Abstract
Ecosystems can be conceptually thought of as interconnected environmental and metabolic systems, in which small molecules to macro-molecules interact through diverse networks. State-of-the-art technologies in post-genomic science offer ways to inspect and analyze this biomolecular web using omics-based approaches. Exploring useful genes and enzymes, as well as biomass resources responsible for anabolism and catabolism within ecosystems will contribute to a better understanding of environmental functions and their application to biotechnology. Here we present ECOMICS, a suite of web-based tools for ECosystem trans-OMICS investigation that target metagenomic, metatranscriptomic, and meta-metabolomic systems, including biomacromolecular mixtures derived from biomass. ECOMICS is made of four integrated webtools. E-class allows for the sequence-based taxonomic classification of eukaryotic and prokaryotic ribosomal data and the functional classification of selected enzymes. FT2B allows for the digital processing of NMR spectra for downstream metabolic or chemical phenotyping. Bm-Char allows for statistical assignment of specific compounds found in lignocellulose-based biomass, and HetMap is a data matrix generator and correlation calculator that can be applied to trans-omics datasets as analyzed by these and other web tools. This web suite is unique in that it allows for the monitoring of biomass metabolism in a particular environment, i.e., from macromolecular complexes (FT2DB and Bm-Char) to microbial composition and degradation (E-class), and makes possible the understanding of relationships between molecular and microbial elements (HetMap). This website is available to the public domain at: https://database.riken.jp/ecomics/.
Highlights
Natural ecosystems can be conceptually thought of as interconnected environmental and metabolic systems
We have reported on methodologies for analyzing metabolic dynamics in plant and bacterial systems [21,22,23,24, 25,26,27], annotating metabolites [28,29,30], and revealing enzymatic networks [31,32,33]
To validate the utility of the E-class, FT2DB and HetMap tools, we prepared a small microcosm experiment to survey if any metabolite – community relationships could be revealed in an unbiased manner using the ECOMICS tools
Summary
Natural ecosystems can be conceptually thought of as interconnected environmental and metabolic systems. Humans and their activities affect and are a part of these ecosystems. Excessive nitrogen fertilizer may result in an alteration of soil, freshwater and marine ecosystems because of nitrate accumulation [1,2]. Considering a more applied perspective of human activities within ecosystems, it is important to gain an understanding of natural ecology and its metabolic processes in various environments. From this perspective, biomass production is at the forefront of current research
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