title: Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses.
abstract: We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (1H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing is a successful technique for elucidating the sub-systems of organismal communities with associated chemical profiles in complex ecosystems.
authors.affiliation: Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil; Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceara, Fortaleza, CE, Brazil; Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil; RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan.
authors.forename: Diogo M O
authors.initials: DM
authors.lastname: Ogawa
authors.affiliation: RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan; RIKEN Antibiotics Laboratory, Yokohama, Japan; Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama, Japan.
authors.forename: Shigeharu
authors.initials: S
authors.lastname: Moriya
authors.affiliation: RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan.
authors.forename: Yuuri
authors.initials: Y
authors.lastname: Tsuboi
authors.affiliation: RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan; Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama, Japan.
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Date
authors.affiliation: Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil; Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil; Laboratory of Genetics, Butantan Institute, Sao Paulo, SP, Brazil.
authors.forename: Álvaro R B
authors.initials: ÁR
authors.lastname: Prieto-da-Silva
authors.affiliation: Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil; Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceara, Fortaleza, CE, Brazil; Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil.
authors.forename: Gandhi
authors.initials: G
authors.lastname: Rádis-Baptista
authors.affiliation: Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil; Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil; Center of Biotechnology of Amazon, Manaus, AM, Brazil.
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Yamane
authors.affiliation: RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan; Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama, Japan; Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Kikuchi
mesh_terms: D030541:Databases, Genetic; D017753:Ecosystem; D054892:Metagenome