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      Denitrification in hypersaline and coastal environments

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          Abstract

          As the association of denitrification with global warming and nitrogen removal from ecosystems has gained attention in recent decades, numerous studies have examined denitrification rates and the distribution of denitrifiers across different environments. In this minireview, reported studies focused on coastal saline environments, including estuaries, mangroves, and hypersaline ecosystems, have been analysed to identify the relationship between denitrification and saline gradients. The analyses of the literature and databases stated the direct effect of salinity on the distribution patterns of denitrifiers. However, few works do not support this hypothesis thus making this topic controversial. The specific mechanisms by which salinity influences denitrifier distribution are not fully understood. Nevertheless, several physical and chemical environmental parameters, in addition to salinity, have been shown to play a role in structuring the denitrifying microbial communities. The prevalence of nirS or nirK denitrifiers in ecosystems is a subject of debate in this work. In general terms, in mesohaline environments, the predominant nitrite reductase is NirS type and, NirK is found predominantly in hypersaline environments. Moreover, the approaches used by different researchers are quite different, resulting in a huge amount of unrelated information, making it difficult to establish comparative analysis. The main techniques used to analyse the distribution of denitrifying populations along salt gradients have been also discussed.

          Abstract

          Importance of denitrification in saline and hypersaline environments in terms of denitrification rates and expression and abundance of denitrification genes in salinity gradients.

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          Most cited references85

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          An Earth-system perspective of the global nitrogen cycle.

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            Cell biology and molecular basis of denitrification.

            W Zumft (1997)
            Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.
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              NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

              NCBI's reference sequence (RefSeq) database () is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. The database includes 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2 879 860 proteins (RefSeq release 19). RefSeq records integrate information from multiple sources, when additional data are available from those sources and therefore represent a current description of the sequence and its features. Annotations include coding regions, conserved domains, tRNAs, sequence tagged sites (STS), variation, references, gene and protein product names, and database cross-references. Sequence is reviewed and features are added using a combined approach of collaboration and other input from the scientific community, prediction, propagation from GenBank and curation by NCBI staff. The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence.
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                Author and article information

                Contributors
                Journal
                FEMS Microbiol Lett
                FEMS Microbiol Lett
                femsle
                FEMS Microbiology Letters
                Oxford University Press
                0378-1097
                1574-6968
                2023
                08 July 2023
                08 July 2023
                : 370
                : fnad066
                Affiliations
                Biochemistry and Molecular Biology, and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante , Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
                Biochemistry and Molecular Biology, and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante , Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
                Biochemistry and Molecular Biology, and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante , Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
                Biochemistry and Molecular Biology, and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante , Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
                Multidisciplinary Institute for Environmental Studies “Ramón Margalef” (IMEM), University of Alicante , Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
                Biochemistry and Molecular Biology, and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante , Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
                Multidisciplinary Institute for Environmental Studies “Ramón Margalef” (IMEM), University of Alicante , Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
                Author notes
                Corresponding author. Biochemistry and Molecular Biology, and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain. Tel: +34 96 5903400 ext. 1258; Fax: +34 96 590 3464. E-mail: carmen.pire@ 123456ua.es
                Author information
                https://orcid.org/0000-0002-8956-4851
                https://orcid.org/0000-0003-2679-135X
                Article
                fnad066
                10.1093/femsle/fnad066
                10423024
                37422443
                fa1d5f97-e4b0-4437-a433-ea3b7e524b52
                © The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License ( https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                : 03 April 2023
                : 09 June 2023
                : 05 July 2023
                : 12 August 2023
                Page count
                Pages: 11
                Categories
                Minireview
                Taxonomy, Systematics and Evolutionary Microbiology
                AcademicSubjects/SCI01150

                Microbiology & Virology
                denitrification,saline ecosystem,halophilic microorganisms,nitrite reductase,denitrifiers distribution,coastal ecosystem

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