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Metabolites
Special Issues
Ecometabolomics
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Ecometabolomics

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

Deadline for manuscript submissions: closed (31 January 2020) | Viewed by 25038

Special Issue Editors

Dr. Jordi Sardans

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Guest Editor
Ecological and Forestry Applications Research Centre (CREAF), Cerdanyola del Vallès, 08193 Barcelona, Spain
Interests: chemical ecology; ecotoxicology and metabolomics; reserves and flows of carbon and nutrients; species interactions
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Josep Peñuelas

grade E-Mail Website
Guest Editor
Global Ecology Unit CREAF‐CSIC‐UAB, CSIC, 08193 Bellaterra, Spain
Interests: biodiversity; terrestrial ecosystems; global ecology; global change; climate change; pollution; atmosphere-biosphere; biogenic volatile organic compounds; remote sensing; plant ecophysiology; functioning and structure of terrestrial plants and ecosystems; chemical ecology; ecometabolomics; microbial ecology; macroecology and evolutionary ecology; biogeochemistry with special focus on phosphorus; environmental sustainability; food security and global health
Special Issues, Collections and Topics in MDPI journals
Dr. Albert Gargallo-Garriga

E-Mail Website
Guest Editor
Global Ecology Unit CREAF‐UAB-CSIC, Cerdanyola del Vallès, 08193 Catalonia, Spain
Interests: ecometabolomics; chemical ecology; global change

Special Issue Information

Dear Colleagues,

Ecometabolomics is an emerging tool for ecological and environmental sciences. It aims to provide knowledge of the metabolic mechanisms underlying the responses of organisms, communities, and ecosystems to environmental shifts. Ecoetabolomics is especially timely now in the frame of current global change. The number of studies on this topic has exponentially grown since only ten years ago, when only a few seminal studies had begun to couple metabolomics to ecological studies in field conditions. This Special Issue of Metabolites on “Ecometabolomics” aims to provide the status-of-the art of Ecometabolomic studies, firstly presenting the most powerful metabolomic analysis techniques (different analytical platforms, tools for data processing and statistical analysis, sampling, and sample preparation) to be used as metabolomics analytical tools in ecological studies in field conditions. Second, this Special Issue aims to provide an overview of current studies showing the successful use of ecometabolomics in organisms’ responses to abiotic and biotic environmental changes in field conditions. Third, it aims to present the ecological and environmental studies where ecometabolomics can be of key use in the coming years. Manuscripts dealing with other pertinent challenging metabolomics issues are also highly desired.

Dr. Jordi Sardans
Prof. Dr. Josep Peñuelas
Dr. Albert Gargallo-Garriga
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Ecometabolomics
  • Bioelements and metabolism
  • Biomarkers
  • Metabolomic modeling
  • Atmospheric metabolome
  • Soil metabolome
  • Stress metabolome
  • Ecometabolomic data bases
  • Environmental metabolome
  • Metabolomic niche
  • Metabolomics and transcriptomics
  • Metabolomics and phyllosphere
  • Metabolomics and gut microbiota

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Published Papers (4 papers)

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Research

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17 pages, 1575 KiB  
Article
Intracellular Metabolites in Marine Microorganisms during an Experiment Evaluating Microbial Mortality
by Krista Longnecker and Elizabeth B. Kujawinski
Metabolites 2020, 10(3), 105; https://doi.org/10.3390/metabo10030105 - 12 Mar 2020
Cited by 4 | Viewed by 3407
Abstract
Metabolomics is a tool with immense potential for providing insight into the impact of biological processes on the environment. Here, we used metabolomics methods to characterize intracellular metabolites within marine microorganisms during a manipulation experiment that was designed to test the impact of [...] Read more.
Metabolomics is a tool with immense potential for providing insight into the impact of biological processes on the environment. Here, we used metabolomics methods to characterize intracellular metabolites within marine microorganisms during a manipulation experiment that was designed to test the impact of two sources of microbial mortality, protozoan grazing and viral lysis. Intracellular metabolites were analyzed with targeted and untargeted mass spectrometry methods. The treatment with reduced viral mortality showed the largest changes in metabolite concentrations, although there were organic compounds that shifted when the impact of protozoan grazers was reduced. Intracellular concentrations of guanine, phenylalanine, glutamic acid, and ectoine presented significant responses to changes in the source of mortality. Unexpectedly, variability in metabolite concentrations were not accompanied by increases in microbial abundance which indicates that marine microorganisms altered their internal organic carbon stores without changes in biomass or microbial growth. We used Weighted Correlation Network Analysis (WGCNA) to identify correlations between the targeted and untargeted mass spectrometry data. This analysis revealed multiple unknown organic compounds were correlated with compatible solutes, also called osmolytes or chemical chaperones, which emphasizes the dominant role of compatible solutes in marine microorganisms. Full article
(This article belongs to the Special Issue Ecometabolomics)
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18 pages, 2777 KiB  
Article
Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species
by Kristian Peters, Hendrik Treutler, Stefanie Döll, Alida S. D. Kindt, Thomas Hankemeier and Steffen Neumann
Metabolites 2019, 9(10), 222; https://doi.org/10.3390/metabo9100222 - 11 Oct 2019
Cited by 33 | Viewed by 6983
Abstract
The central aim in ecometabolomics and chemical ecology is to pinpoint chemical features that explain molecular functioning. The greatest challenge is the identification of compounds due to the lack of constitutive reference spectra, the large number of completely unknown compounds, and bioinformatic methods [...] Read more.
The central aim in ecometabolomics and chemical ecology is to pinpoint chemical features that explain molecular functioning. The greatest challenge is the identification of compounds due to the lack of constitutive reference spectra, the large number of completely unknown compounds, and bioinformatic methods to analyze the big data. In this study we present an interdisciplinary methodological framework that extends ultra-performance liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) and the automated in silico classification of fragment peaks into compound classes. We synthesize findings from a prior study that explored the influence of seasonal variations on the chemodiversity of secondary metabolites in nine bryophyte species. Here we reuse and extend the representative dataset with DDA-MS data. Hierarchical clustering, heatmaps, dbRDA, and ANOVA with post-hoc Tukey HSD were used to determine relationships of the study factors species, seasons, and ecological characteristics. The tested bryophytes showed species-specific metabolic responses to seasonal variations (50% vs. 5% of explained variation). Marchantia polymorpha, Plagiomnium undulatum, and Polytrichum strictum were biochemically most diverse and unique. Flavonoids and sesquiterpenoids were upregulated in all bryophytes in the growing seasons. We identified ecological functioning of compound classes indicating light protection (flavonoids), biotic and pathogen interactions (sesquiterpenoids, flavonoids), low temperature and desiccation tolerance (glycosides, sesquiterpenoids, anthocyanins, lactones), and moss growth supporting anatomic structures (few methoxyphenols and cinnamic acids as part of proto-lignin constituents). The reusable bioinformatic framework of this study can differentiate species based on automated compound classification. Our study allows detailed insights into the ecological roles of biochemical constituents of bryophytes with regard to seasonal variations. We demonstrate that compound classification can be improved with adding constitutive reference spectra to existing spectral libraries. We also show that generalization on compound classes improves our understanding of molecular ecological functioning and can be used to generate new research hypotheses. Full article
(This article belongs to the Special Issue Ecometabolomics)
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Review

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30 pages, 943 KiB  
Review
Unraveling Arbuscular Mycorrhiza-Induced Changes in Plant Primary and Secondary Metabolome
by Sukhmanpreet Kaur and Vidya Suseela
Metabolites 2020, 10(8), 335; https://doi.org/10.3390/metabo10080335 - 18 Aug 2020
Cited by 153 | Viewed by 9200
Abstract
Arbuscular mycorrhizal fungi (AMF) is among the most ubiquitous plant mutualists that enhance plant growth and yield by facilitating the uptake of phosphorus and water. The countless interactions that occur in the rhizosphere between plants and its AMF symbionts are mediated through the [...] Read more.
Arbuscular mycorrhizal fungi (AMF) is among the most ubiquitous plant mutualists that enhance plant growth and yield by facilitating the uptake of phosphorus and water. The countless interactions that occur in the rhizosphere between plants and its AMF symbionts are mediated through the plant and fungal metabolites that ensure partner recognition, colonization, and establishment of the symbiotic association. The colonization and establishment of AMF reprogram the metabolic pathways of plants, resulting in changes in the primary and secondary metabolites, which is the focus of this review. During initial colonization, plant–AMF interaction is facilitated through the regulation of signaling and carotenoid pathways. After the establishment, the AMF symbiotic association influences the primary metabolism of the plant, thus facilitating the sharing of photosynthates with the AMF. The carbon supply to AMF leads to the transport of a significant amount of sugars to the roots, and also alters the tricarboxylic acid cycle. Apart from the nutrient exchange, the AMF imparts abiotic stress tolerance in host plants by increasing the abundance of several primary metabolites. Although AMF initially suppresses the defense response of the host, it later primes the host for better defense against biotic and abiotic stresses by reprogramming the biosynthesis of secondary metabolites. Additionally, the influence of AMF on signaling pathways translates to enhanced phytochemical content through the upregulation of the phenylpropanoid pathway, which improves the quality of the plant products. These phytometabolome changes induced by plant–AMF interaction depends on the identity of both plant and AMF species, which could contribute to the differential outcome of this symbiotic association. A better understanding of the phytochemical landscape shaped by plant–AMF interactions would enable us to harness this symbiotic association to enhance plant performance, particularly under non-optimal growing conditions. Full article
(This article belongs to the Special Issue Ecometabolomics)
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20 pages, 5340 KiB  
Review
Ecometabolomics for a Better Understanding of Plant Responses and Acclimation to Abiotic Factors Linked to Global Change
by Jordi Sardans, Albert Gargallo-Garriga, Otmar Urban, Karel Klem, Tom W.N. Walker, Petr Holub, Ivan A. Janssens and Josep Peñuelas
Metabolites 2020, 10(6), 239; https://doi.org/10.3390/metabo10060239 - 9 Jun 2020
Cited by 42 | Viewed by 4620
Abstract
The number of ecometabolomic studies, which use metabolomic analyses to disentangle organisms’ metabolic responses and acclimation to a changing environment, has grown exponentially in recent years. Here, we review the results and conclusions of ecometabolomic studies on the impacts of four main drivers [...] Read more.
The number of ecometabolomic studies, which use metabolomic analyses to disentangle organisms’ metabolic responses and acclimation to a changing environment, has grown exponentially in recent years. Here, we review the results and conclusions of ecometabolomic studies on the impacts of four main drivers of global change (increasing frequencies of drought episodes, heat stress, increasing atmospheric carbon dioxide (CO2) concentrations and increasing nitrogen (N) loads) on plant metabolism. Ecometabolomic studies of drought effects confirmed findings of previous target studies, in which most changes in metabolism are characterized by increased concentrations of soluble sugars and carbohydrate derivatives and frequently also by elevated concentrations of free amino acids. Secondary metabolites, especially flavonoids and terpenes, also commonly exhibited increased concentrations when drought intensified. Under heat and increasing N loads, soluble amino acids derived from glutamate and glutamine were the most responsive metabolites. Foliar metabolic responses to elevated atmospheric CO2 concentrations were dominated by greater production of monosaccharides and associated synthesis of secondary metabolites, such as terpenes, rather than secondary metabolites synthesized along longer sugar pathways involving N-rich precursor molecules, such as those formed from cyclic amino acids and along the shikimate pathway. We suggest that breeding for crop genotypes tolerant to drought and heat stress should be based on their capacity to increase the concentrations of C-rich compounds more than the concentrations of smaller N-rich molecules, such as amino acids. This could facilitate rapid and efficient stress response by reducing protein catabolism without compromising enzymatic capacity or increasing the requirement for re-transcription and de novo biosynthesis of proteins. Full article
(This article belongs to the Special Issue Ecometabolomics)
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