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Metabolites
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Environmental Metabolomics
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Environmental Metabolomics

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Environmental Metabolomics".

Deadline for manuscript submissions: closed (31 August 2017) | Viewed by 39589

Special Issue Editor

Dr. Manuel Liebeke

E-Mail Website
Guest Editor
Department of Symbiosis, Max Planck Institute for Marine Microbiology, Celsius Strasse 1, 28359 Bremen, Germany
Interests: mass spectral imaging; metabolic profiling; symbiosis; microbial metabolomics; marine and terrestrial invertebrate metabolism; host-pathogen interactions; mass spectrometry; gas chromatography; sample preparation for metabolomics

Special Issue Information

Dear Colleagues,

With emerging technologies in mass spectrometry and nuclear magnetic resonance spectroscopy, hundreds to thousands of metabolites can now be quantitatively measured from minimal amounts of biological material. This has thereby enabled in-depth insight into the metabolism of living organisms and the biochemistry of their environment. Metabolite profiling, or metabolomics, has become a powerful approach that has been widely adopted in many areas and is by now a solid pillar next to genomics, proteomics and transcriptomics. Yet, the comprehensive integration of metabolomics data with other ‘omics’ is still in the early developmental phase.  However, environmental metabolomics should now step up and deliver profound data on the complexity, variability and plasticity of the environment and natural populations to build a basis for future research directions. An expansion towards cells and organisms from diverse environments will without doubt increase the current metabolome inventory and tasks should be taken to implement such data into current or future databases including tools to help annotate so far undescribed metabolites. Here, high throughput and robust analytical tools are needed to deliver accurate metabolic profiling data. Due to the enormous improvements in mass-spectrometry technologies, possibilities like mass-spectrometry imaging should be used increasingly to also give spatial information to certain metabolites of interest.  

In this Special Issue of Metabolites, original papers, which are describing novel metabolomics methods for the diverse nature of environmental samples from the terrestrial to the marine realm, are welcome. Work which shows new directions of metabolomics applied to monitor environmental factors (abiotic or biotic) towards populations of organisms is of interest for this Special Issue. Comprehensive descriptions of metabolome data, either from extracts or via direct MS imaging studies are welcome here. Manuscripts dealing with other challenging issues in the environmental metabolomics field including software tools and databases for metabolite annotation or combination with other –omics are also highly welcome.

Dr. Manuel Liebeke
Guest Editor

Relevant special issue can be found here: https://www.mdpi.com/journal/metabolites/special_issues/stress-metabolism.

Keywords

  • Environmental stressors of metabolism and stress responses
  • Mass spectrometry and NMR methods for high content analysis
  • Bioinformatic tools for metabolite assignment and data analysis (e.g. multi-omics)

Published Papers (7 papers)

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Research

19 pages, 1495 KiB  
Article
Evaluation of Sample Preparation Methods for the Analysis of Reef-Building Corals Using 1H-NMR-Based Metabolomics
by Erik R. Andersson, Rusty D. Day, Julie M. Loewenstein, Cheryl M. Woodley and Tracey B. Schock
Metabolites 2019, 9(2), 32; https://doi.org/10.3390/metabo9020032 - 13 Feb 2019
Cited by 11 | Viewed by 7351
Abstract
The field of metabolomics generally lacks standardized methods for the preparation of samples prior to analysis. This is especially true for metabolomics of reef-building corals, where the handful of studies that were published employ a range of sample preparation protocols. The utilization of [...] Read more.
The field of metabolomics generally lacks standardized methods for the preparation of samples prior to analysis. This is especially true for metabolomics of reef-building corals, where the handful of studies that were published employ a range of sample preparation protocols. The utilization of metabolomics may prove essential in understanding coral biology in the face of increasing environmental threats, and an optimized method for preparing coral samples for metabolomics analysis would aid this cause. The current study evaluates three important steps during sample processing of stony corals: (i) metabolite extraction, (ii) metabolism preservation, and (iii) subsampling. Results indicate that a modified Bligh and Dyer extraction is more reproducible across multiple coral species compared to methyl tert-butyl ether and methanol extractions, while a methanol extraction is superior for feature detection. Additionally, few differences were detected between spectra from frozen or lyophilized coral samples. Finally, extraction of entire coral nubbins increased feature detection, but decreased throughput and was more susceptible to subsampling error compared to a novel tissue powder subsampling method. Overall, we recommend the use of a modified Bligh and Dyer extraction, lyophilized samples, and the analysis of brushed tissue powder for the preparation of reef-building coral samples for 1H NMR metabolomics. Full article
(This article belongs to the Special Issue Environmental Metabolomics)
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4867 KiB  
Article
Metabolomic Profiles of a Midge (Procladius villosimanus, Kieffer) Are Associated with Sediment Contamination in Urban Wetlands
by Katherine J. Jeppe, Konstantinos A. Kouremenos, Kallie R. Townsend, Daniel F. MacMahon, David Sharley, Dedreia L. Tull, Ary A. Hoffmann, Vincent Pettigrove and Sara M. Long
Metabolites 2017, 7(4), 64; https://doi.org/10.3390/metabo7040064 - 18 Dec 2017
Cited by 4 | Viewed by 3964
Abstract
Metabolomic techniques are powerful tools for investigating organism-environment interactions. Metabolite profiles have the potential to identify exposure or toxicity before populations are disrupted and can provide useful information for environmental assessment. However, under complex environmental scenarios, metabolomic responses to exposure can be distorted [...] Read more.
Metabolomic techniques are powerful tools for investigating organism-environment interactions. Metabolite profiles have the potential to identify exposure or toxicity before populations are disrupted and can provide useful information for environmental assessment. However, under complex environmental scenarios, metabolomic responses to exposure can be distorted by background and/or organismal variation. In the current study, we use LC-MS (liquid chromatography-mass spectrometry) and GC-MS (gas chromatography-mass spectrometry) to measure metabolites of the midge Procladius villosimanus inhabiting 21 urban wetlands. These metabolites were tested against common sediment contaminants using random forest models and metabolite enrichment analysis. Sediment contaminant concentrations in the field correlated with several P. villosimanus metabolites despite natural environmental and organismal variation. Furthermore, enrichment analysis indicated that metabolite sets implicated in stress responses were enriched, pointing to specific cellular functions affected by exposure. Methionine metabolism, sugar metabolism and glycerolipid metabolism associated with total petroleum hydrocarbon and metal concentrations, while mitochondrial electron transport and urea cycle sets associated only with bifenthrin. These results demonstrate the potential for metabolomics approaches to provide useful information in field-based environmental assessments. Full article
(This article belongs to the Special Issue Environmental Metabolomics)
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1842 KiB  
Article
Exometabolomic Analysis of Cross-Feeding Metabolites
by Andrea Lubbe, Benjamin P. Bowen and Trent Northen
Metabolites 2017, 7(4), 50; https://doi.org/10.3390/metabo7040050 - 04 Oct 2017
Cited by 9 | Viewed by 5214
Abstract
Microbial consortia have the potential to perform complex, industrially important tasks. The design of microbial consortia requires knowledge of the substrate preferences and metabolic outputs of each member, to allow understanding of potential interactions such as competition and beneficial metabolic exchange. Here, we [...] Read more.
Microbial consortia have the potential to perform complex, industrially important tasks. The design of microbial consortia requires knowledge of the substrate preferences and metabolic outputs of each member, to allow understanding of potential interactions such as competition and beneficial metabolic exchange. Here, we used exometabolite profiling to follow the resource processing by a microbial co-culture of two biotechnologically relevant microbes, the bacterial cellulose degrader Cellulomonas fimi, and the oleaginous yeast Yarrowia lipolytica. We characterized the substrate preferences of the two strains on compounds typically found in lignocellulose hydrolysates. This allowed prediction that specific sugars resulting from hemicellulose polysaccharide degradation by C. fimi may serve as a cross-feeding metabolites to Y. lipolytica in co-culture. We also showed that products of ionic liquid-treated switchgrass lignocellulose degradation by C. fimi were channeled to Y. lipolytica in a co-culture. Additionally, we observed metabolites, such as shikimic acid accumulating in the co-culture supernatants, suggesting the potential for producing interesting co-products. Insights gained from characterizing the exometabolite profiles of individual and co-cultures of the two strains can help to refine this interaction, and guide strategies for making this an industrially viable co-culture to produce valuable products from lignocellulose material. Full article
(This article belongs to the Special Issue Environmental Metabolomics)
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3995 KiB  
Article
Impact of Soil Warming on the Plant Metabolome of Icelandic Grasslands
by Albert Gargallo-Garriga, Marta Ayala-Roque, Jordi Sardans, Mireia Bartrons, Victor Granda, Bjarni D. Sigurdsson, Niki I. W. Leblans, Michal Oravec, Otmar Urban, Ivan A. Janssens and Josep Peñuelas
Metabolites 2017, 7(3), 44; https://doi.org/10.3390/metabo7030044 - 23 Aug 2017
Cited by 14 | Viewed by 5057
Abstract
Climate change is stronger at high than at temperate and tropical latitudes. The natural geothermal conditions in southern Iceland provide an opportunity to study the impact of warming on plants, because of the geothermal bedrock channels that induce stable gradients of soil temperature. [...] Read more.
Climate change is stronger at high than at temperate and tropical latitudes. The natural geothermal conditions in southern Iceland provide an opportunity to study the impact of warming on plants, because of the geothermal bedrock channels that induce stable gradients of soil temperature. We studied two valleys, one where such gradients have been present for centuries (long-term treatment), and another where new gradients were created in 2008 after a shallow crustal earthquake (short-term treatment). We studied the impact of soil warming (0 to +15 °C) on the foliar metabolomes of two common plant species of high northern latitudes: Agrostis capillaris, a monocotyledon grass; and Ranunculus acris, a dicotyledonous herb, and evaluated the dependence of shifts in their metabolomes on the length of the warming treatment. The two species responded differently to warming, depending on the length of exposure. The grass metabolome clearly shifted at the site of long-term warming, but the herb metabolome did not. The main up-regulated compounds at the highest temperatures at the long-term site were saccharides and amino acids, both involved in heat-shock metabolic pathways. Moreover, some secondary metabolites, such as phenolic acids and terpenes, associated with a wide array of stresses, were also up-regulated. Most current climatic models predict an increase in annual average temperature between 2–8 °C over land masses in the Arctic towards the end of this century. The metabolomes of A. capillaris and R. acris shifted abruptly and nonlinearly to soil warming >5 °C above the control temperature for the coming decades. These results thus suggest that a slight warming increase may not imply substantial changes in plant function, but if the temperature rises more than 5 °C, warming may end up triggering metabolic pathways associated with heat stress in some plant species currently dominant in this region. Full article
(This article belongs to the Special Issue Environmental Metabolomics)
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966 KiB  
Article
Analysis of Sub-Lethal Toxicity of Perfluorooctane Sulfonate (PFOS) to Daphnia magna Using 1H Nuclear Magnetic Resonance-Based Metabolomics
by Martha N. Kariuki, Edward G. Nagato, Brian P. Lankadurai, André J. Simpson and Myrna J. Simpson
Metabolites 2017, 7(2), 15; https://doi.org/10.3390/metabo7020015 - 14 Apr 2017
Cited by 47 | Viewed by 5933
Abstract
1H nuclear magnetic resonance (NMR)-based metabolomics was used to characterize the response of Daphnia magna after sub-lethal exposure to perfluorooctane sulfonate (PFOS), a commonly found environmental pollutant in freshwater ecosystems. Principal component analysis (PCA) scores plots showed significant separation in the exposed [...] Read more.
1H nuclear magnetic resonance (NMR)-based metabolomics was used to characterize the response of Daphnia magna after sub-lethal exposure to perfluorooctane sulfonate (PFOS), a commonly found environmental pollutant in freshwater ecosystems. Principal component analysis (PCA) scores plots showed significant separation in the exposed samples relative to the controls. Partial least squares (PLS) regression analysis revealed a strong linear correlation between the overall metabolic response and PFOS exposure concentration. More detailed analysis showed that the toxic mode of action is metabolite-specific with some metabolites exhibiting a non-monotonic response with higher PFOS exposure concentrations. Our study indicates that PFOS exposure disrupts various energy metabolism pathways and also enhances protein degradation. Overall, we identified several metabolites that are sensitive to PFOS exposure and may be used as bioindicators of D. magna health. In addition, this study also highlights the important utility of environmental metabolomic methods when attempting to elucidate acute and sub-lethal pollutant stressors on keystone organisms such as D. magna. Full article
(This article belongs to the Special Issue Environmental Metabolomics)
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1575 KiB  
Article
Defining the Baseline and Oxidant Perturbed Lipidomic Profiles of Daphnia magna
by Nadine S. Taylor, Thomas A. White and Mark R. Viant
Metabolites 2017, 7(1), 11; https://doi.org/10.3390/metabo7010011 - 15 Mar 2017
Cited by 10 | Viewed by 5588
Abstract
Recent technological advancement has enabled the emergence of lipidomics as an important tool for assessing molecular stress, one which has yet to be assessed fully as an approach in an environmental toxicological context. Here we have applied a high-resolution, non-targeted, nanoelectrospray ionisation (nESI) [...] Read more.
Recent technological advancement has enabled the emergence of lipidomics as an important tool for assessing molecular stress, one which has yet to be assessed fully as an approach in an environmental toxicological context. Here we have applied a high-resolution, non-targeted, nanoelectrospray ionisation (nESI) direct infusion mass spectrometry (DIMS) technique to assess the effects of oxidative stress to Daphnia magna both in vitro (air exposure of daphniid extracts) and in vivo (Cu2+ exposure). Multivariate and univariate statistical analyses were used to distinguish any perturbations including oxidation to the D. magna baseline lipidome. This approach enabled the putative annotation of the baseline lipidome of D. magna with 65% of the lipid species discovered previously not reported. In vitro exposure of lipid extracts to air, primarily to test the methodology, revealed a significant perturbation to this baseline lipidome with detectable oxidation of peaks, in most cases attributed to single oxygen addition. Exposure of D. magna to Cu2+ in vivo also caused a significant perturbation to the lipidome at an environmentally relevant concentration of 20 µg/L. This nESI DIMS approach has successfully identified perturbations and oxidative modifications to the D. magna lipidome in a high-throughput manner, highlighting its suitability for environmental lipidomic studies. Full article
(This article belongs to the Special Issue Environmental Metabolomics)
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1367 KiB  
Article
Application of Passive Sampling to Characterise the Fish Exometabolome
by Mark R. Viant, Jessica Elphinstone Davis, Cathleen Duffy, Jasper Engel, Craig Stenton, Marion Sebire and Ioanna Katsiadaki
Metabolites 2017, 7(1), 8; https://doi.org/10.3390/metabo7010008 - 14 Feb 2017
Cited by 4 | Viewed by 5225
Abstract
The endogenous metabolites excreted by organisms into their surrounding environment, termed the exometabolome, are important for many processes including chemical communication. In fish biology, such metabolites are also known to be informative markers of physiological status. While metabolomics is increasingly used to investigate [...] Read more.
The endogenous metabolites excreted by organisms into their surrounding environment, termed the exometabolome, are important for many processes including chemical communication. In fish biology, such metabolites are also known to be informative markers of physiological status. While metabolomics is increasingly used to investigate the endogenous biochemistry of organisms, no non-targeted studies of the metabolic complexity of fish exometabolomes have been reported to date. In environmental chemistry, Chemcatcher® (Portsmouth, UK) passive samplers have been developed to sample for micro-pollutants in water. Given the importance of the fish exometabolome, we sought to evaluate the capability of Chemcatcher® samplers to capture a broad spectrum of endogenous metabolites excreted by fish and to measure these using non-targeted direct infusion mass spectrometry metabolomics. The capabilities of C18 and styrene divinylbenzene reversed-phase sulfonated (SDB-RPS) Empore™ disks for capturing non-polar and polar metabolites, respectively, were compared. Furthermore, we investigated real, complex metabolite mixtures excreted from two model fish species, rainbow trout (Oncorhynchus mykiss) and three-spined stickleback (Gasterosteus aculeatus). In total, 344 biological samples and 28 QC samples were analysed, revealing 646 and 215 m/z peaks from trout and stickleback, respectively. The measured exometabolomes were principally affected by the type of Empore™ (Hemel Hempstead, UK) disk and also by the sampling time. Many peaks were putatively annotated, including several bile acids (e.g., chenodeoxycholate, taurocholate, glycocholate, glycolithocholate, glycochenodeoxycholate, glycodeoxycholate). Collectively these observations show the ability of Chemcatcher® passive samplers to capture endogenous metabolites excreted from fish. Full article
(This article belongs to the Special Issue Environmental Metabolomics)
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