3
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

      review-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Biological dinitrogen (N 2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N 2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N 2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.

          Abstract

          The authors discuss recent advances that highlight marine non-cyanobacterial diazotrophs in marine ecosystems, with a focus on diversity, drivers of their global biogeography and potential ecophysiologies, and their significance to the nitrogen cycle in well-lit oxygenated euphotic waters.

          Related collections

          Most cited references300

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

          Background We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability. Methodology/Principal Findings Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion to improve the tree, FastTree 2 adds minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood NNIs. FastTree 2 uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site (the “CAT” approximation). Nevertheless, for both simulated and genuine alignments, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs (PhyML 3 with default settings). Although FastTree 2 is not quite as accurate as methods that use maximum-likelihood SPRs, most of the splits that disagree are poorly supported, and for large alignments, FastTree 2 is 100–1,000 times faster. FastTree 2 inferred a topology and likelihood-based local support values for 237,882 distinct 16S ribosomal RNAs on a desktop computer in 22 hours and 5.8 gigabytes of memory. Conclusions/Significance FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

            The Interactive Tree Of Life ( https://itol.embl.de ) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users. Graphical Abstract iTOL: an online tool for the tree display and annotation.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              HMMER web server: interactive sequence similarity searching

              HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.
                Bookmark

                Author and article information

                Contributors
                Journal
                FEMS Microbiol Rev
                FEMS Microbiol Rev
                femsre
                FEMS Microbiology Reviews
                Oxford University Press
                0168-6445
                1574-6976
                November 2023
                23 November 2022
                23 November 2022
                : 47
                : 6
                : fuac046
                Affiliations
                Ocean Sciences Department, University of California, Santa Cruz , 1156 High Street, Santa Cruz, CA 95064, United States
                Ocean Sciences Department, University of California, Santa Cruz , 1156 High Street, Santa Cruz, CA 95064, United States
                Columbia River Inter-Tribal Fish Commission , Portland, OR, United States
                Ocean Sciences Department, University of California, Santa Cruz , 1156 High Street, Santa Cruz, CA 95064, United States
                Ocean Sciences Department, University of California, Santa Cruz , 1156 High Street, Santa Cruz, CA 95064, United States
                Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC) , Pg. Marítim Barceloneta, 37-49 08003 Barcelona, Spain
                Ocean Sciences Department, University of California, Santa Cruz , 1156 High Street, Santa Cruz, CA 95064, United States
                Marine Biology Research Division, Scripps Institute of Oceanography , 9500 Gilman Drive, La Jolla, CA 92093, United States
                Ocean Sciences Department, University of California, Santa Cruz , 1156 High Street, Santa Cruz, CA 95064, United States
                Department of Earth System Science, Stanford University , 473 Via Ortega, Stanford, CA 94305, United States
                Ocean Sciences Department, University of California, Santa Cruz , 1156 High Street, Santa Cruz, CA 95064, United States
                Author notes
                Corresponding author: Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States. Tel: (831) 459-4490; E-mail: kturk@ 123456ucsc.edu

                Equal contribution

                Author information
                https://orcid.org/0000-0002-9847-7514
                https://orcid.org/0000-0001-8431-9278
                Article
                fuac046
                10.1093/femsre/fuac046
                10719068
                36416813
                1e4b9b22-8e1d-4824-bba3-d908bfac5dc6
                © The Author(s) 2022. Published by Oxford University Press on behalf of FEMS.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                : 01 June 2022
                : 15 September 2022
                : 17 November 2022
                : 15 December 2022
                Page count
                Pages: 25
                Funding
                Funded by: National Science Foundation, DOI 10.13039/100000001;
                Award ID: OCE-2023498
                Funded by: Simons Foundation, DOI 10.13039/100000893;
                Award ID: 824082
                Award ID: 724220
                Funded by: 'la Caixa' Foundation, DOI 10.13039/100010434;
                Award ID: 105090
                Funded by: Horizon 2020, DOI 10.13039/100010661;
                Funded by: H2020 Marie Skłodowska-Curie Actions, DOI 10.13039/100010665;
                Award ID: 847648
                Award ID: CEX2019-000928-S
                Categories
                Review Article
                AcademicSubjects/SCI01150

                Microbiology & Virology
                diazotrophs,marine nitrogen cycle,nitrogen fixation,non-cyanobacterial diazotrophs

                Comments

                Comment on this article