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      Inhibition of phototrophic iron oxidation by nitric oxide in ferruginous environments

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          Abstract

          Anoxygenic phototrophic Fe(II) oxidizers (photoferrotrophs) are thought to have thrived in Earth’s ancient ferruginous oceans and played a primary role in the precipitation of Archaean and Palaeoproterozoic (3.8–1.85-billion-year-old) banded iron formations (BIFs). The end of BIF deposition by photoferrotrophs has been interpreted as the result of a deepening of water-column oxygenation below the photic zone, concomitant with the proliferation of cyanobacteria. However, photoferrotrophs may have experienced competition from other anaerobic Fe(II)-oxidizing microorganisms, altering the formation mechanism of BIFs. Here we utilize microbial incubations to show that nitrate-reducing Fe(II) oxidizers metabolically outcompete photoferrotrophs for dissolved Fe(II). Moreover, both experiments and numerical modelling show that the nitrate-reducing Fe(II) oxidizers inhibit photoferrotrophy via the production of toxic intermediates. Four different photoferrotrophs, representing both green sulfur and purple non-sulfur bacteria, are susceptible to this toxic effect despite having genomic capabilities for nitric oxide detoxification. Indeed, despite nitric oxide detoxification mechanisms being ubiquitous in some groups of phototrophs at the genomic level (for example, Chlorobi and Cyanobacteria) it is likely that they would still be affected. We suggest that the production of reactive nitrogen species during nitrate-reducing Fe(II) oxidation in ferruginous environments may have inhibited the activity of photoferrotrophs in the ancient oceans and thus impeded their role in the precipitation of BIFs.

          Abstract

          Banded iron formation deposition by photoferrotrophic organisms in the early Earth’s oceans may have been inhibited by competition for iron and toxicity from nitrate-reducing microorganisms, according to a microbial incubation and numerical modelling study.

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          Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

          The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
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            The microbial nitrogen-cycling network

            Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet. By far, the largest inventory of freely accessible nitrogen is atmospheric dinitrogen, but most organisms rely on more bioavailable forms of nitrogen, such as ammonium and nitrate, for growth. The availability of these substrates depends on diverse nitrogen-transforming reactions that are carried out by complex networks of metabolically versatile microorganisms. In this Review, we summarize our current understanding of the microbial nitrogen-cycling network, including novel processes, their underlying biochemical pathways, the involved microorganisms, their environmental importance and industrial applications.
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              Ferrozine---a new spectrophotometric reagent for iron

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                Author and article information

                Contributors
                casey.bryce@bristol.ac.uk
                Journal
                Nat Geosci
                Nat Geosci
                Nature Geoscience
                Nature Publishing Group UK (London )
                1752-0894
                1752-0908
                4 October 2024
                4 October 2024
                2024
                : 17
                : 11
                : 1169-1174
                Affiliations
                [1 ]Geomicrobiology, University of Tübingen, ( https://ror.org/03a1kwz48) Tübingen, Germany
                [2 ]NORCE Norwegian Research Center, ( https://ror.org/02gagpf75) Bergen, Norway
                [3 ]Civil and Environmental Engineering, University of Kassel, ( https://ror.org/04zc7p361) Kassel, Germany
                [4 ]School of Geographical Sciences, University of Bristol, ( https://ror.org/0524sp257) Bristol, UK
                [5 ]Department of Earth System Science, Stanford University, ( https://ror.org/00f54p054) Stanford, CA USA
                [6 ]School of Life Sciences, Arizona State University, ( https://ror.org/03efmqc40) Tempe, AZ USA
                [7 ]Department of Earth and Atmospheric Sciences, University of Alberta, ( https://ror.org/0160cpw27) Edmonton, Alberta Canada
                [8 ]Blue Marble Space Institute of Science, ( https://ror.org/04yhya597) Seattle, WA USA
                [9 ]GRID grid.517304.4, Cluster of Excellence EXC 2124: Controlling Microbes to Fight Infections, ; Tübingen, Germany
                [10 ]School of Earth Sciences, University of Bristol, ( https://ror.org/0524sp257) Bristol, UK
                Author information
                http://orcid.org/0000-0003-2708-4518
                http://orcid.org/0000-0003-0223-0339
                http://orcid.org/0000-0002-1376-8049
                http://orcid.org/0000-0003-0755-3364
                http://orcid.org/0000-0001-7722-7068
                http://orcid.org/0000-0003-2324-1619
                http://orcid.org/0000-0002-5216-2664
                http://orcid.org/0000-0002-3558-9500
                http://orcid.org/0000-0002-1132-5201
                Article
                1560
                10.1038/s41561-024-01560-9
                11543593
                8250ac0c-37bd-4395-ae8b-408a466a4aaa
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 22 September 2021
                : 13 September 2024
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft (German Research Foundation);
                Award ID: BR-5927/2-1
                Award ID: BR-5927/2-1
                Award ID: EXC2124, project ID 390838134
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000104, National Aeronautics and Space Administration (NASA);
                Award ID: Nexus for Exoplanet System Science (NExSS)
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100000288, Royal Society;
                Award ID: University Research Fellowship
                Award Recipient :
                Categories
                Article
                Custom metadata
                © Springer Nature Limited 2024

                Geosciences
                element cycles,geochemistry
                Geosciences
                element cycles, geochemistry

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