The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn; Knight, Rob; Cole, James R.; Amaral‐Zettler, Linda; Gilbert, Jack A.; Karsch‐Mizrachi, Ilene; Johnston, Anjanette; Cochrane, Guy; Vaughan, R. W.; Hunter, Christopher I.; Park, Joonhong; Morrison, Norman; Rocca-Serra, Phillipe; Sterk, Peter J.; Arumugam, Mani; Baumgartner, Laura K.; Birren, Bruce W.; Bonazzi, Vivien; Bork, Peer; Buttigieg, Pier Luigi; Chain, Patrick; Costello, Elizabeth K.; Huot-Creasy, Heather; Dawyndt, Peter; DeSantis, Todd Z.; Fierer, Noah; Fuhrman, Jed A.; Gallery, Rachel E.; Gibbs, Richard A.; Giglio, Michelle; Gil, Inigo San; Glass, Elizabeth M.; González, Antonio G.; Gordon, Jeffrey I.; Guralnick, Robert; Hankeln, Wolfgang; Highlander, Sarah K.; Hugenholtz, Philip; Jansson, Janet K.; Kennedy, Jerry; Knights, Dan; Koren, Omry; Kuczynski, Justin; Kyrpides, Nikos; Larsen, Robert D.; Lauber, Christian L.; Legg, Teresa M.; Ley, Ruth E.; Lozupone, Catherine; Ludwig, Wolfgang; Lyons, Donna; Maguire, Eamonn; Methé, Barbara A.; Meyer, Folker; Nakielny, Sara; Nelson, Karen E.; Nemergut, Diana R.; Neufeld, Josh D.; Pace, Norman R.; Palanisamy, Giri; Peplies, Jörg; Peterson, Jane; Petrosino, Joseph; Proctor, Lita M.; Raes, Jeroen; Ratnasingham, Sujeevan; Ravel, Jacques; Relman, David A.; Assunta-Sansone, Susanna; Sodergren, Erica; Spor, Aymé; Stombaugh, Jesse; Tiedje, James M.; Ward, Doyle V.; Weinstock, George M.; Wendel, Doug; White, Owen; Wilke, Andreas; Wortmann, Jennifer; Glöckner, Frank Oliver

doi:10.1038/npre.2010.5252.1

Cited by 3 publications

(1 citation statement)

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“…The 16S rRNA gene sequences determined in this study have been deposited in the GenBank database under accession numbers. HQ730609 to HQ730756, HQ853235 to HQ853236, and HQ916664 to HQ916667, combining sequence and contextual data in compliance with the Genomic Standards Consortium (GSC) with the CDinFusion tool (51).…”

Section: Fieldmentioning

confidence: 99%

Microbial Diversity in Anaerobic Sediments at Río Tinto, a Naturally Acidic Environment with a High Heavy Metal Content

Sánchez‐Andrea

Rodríguez

Amils

et al. 2011

Appl Environ Microbiol

174

126

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The Tinto River is an extreme environment located at the core of the Iberian Pyritic Belt (IPB). It is an unusual ecosystem due to its size (100 km long), constant acidic pH (mean pH, 2.3), and high concentration of heavy metals, iron, and sulfate in its waters, characteristics that make the Tinto River Basin comparable to acidic mine drainage (AMD) systems. In this paper we present an extensive survey of the Tinto River sediment microbiota using two culture-independent approaches: denaturing gradient gel electrophoresis and cloning of 16S rRNA genes. The taxonomic affiliation of the Bacteria showed a high degree of biodiversity, falling into 5 different phyla: Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and Actinobacteria; meanwhile, all the Archaea were affiliated with the order Thermoplasmatales. Microorganisms involved in the iron (Acidithiobacillus ferrooxidans, Sulfobacillus spp., Ferroplasma spp., etc.), sulfur (Desulfurella spp., Desulfosporosinus spp., Thermodesulfobium spp., etc.), and carbon (Acidiphilium spp., Bacillus spp., Clostridium spp., Acidobacterium spp., etc.) cycles were identified, and their distribution was correlated with physicochemical parameters of the sediments. Ferric iron was the main electron acceptor for the oxidation of organic matter in the most acid and oxidizing layers, so acidophilic facultative Fe(III)-reducing bacteria appeared widely in the clone libraries. With increasing pH, the solubility of iron decreases and sulfate-reducing bacteria become dominant, with the ecological role of methanogens being insignificant. Considering the identified microorganisms-which, according to the rarefaction curves and Good's coverage values, cover almost all of the diversity-and their corresponding metabolism, we suggest a model of the iron, sulfur, and organic matter cycles in AMD-related sediments.

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Section: Fieldmentioning

confidence: 99%

Microbial Diversity in Anaerobic Sediments at Río Tinto, a Naturally Acidic Environment with a High Heavy Metal Content

Sánchez‐Andrea

Rodríguez

Amils

et al. 2011

Appl Environ Microbiol

174

126

View full text Add to dashboard Cite

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Microbial dynamics and bioreactor performance are interlinked with organic matter removal from wastewater treatment plant effluent

Atasoy

Scott

Gijn

et al. 2023

Bioresource Technology

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Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB)

Martorelli

Helwerda

Kerkvliet

et al. 2020

Journal of Integrative Bioinformatics

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Fungi have crucial roles in ecosystems, and are important associates for many organisms. They are adapted to a wide variety of habitats, however their global distribution and diversity remains poorly documented. The exponential growth of DNA barcode information retrieved from the environment is assisting considerably the traditional ways for unraveling fungal diversity and detection. The raw DNA data in association to environmental descriptors of metabarcoding studies are made available in public sequence read archives. While this is potentially a valuable source of information for the investigation of Fungi across diverse environmental conditions, the annotation used to describe environment is heterogenous. Moreover, a uniform processing pipeline still needs to be applied to the available raw DNA data. Hence, a comprehensive framework to analyses these data in a large context is still lacking. We introduce the MycoDiversity DataBase, a database which includes public fungal metabarcoding data of environmental samples for the study of biodiversity patterns of Fungi. The framework we propose will contribute to our understanding of fungal biodiversity and aims to become a valuable source for large-scale analyses of patterns in space and time, in addition to assisting evolutionary and ecological research on Fungi.

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The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Cited by 3 publications

References 0 publications

Microbial Diversity in Anaerobic Sediments at Río Tinto, a Naturally Acidic Environment with a High Heavy Metal Content

Microbial Diversity in Anaerobic Sediments at Río Tinto, a Naturally Acidic Environment with a High Heavy Metal Content

Microbial dynamics and bioreactor performance are interlinked with organic matter removal from wastewater treatment plant effluent

Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB)

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