrobiology given the time span that the geological ages of planetary bodies encompass. This work gathers studies that have employed lipid biomarker approaches for paleoenvironmental surveys and life detection purposes in terrestrial environments with extreme conditions: hydrothermal, hyperarid, hypersaline, and highly acidic, among others; all of which are analogous to current or past conditions on Mars. Although some of the compounds discussed in this review may be abiotically synthesized, we focus on those with a biological origin, namely lipid biomarkers. Therefore, along with appropriate complementary techniques such as bulk and compound-specific stable carbon isotope analysis, this work recapitulates and reevaluates the potential of lipid biomarkers as an additional, powerful tool to interrogate whether there is life on Mars, or if there ever was.
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Affiliation(s)
- Pablo L Finkel
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
- Department of Physics and Mathematics and Department of Automatics, University of Alcalá, Madrid, Spain
| | | | - Victor Parro
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
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6
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Impact of crop residue burning and tillage practices on soil biological parameters of rice–wheat agro-ecosystems. Trop Ecol 2023. [DOI: 10.1007/s42965-022-00287-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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7
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Wen L, Li D, Xiao X, Tang H. Alterations in soil microbial phospholipid fatty acid profile with soil depth following cropland conversion in karst region, southwest China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:1502-1519. [PMID: 35918580 DOI: 10.1007/s11356-022-22178-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
The soil microbial community is a key indicator used to evaluate the effectiveness of land use changes in degraded ecosystems. However, there is currently limited information on the vertical variations of soil microbial communities under different cropland types in the karst region of southwest China. In this study, three different cropland types (sugarcane, mulberry, and forage grass) were selected to replace maize-soybean cultivation in a karst area of southwest China. Secondary forest was included for comparison. Soil was collected at soil depths of 0-10 cm, 10-20 cm, 20-30 cm, and 30-50 cm to conduct a phospholipid fatty acid (PLFA) analysis of the soil microbial communities. The results showed that the abundances of total PLFAs and PLFAs of bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi were significantly higher in forage grass cultivation and secondary forest areas than those in other three cropland types. The abundance of total PLFA and its functional groups significantly decreased with increasing soil depth. Bacteria was the predominant community (> 52%) across all land use types and soil depths. A principal component analysis indicated that soil microbial PLFA composition in forage grass field and secondary forest areas differed significantly from that in mulberry, sugarcane, and maize-soybean fields across 0-50-cm soil layer. Soil organic carbon was identified as the primary factor affecting the abundance and structure of soil microbial communities in the four soil layers. These results suggest that greater improvements in soil quality and fertility could be made by replacing the maize-soybean rotation system with forage grass cultivation than by replacing it with mulberry or sugarcane cultivation in the karst region of southwest China.
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Affiliation(s)
- Li Wen
- Hunan Soil and Fertilizer Institute, Changsha, 410125, Hunan, China.
| | - Dejun Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Huangjiang 547100, Guangxi, China
| | - Xiaoping Xiao
- Hunan Soil and Fertilizer Institute, Changsha, 410125, Hunan, China
| | - Haiming Tang
- Hunan Soil and Fertilizer Institute, Changsha, 410125, Hunan, China
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8
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Pogăcean F, Varodi C, Măgeruşan L, Stefan-van Staden RI, Pruneanu S. Highly Sensitive Electrochemical Detection of Azithromycin with Graphene-Modified Electrode. SENSORS (BASEL, SWITZERLAND) 2022; 22:6181. [PMID: 36015941 PMCID: PMC9413463 DOI: 10.3390/s22166181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
An electrochemical cell containing two graphite rods was filled with the appropriate electrolyte (0.2 M ammonia + 0.2 M ammonium sulphate) and connected to the exfoliation system to synthesize graphene (EGr). A bias of 7 V was applied between the anode and cathode for 3 h. After synthesis, the morphology and structure of the sample was characterized by SEM, XRD, and FTIR techniques. The material was deposited onto the surface of a glassy carbon (GC) electrode (EGr/GC) and employed for the electrochemical detection of azithromycin (AZT). The DPV signals recorded in pH 5 acetate containing 6 × 10-5 M AZT revealed significant differences between the GC and EGr/GC electrodes. For EGr/GC, the oxidation peak was higher and appeared at lower potential (+1.12 V) compared with that of bare GC (+1.35 V). The linear range for AZT obtained with the EGr/GC electrode was very wide, 10-8-10-5 M, the sensitivity was 0.68 A/M, and the detection limit was 3.03 × 10-9 M. It is important to mention that the sensitivity of EGr/GC was three times higher than that of bare GC (0.23 A/M), proving the advantages of using graphene-modified electrodes in the electrochemical detection of AZT.
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Affiliation(s)
- Florina Pogăcean
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103, Donat Street, 400293 Cluj-Napoca, Romania
| | - Codruţa Varodi
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103, Donat Street, 400293 Cluj-Napoca, Romania
| | - Lidia Măgeruşan
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103, Donat Street, 400293 Cluj-Napoca, Romania
| | - Raluca-Ioana Stefan-van Staden
- Laboratory of Electrochemistry and PATLAB, National Institute of Research for Electrochemistry and Condensed Matter, 202 Splaiul Independentei Str., 060021 Bucharest, Romania
- Faculty of Applied Chemistry and Material Science, Politehnica University of Bucharest, 060042 Bucharest, Romania
| | - Stela Pruneanu
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103, Donat Street, 400293 Cluj-Napoca, Romania
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9
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Szamosvári D, Bae M, Bang S, Tusi BK, Cassilly CD, Park SM, Graham DB, Xavier RJ, Clardy J. Lyme Disease, Borrelia burgdorferi, and Lipid Immunogens. J Am Chem Soc 2022; 144:2474-2478. [PMID: 35129341 DOI: 10.1021/jacs.1c12202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The human immune system detects potentially pathogenic microbes with receptors that respond to microbial metabolites. While the overall immune signaling pathway is known in considerable detail, the initial molecular signals, the microbially produced immunogens, for important diseases like Lyme disease (LD) are often not well-defined. The immunogens for LD are produced by the spirochete Borrelia burgdorferi, and a galactoglycerolipid (1) has been identified as a key trigger for the inflammatory immune response that characterizes LD. This report corrects the original structural assignment of 1 to 3, a change of an α-galactopyranose to an α-galactofuranose headgroup. The seemingly small change has important implications for the diagnosis, prevention, and treatment of LD.
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Affiliation(s)
- Dávid Szamosvári
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
| | - Munhyung Bae
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
| | - Sunghee Bang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
| | - Betsabeh Khoramian Tusi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Chelsi D Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
| | - Sung-Moo Park
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Blavatnik Institute, Boston, Massachusetts 02115, United States
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10
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Burchill L, Williams SJ. From the banal to the bizarre: unravelling immune recognition and response to microbial lipids. Chem Commun (Camb) 2022; 58:925-940. [PMID: 34989357 DOI: 10.1039/d1cc06003a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Microbes produce a rich array of lipidic species that through their location in the cell wall and ability to mingle with host lipids represent a privileged class of immune-active molecules. Lipid-sensing immunity recognizes microbial lipids from pathogens and commensals causing immune responses. Yet microbial lipids are often heterogeneous, in limited supply and in some cases their structures are incompletely defined. Total synthesis can assist in structural determination, overcome supply issues, and provide access to high-purity, homogeneous samples and analogues. This account highlights synthetic approaches to lipidic species from pathogenic and commensal bacteria and fungi that have supported immunological studies involving lipid sensing through the pattern recognition receptor Mincle and cell-mediated immunity through the CD1-T cell axis.
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Affiliation(s)
- Laura Burchill
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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11
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Law KP, He W, Tao J, Zhang C. A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry. Front Microbiol 2021; 12:735878. [PMID: 34925256 PMCID: PMC8674956 DOI: 10.3389/fmicb.2021.735878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable, or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, Nitrosopumilus maritimus (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics.
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Affiliation(s)
- Kai P Law
- Southern University of Science and Technology, SUSTech Academy for Advanced Interdisciplinary Studies, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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12
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13
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Microbial lipid biosynthesis from lignocellulosic biomass pyrolysis products. Biotechnol Adv 2021; 54:107791. [PMID: 34192583 DOI: 10.1016/j.biotechadv.2021.107791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/18/2021] [Accepted: 06/24/2021] [Indexed: 01/08/2023]
Abstract
Lipids are a biorefinery platform to prepare fuel, food and health products. They are traditionally obtained from plants, but those of microbial origin allow for a better use of land and C resources, among other benefits. Several (thermo)chemical and biochemical strategies are used for the conversion of C contained in lignocellulosic biomass into lipids. In particular, pyrolysis can process virtually any biomass and is easy to scale up. Products offer cost-effective, renewable C in the form of readily fermentable molecules and other upgradable intermediates. Although the production of microbial lipids has been studied for 30 years, their incorporation into biorefineries was only described a few years ago. As pyrolysis becomes a profitable technology to depolymerize lignocellulosic biomass into assimilable C, the number of investigations on it raises significantly. This article describes the challenges and opportunities resulting from the combination of lignocellulosic biomass pyrolysis and lipid biosynthesis with oleaginous microorganisms. First, this work presents the basics of the individual processes, and then it shows state-of-the-art processes for the preparation of microbial lipids from biomass pyrolysis products. Advanced knowledge on separation techniques, structure analysis, and fermentability is detailed for each biomass pyrolysis fraction. Finally, the microbial fatty acid platform comprising biofuel, human food and animal feed products, and others, is presented. Literature shows that the microbial lipid production from anhydrosugars, like levoglucosan, and short-chain organic acids, like acetic acid, is straightforward. Indeed, processes achieving nearly theoretical yields form the latter have been described. Some authors have shown that lipid biosynthesis from different lignin sources is biochemically feasible. However, it still imposes major challenges regarding strain performance. No report on the fermentation of pyrolytic lignin is yet available. Research on the microbial uptake of pyrolytic humins remains vacant. Microorganisms that make use of methane show promising results at the proof-of-concept level. Overall, despite some issues need to be tackled, it is now possible to conceive new versatile biorefinery models by combining lignocellulosic biomass pyrolysis products and robust oleaginous microbial cell factories.
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Zosso CU, Wiesenberg GLB. Methylation procedures affect PLFA results more than selected extraction parameters. J Microbiol Methods 2021; 182:106164. [PMID: 33582123 DOI: 10.1016/j.mimet.2021.106164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022]
Abstract
Microorganisms are key players in organic matter and nutrient cycles of terrestrial ecosystems. The analysis of microbial membrane lipids, phospholipid fatty acids (PLFAs) has strongly improved our understanding of how microbial processes contribute to these cycles. The analysis has proven to yield robust results, but adaptations of analytical parameters to laboratory needs might lead to pitfalls and impede comparability of PLFA results between different studies. Here, we show how a set of four analytical parameters (freeze-drying vs. field moist, amount of sample extracted, age of solvent mixture, and methylation methods) influence the quantitative and qualitative results of PLFA analysis. Freeze-drying vs. field moist samples and the amount of sample extracted had only minor effects on PLFA concentrations and recovery of the microbial community structure. Nevertheless, these parameters are important to consider, especially if treatment effects in an experiment are expected to be low. The use of a four weeks old extraction solution resulted in 12% lower PLFA concentrations as well as significant differences in the relative abundance of functional microbial groups. This suggests that extraction solution should be prepared on the day of extraction or that the different components of the extraction solution should be added sequentially to the sample. Most importantly, the choice of the methylation method led to differences in both, PLFA concentrations (35%) and the relative abundance of functional microbial groups, making comparisons between studies difficult. Our study provides a valuable ranking of parameters that need to be considered during PLFA method implementation in a laboratory and also highlights the fact that comparability of studies using different methylation methods might be limited.
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Affiliation(s)
- Cyrill U Zosso
- Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Guido L B Wiesenberg
- Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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15
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Kodešová R, Chroňáková A, Grabicová K, Kočárek M, Schmidtová Z, Frková Z, Vojs Staňová A, Nikodem A, Klement A, Fér M, Grabic R. How microbial community composition, sorption and simultaneous application of six pharmaceuticals affect their dissipation in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141134. [PMID: 32768780 DOI: 10.1016/j.scitotenv.2020.141134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/17/2020] [Accepted: 07/19/2020] [Indexed: 05/12/2023]
Abstract
Pharmaceuticals may enter soils due to the application of treated wastewater or biosolids. Their leakage from soils towards the groundwater, and their uptake by plants is largely controlled by sorption and degradation of those compounds in soils. Standard laboratory batch degradation and sorption experiments were performed using soil samples obtained from the top horizons of seven different soil types and 6 pharmaceuticals (carbamazepine, irbesartan, fexofenadine, clindamycin and sulfamethoxazole), which were applied either as single-solute solutions or as mixtures (not for sorption). The highest dissipation half-lives were observed for citalopram (average DT50,S for a single compound of 152 ± 53.5 days) followed by carbamazepine (106.0 ± 17.5 days), irbesartan (24.4 ± 3.5 days), fexofenadine (23.5 ± 20.9 days), clindamycin (10.8 ± 4.2 days) and sulfamethoxazole (9.6 ± 2.0 days). The simultaneous application of all compounds increased the half-lives (DT50,M) of all compounds (particularly carbamazepine, citalopram, fexofenadine and irbesartan), which is likely explained by the negative impact of antibiotics (sulfamethoxazole and clindamycin) on soil microbial community. However, this trend was not consistent in all soils. In several cases, the DT50,S values were even higher than the DT50,M values. Principal component analyses showed that while knowledge of basic soil properties determines grouping of soils according sorption behavior, knowledge of the microbial community structure could be used to group soils according to the dissipation behavior of tested compounds in these soils. The derived multiple linear regression models for estimating dissipation half-lives (DT50,S) for citalopram, clindamycin, fexofenadine, irbesartan and sulfamethoxazole always included at least one microbial factor (either amount of phosphorus in microbial biomass or microbial biomarkers derived from phospholipid fatty acids) that deceased half-lives (i.e., enhanced dissipations). Equations for citalopram, clindamycin, fexofenadine and sulfamethoxazole included the Freundlich sorption coefficient, which likely increased half-lives (i.e., prolonged dissipations).
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Affiliation(s)
- Radka Kodešová
- Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Dept. of Soil Science and Soil Protection, Kamýcká 129, CZ-16500 Prague 6, Czech Republic.
| | - Alica Chroňáková
- Institute of Soil Biology, Biology Centre CAS, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic
| | - Kateřina Grabicová
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, CZ-38925 Vodňany, Czech Republic
| | - Martin Kočárek
- Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Dept. of Soil Science and Soil Protection, Kamýcká 129, CZ-16500 Prague 6, Czech Republic
| | - Zuzana Schmidtová
- Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Dept. of Soil Science and Soil Protection, Kamýcká 129, CZ-16500 Prague 6, Czech Republic
| | - Zuzana Frková
- Institute of Soil Biology, Biology Centre CAS, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic; University of Luxembourg, Faculty of Science, Technology and Communication, 6, rue Richard Coudenhove-Kalergi, L-1359, Luxembourg
| | - Andrea Vojs Staňová
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, CZ-38925 Vodňany, Czech Republic; Comenius University in Bratislava, Faculty of Natural Sciences, Department of Analytical Chemistry, Ilkovičova 6, SK-84215 Bratislava, Slovak Republic
| | - Antonín Nikodem
- Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Dept. of Soil Science and Soil Protection, Kamýcká 129, CZ-16500 Prague 6, Czech Republic
| | - Aleš Klement
- Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Dept. of Soil Science and Soil Protection, Kamýcká 129, CZ-16500 Prague 6, Czech Republic
| | - Miroslav Fér
- Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Dept. of Soil Science and Soil Protection, Kamýcká 129, CZ-16500 Prague 6, Czech Republic
| | - Roman Grabic
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, CZ-38925 Vodňany, Czech Republic
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Exploration of Microbial Diversity of Himalayan Glacier Moraine Soil Using 16S Amplicon Sequencing and Phospholipid Fatty Acid Analysis Approaches. Curr Microbiol 2020; 78:78-85. [PMID: 33112975 DOI: 10.1007/s00284-020-02259-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/15/2020] [Indexed: 10/23/2022]
Abstract
Changme Khangpu glacier is located in the northern district of Sikkim which comes under UNESCO heritage site Kanchenjunga Biosphere Reserve which is considered as one of the important biological hotspot regions in the Eastern Himalayas. This is the first report on microbial diversity analysis of moraine soil from one of the unexplored glaciers of Sikkim using high throughput sequencing platform and phospholipid fatty acids analysis (PLFA). It was found that the 16S amplicon sequence comprised 362,902 raw sequences with a sequence length of 150 bp and (G + C) content 52%. A total of 156,821 pre-processed reads were clustered into 378 OTUs (operational taxonomic units) comprising 6 bacterial phyla. The top four dominant phyla based on the 16S amplicon sequences were Proteobacteria (56%), Firmicutes (16%), Actinobacteria (12%), and Bacteroidetes (8%), respectively. PLFA analysis confirmed the dominance of Gram positive bacteria (72%) followed by Gram negative bacteria (32%) and the major fatty acids which are present in the moraine soil sample were PUFA (61%), and 18:2ω6,9c (29%). This is the primary study and first of its kind done on moraine soil from glaciers of Sikkim. Based on 16S amplicon sequencing and PLFA analysis of moraine soil samples from glaciers of Sikkim suggest that this glaciers harbours rich microbial diversity and thus can have wide industrial and biotechnological potential. Thus, there is an escalating scope to further study these extreme biomes with respect to their microbial diversity and their functional capabilities.
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Hassan N, Anesio AM, Rafiq M, Holtvoeth J, Bull I, Haleem A, Shah AA, Hasan F. Temperature Driven Membrane Lipid Adaptation in Glacial Psychrophilic Bacteria. Front Microbiol 2020; 11:824. [PMID: 32477293 PMCID: PMC7240044 DOI: 10.3389/fmicb.2020.00824] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/07/2020] [Indexed: 11/30/2022] Open
Abstract
Bacteria inhabiting non-polar glaciers are exposed to large variations in temperature, which significantly affects the fluidity of bacterial cell membranes. In order to maintain normal functions of the cell membranes, psychrophilic bacteria adapt by changing the composition of cell membrane fatty acids. However, information on the exact pattern of cell membrane adaptability in non-polar low-temperature habitats is scarce. In the present study, 42 bacterial strains were isolated from the Ghulmet, Ghulkin, and Hopar glaciers of the Hunza Valley in the Karakoram Mountain Range, Pakistan and their cell membrane fatty acid distributions studied, using gas chromatography/mass spectrometry (GC-MS) for the analysis of fatty acid methyl esters (FAMEs) liberated by acid-catalyzed methanolysis. Furthermore, Gram-negative and Gram-positive groups were grown under different temperature settings (5, 15, 25, and 35°C) in order to determine the effect of temperature on cell membrane (CM) fatty acid distribution. The analyses identified the major groups of cell membrane fatty acids (FA) as straight-chain monounsaturated fatty acids (n-MUFAs) and branched fatty acids (br-FAs), accounting for more than 70% of the fatty acids analyzed. The distribution of br-FAs and n-FAs in bacterial cell membranes was significantly affected by temperature, with the level of br-FAs decreasing relative to n-FAs with increasing temperature. Notably, the production of polyunsaturated fatty acids (PUFAs) was only seen at lower temperatures. This study contributes to understanding, for the first time, the role of br-FAs in the maintenance of cell membrane fluidity of bacteria inhabiting non-polar habitats.
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Affiliation(s)
- Noor Hassan
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
- Bristol Glaciology Centre, School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, United Kingdom
| | | | - Muhammad Rafiq
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
- Bristol Glaciology Centre, School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, United Kingdom
- Department of Microbiology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Jens Holtvoeth
- Organic Geochemistry Unit, School of Chemistry, Cantock’s Close, University of Bristol, Bristol, United Kingdom
| | - Ian Bull
- Organic Geochemistry Unit, School of Chemistry, Cantock’s Close, University of Bristol, Bristol, United Kingdom
| | - Abdul Haleem
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aamer Ali Shah
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fariha Hasan
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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Drotleff B, Roth SR, Henkel K, Calderón C, Schlotterbeck J, Neukamm MA, Lämmerhofer M. Lipidomic profiling of non-mineralized dental plaque and biofilm by untargeted UHPLC-QTOF-MS/MS and SWATH acquisition. Anal Bioanal Chem 2020; 412:2303-2314. [PMID: 31942654 PMCID: PMC7118048 DOI: 10.1007/s00216-019-02364-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/29/2019] [Accepted: 12/18/2019] [Indexed: 12/22/2022]
Abstract
Dental plaque is a structurally organized biofilm which consists of diverse microbial colonies and extracellular matrix. Its composition may change when pathogenic microorganisms become dominating. Therefore, dental biofilm or plaque has been frequently investigated in the context of oral health and disease. Furthermore, its potential as an alternative matrix for analytical purposes has also been recognized in other disciplines like archeology, food sciences, and forensics. Thus, a careful in-depth characterization of dental plaque is worthwhile. Most of the conducted studies focused on the screening of microbial populations in dental plaque. Their lipid membranes, on the other hand, may significantly impact substance (metabolite) exchange within microbial colonies as well as xenobiotics uptake and incorporation into teeth. Under this umbrella, a comprehensive lipidomic profiling for determination of lipid compositions of in vivo dental plaque samples and of in vitro cultivated biofilm as surrogate matrix to be used for analytical purposes has been performed in this work. An untargeted lipidomics workflow utilizing a ultra-high-performance liquid chromatography (UHPLC)-quadrupole-time-of-flight (QTOF) platform together with comprehensive SWATH (sequential window acquisition of all theoretical fragment ion mass spectra) acquisition and compatible software (MS-DIAL) that comprises a vast lipid library has been adopted to establish an extensive lipidomic fingerprint of dental plaque. The main lipid components in dental plaque were identified as triacylglycerols, followed by cholesterol, cholesteryl esters as well as diacylglycerols, and various phospholipid classes. In vivo plaque is a rare matrix which is usually available in very low amounts. When higher quantities for specific research assays are required, efficient ways to produce an appropriate surrogate matrix are mandatory. A potential surrogate matrix substituting dental plaque was prepared by cultivation of in vitro biofilm from saliva and similarities and differences in the lipidomics profile to in vivo plaque were mapped by statistical evaluation post-analysis. It was discovered that most lipid classes were highly elevated in the in vitro biofilm samples, in particular diacylglycerols, phosphatidylglycerols, and phosphatidylethanolamines (PEs). Furthermore, an overall shift from even-chain lipid species to odd-chain lipids was observed in the cultivated biofilms. On the other hand, even-chain phosphatidylcholines (PCs), lysoPCs, cholesteryl esters, and cholesterol-sulfate were shown to be specifically increased in plaque samples. Graphical abstract ![]()
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Affiliation(s)
- Bernhard Drotleff
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Simon R Roth
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstraße 9, 79104, Freiburg, Germany
| | - Kerstin Henkel
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstraße 9, 79104, Freiburg, Germany
| | - Carlos Calderón
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Jörg Schlotterbeck
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Merja A Neukamm
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstraße 9, 79104, Freiburg, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
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19
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Garcia-Mazcorro JF, Kawas JR, Marroquin-Cardona AG. Descriptive Bacterial and Fungal Characterization of Propolis Using Ultra-High-Throughput Marker Gene Sequencing. INSECTS 2019; 10:insects10110402. [PMID: 31726746 PMCID: PMC6920825 DOI: 10.3390/insects10110402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/31/2019] [Accepted: 11/08/2019] [Indexed: 02/07/2023]
Abstract
Bees harbor microorganisms that are important for host health, physiology, and survival. Propolis helps modulate the immune system and health of the colony, but little information is available about its microbial constituents. Total genomic DNA from samples of natural propolis from Apis mellifera production hives from four locations in Mexico were used to amplify a region of the 16S rRNA gene (bacteria) and the internal transcriber spacer (fungi), using PCR. The Illumina MiSeq platform was used to sequence PCR amplicons. Extensive variation in microbial composition was observed between the propolis samples. The most abundant bacterial group was Rhodopila spp. (median: 14%; range: 0.1%–27%), a group with one of the highest redox potential in the microbial world. Other high abundant groups include Corynebacterium spp. (median: 8.4%; 1.6%–19.5%) and Sphingomonas spp. (median: 5.9%; 0.03%–14.3%), a group that has been used for numerous biotechnological applications because of its biodegradative capabilities. Bacillus and Prevotella spp. alone comprised as much as 88% (53% and 35%, respectively) of all bacterial microbiota in one sample. Candida (2%–43%), Acremonium (0.03%–25.2%), and Aspergillus (0.1%–43%) were among the most abundant fungi. The results contribute to a better understanding of the factors associated with the health of Apis mellifera production hives.
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Affiliation(s)
- Jose F. Garcia-Mazcorro
- MNA de Mexico, Research and Development, San Nicolas de los Garza, Nuevo Leon 66477, Mexico;
| | - Jorge R. Kawas
- Faculty of Agronomy, Universidad Autonoma de Nuevo Leon, General Escobedo, Nuevo Leon 66050, Mexico;
| | - Alicia G. Marroquin-Cardona
- Faculty of Veterinary Medicine, Universidad Autonoma de Nuevo Leon, General Escobedo, Nuevo Leon 66050, Mexico
- Correspondence: ; Tel.: +52-81-1340-4390
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Safafar H, Ljubic A, Møller P, Jacobsen C. Two‐Step Direct Transesterification as a Rapid Method for the Analysis of Fatty Acids in Microalgae Biomass. EUR J LIPID SCI TECH 2019. [DOI: 10.1002/ejlt.201700409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hamed Safafar
- Technical University of DenmarkNational Food, Søltofts PladsBuilding 2212800Kongens LyngbyDenmark
| | - Anita Ljubic
- Technical University of DenmarkNational Food, Søltofts PladsBuilding 2212800Kongens LyngbyDenmark
| | - Per Møller
- Kalundborg MunicipalityDept. DevelopmentTorvet 3A4400KalundborgDenmark
| | - Charlotte Jacobsen
- Technical University of DenmarkNational Food, Søltofts PladsBuilding 2212800Kongens LyngbyDenmark
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Oates LG, Read HW, Gutknecht JLM, Duncan DS, Balser TB, Jackson RD. A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples. J Vis Exp 2017:55310. [PMID: 28745639 PMCID: PMC5553326 DOI: 10.3791/55310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes. The PLFA method has been shown to be sensitive to detecting shifts in microbial community composition. An alternative method, fatty acid methyl ester extraction and analysis (MIDI-FA) was developed for rapid extraction of total lipids, without separation of the phospholipid fraction, from pure cultures as a microbial identification technique. This method is rapid but is less suited for soil samples because it lacks an initial step separating soil particles and begins instead with a saponification reaction that likely produces artifacts from the background organic matter in the soil. This article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples. The method combines the accuracy achieved through PLFA profiling by extracting and concentrating soil lipids as a first step, and a reduction in effort by saponifying the organic material extracted and processing with the MIDI-FA method as a second step.
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Affiliation(s)
- Lawrence G Oates
- Department of Agronomy and Great Lakes Bioenergy Research Center, University of Wisconsin - Madison;
| | - Harry W Read
- Department of Soil Science, University of Wisconsin - Madison
| | | | - David S Duncan
- Department of Agronomy and Great Lakes Bioenergy Research Center, University of Wisconsin - Madison
| | - Teri B Balser
- Faculty of Science and Engineering, Curtin University
| | - Randall D Jackson
- Department of Agronomy and Great Lakes Bioenergy Research Center, University of Wisconsin - Madison
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Willers C, Jansen van Rensburg P, Claassens S. Phospholipid fatty acid profiling of microbial communities-a review of interpretations and recent applications. J Appl Microbiol 2015; 119:1207-18. [PMID: 26184497 DOI: 10.1111/jam.12902] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/02/2015] [Accepted: 07/03/2015] [Indexed: 11/29/2022]
Affiliation(s)
- C. Willers
- Unit for Environmental Sciences and Management; North-West University; Potchefstroom South Africa
| | | | - S. Claassens
- Unit for Environmental Sciences and Management; North-West University; Potchefstroom South Africa
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