Karl D, Michaels A, Bergman B, Capone D, Carpenter E, Letelier R, et al. Dinitrogen fixation in the world’s oceans. In: Boyer EW, Howarth RW, editors. The nitrogen cycle at regional to global scales. Dordrecht: Springer; 2002. p. 47–98.
Berthelot H, Benavides M, Moisander PH, Grosso O, Bonnet S. High-nitrogen fixation rates in the particulate and dissolved pools in the Western Tropical Pacific (Solomon and Bismarck Seas): N2 fixation in the Western Pacific. Geophys Res Lett. 2017;44:8414–23.
Google Scholar
Rahav E, Bar-Zeev E, Ohayion S, Elifantz H, Belkin N, Herut B, et al. Dinitrogen fixation in aphotic oxygenated marine environments. Front Microbiol. 2013;4:227.
Google Scholar
Bentzon-Tilia M, Traving SJ, Mantikci M, Knudsen-Leerbeck H, Hansen JL, Markager S, et al. Significant N2 fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries. ISME J. 2015;9:273–85.
Google Scholar
Messer LF, Doubell M, Jeffries TC, Brown MV, Seymour JR. Prokaryotic and diazotrophic population dynamics within a large oligotrophic inverse estuary. Aquat Micro Ecol. 2015;74:1–15.
Google Scholar
Sipler RE, Gong D, Baer SE, Sanderson MP, Roberts QN, Mulholland MR, et al. Preliminary estimates of the contribution of Arctic nitrogen fixation to the global nitrogen budget. Limnol Oceanogr Lett. 2017;2:159–66.
Google Scholar
Benavides M, Bonnet S, Berman-Frank I, Riemann L. Deep into oceanic N2 fixation. Front Mar Sci. 2018;5:1–4.
Google Scholar
Mulholland MR, Bernhardt PW, Widner BN, Selden CR, Chappell PD, Clayton S, et al. High rates of N2 fixation in temperate, Western North Atlantic coastal waters expand the realm of marine diazotrophy. Glob Biogeochem Cycles. 2019;33:826–40.
Google Scholar
Zehr JP. Nitrogen fixation by marine cyanobacteria. Trends Microbiol. 2011;19:162–73.
Google Scholar
Riemann L, Farnelid H, Steward G. Nitrogenase genes in non-cyanobacterial plankton: prevalence, diversity and regulation in marine waters. Aquat Micro Ecol. 2010;61:235–47.
Google Scholar
Farnelid H, Andersson AF, Bertilsson S, Al-Soud WA, Hansen LH, Sørensen S, et al. Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria. PLoS ONE. 2011;6:e19223.
Google Scholar
Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018;3:804–13.
Google Scholar
Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh H-J, Cuenca M, et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell. 2019;179:1068–1083.e21.
Google Scholar
Bombar D, Paerl RW, Riemann L. Marine non-cyanobacterial diazotrophs: moving beyond molecular detection. Trends Microbiol. 2016;24:916–27.
Google Scholar
Moisander PH, Benavides M, Bonnet S, Berman-Frank I, White AE, Riemann L. Chasing after non-cyanobacterial nitrogen fixation in marine pelagic environments. Front Microbiol. 2017;8:1736.
Google Scholar
Eady RR, Postgate JR. Nitrogenase. Nature. 1974;249:805–10.
Google Scholar
Wong PP, Burris RH. Nature of oxygen inhibition of nitrogenase from azotobacter vinelandii. Proc Natl Acad Sci USA 1972;69:672–5.
Google Scholar
Berman-Frank I, Quigg A, Finkel ZV, Irwin AJ, Haramaty L. Nitrogen-fixation strategies and Fe requirements in cyanobacteria. Limnol Oceanogr. 2007;52:2260–9.
Google Scholar
Inomura K, Bragg J, Follows MJ. A quantitative analysis of the direct and indirect costs of nitrogen fixation: a model based on Azotobacter vinelandii. ISME J. 2017;11:166–75.
Google Scholar
Paerl HW. Microzone formation: its role in the enhancement of aquatic N2 fixation. Limnol Oceanogr. 1985;30:1246–52.
Google Scholar
Paerl HW, Prufert LE. Oxygen-poor microzones as potential sites of microbial N2 fixation in nitrogen-depleted aerobic marine waters. Appl Env Microbiol. 1987;53:1078–87.
Google Scholar
Riemann L, Rahav E, Passow U, Grossart H-P, de Beer D, Klawonn I, et al. Planktonic aggregates as hotspots for heterotrophic diazotrophy: the plot thickens. Front Microbiol. 2022;13:1092.
Google Scholar
Braun ST, Proctor LM, Zani S, Mellon MT, Zehr JP. Molecular evidence for zooplankton-associated nitrogen-fixing anaerobes based on amplification of the nifH gene. FEMS Microbiol Ecol. 1999;28:273–9.
Google Scholar
Farnelid H, Tarangkoon W, Hansen G, Hansen PJ, Riemann L. Putative N2-fixing heterotrophic bacteria associated with dinoflagellate–Cyanobacteria consortia in the low-nitrogen Indian Ocean. Aquat Micro Ecol. 2010;61:105–17.
Google Scholar
Scavotto RE, Dziallas C, Bentzon-Tilia M, Riemann L, Moisander PH. Nitrogen-fixing bacteria associated with copepods in coastal waters of the North Atlantic Ocean: diazotroph community in association with copepods. Environ Microbiol. 2015;17:3754–65.
Google Scholar
Farnelid H, Turk-Kubo K, Ploug H, Ossolinski JE, Collins JR, Van Mooy BAS, et al. Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre. ISME J. 2019;13:170–82.
Google Scholar
Geisler E, Bogler A, Rahav E, Bar-Zeev E. Direct detection of heterotrophic diazotrophs associated with planktonic aggregates. Sci Rep. 2019;9:1–9.
Google Scholar
Pedersen JN, Bombar D, Paerl RW, Riemann L. Diazotrophs and N2-fixation associated with particles in coastal estuarine waters. Front Microbiol. 2018;9:2759.
Google Scholar
Paerl RW, Hansen TNG, Henriksen NNSE, Olesen AK, Riemann L. N2-fixation and related O2 constraints on model marine diazotroph Pseudomonas stutzeri BAL361. Aquat Micro Ecol. 2018;81:125–36.
Google Scholar
Rahav E, Giannetto MJ, Bar-Zeev E. Contribution of mono and polysaccharides to heterotrophic N2 fixation at the eastern Mediterranean coastline. Sci Rep. 2016;6:27858.
Google Scholar
Chakraborty S, Andersen KH, Visser AW, Inomura K, Follows MJ, Riemann L. Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles. Nat Commun. 2021;12:4085.
Google Scholar
Stocker R, Seymour JR, Samadani A, Hunt DE, Polz MF. Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. Proc Natl Acad Sci USA 2008;105:4209–14.
Google Scholar
Stocker R, Seymour JR. Ecology and physics of bacterial chemotaxis in the ocean. Microbiol Mol Biol Rev. 2012;76:792–812.
Google Scholar
Garren M, Son K, Raina J-B, Rusconi R, Menolascina F, Shapiro OH, et al. A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals. ISME J. 2014;8:999–1007.
Google Scholar
Son K, Menolascina F, Stocker R. Speed-dependent chemotactic precision in marine bacteria. Proc Natl Acad Sci USA 2016;113:8624–9.
Google Scholar
Brumley DR, Carrara F, Hein AM, Yawata Y, Levin SA, Stocker R. Bacteria push the limits of chemotactic precision to navigate dynamic chemical gradients. Proc Natl Acad Sci USA 2019;116:10792–7.
Google Scholar
Müller‐Niklas G, Stefan S, Kaltenböok E, Herndl GJ. Organic content and bacterial metabolism in amorphous aggregations of the northern Adriatic Sea. Limnol Oceanogr. 1994;39:58–68.
Google Scholar
Grossart H-P, Czub G, Simon M. Algae–bacteria interactions and their effects on aggregation and organic matter flux in the sea. Environ Microbiol. 2006;8:1074–84.
Google Scholar
Smith DC, Simon M, Alldredge AL, Azam F. Intense hydrolytic enzyme activity on marine aggregates and implications for rapid particle dissolution. Nature. 1992;359:139–42.
Google Scholar
Kiørboe T, Ploug H, Thygesen UH. Fluid motion and solute distribution around sinking aggregates. I. Small-scale fluxes and heterogeneity of nutrients in the pelagic environment. Mar Ecol Prog Ser. 2001;211:1–13.
Google Scholar
Kiørboe T, Jackson GA. Marine snow, organic solute plumes, and optimal chemosensory behavior of bacteria. Limnol Oceanogr. 2001;46:1309–18.
Google Scholar
Raina J-B, Lambert BS, Parks DH, Rinke C, Siboni N, Bramucci A, et al. Chemotaxis shapes the microscale organisation of the ocean’s microbiome. Nature. 2022;605:132–8.
Google Scholar
Lambert BS, Raina J-B, Fernandez VI, Rinke C, Siboni N, Rubino F, et al. A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nat Microbiol. 2017;2:1344–9.
Google Scholar
Clerc EE, Raina J-B, Lambert BS, Seymour J, Stocker R. In situ chemotaxis assay to examine microbial behavior in aquatic ecosystems. J Vis Exp. 2020;159:e61062.
Boström KH, Riemann L, Kühl M, Hagström Å. Isolation and gene quantification of heterotrophic N2-fixing bacterioplankton in the Baltic Sea. Environ Microbiol. 2007;9:152–64.
Google Scholar
Farnelid H, Harder J, Bentzon-Tilia M, Riemann L. Isolation of heterotrophic diazotrophic bacteria from estuarine surface waters: heterotrophic diazotrophs in the Baltic Sea. Environ Microbiol. 2014;16:3072–82.
Google Scholar
ZoBell CE. Studies on Marine Bacteria I. The cultural requirements of heterotrophic aerobes. J Mar Res. 1941;4:41–75.
Alldredge AL, Gotschalk C, Passow U, Riebesell U. Mass aggregation of diatom blooms: Insights from a mesocosm study. Deep Sea Res Part II Top Stud Oceanogr. 1995;42:9–27.
Google Scholar
Thornton DCO. Diatom aggregation in the sea: mechanisms and ecological implications. Eur J Phycol. 2002;37:149–61.
Google Scholar
Turner J. Zooplankton fecal pellets, marine snow and sinking phytoplankton blooms. Aquat Micro Ecol. 2002;27:57–102.
Google Scholar
Schnetzer A, Lampe RH, Benitez-Nelson CR, Marchetti A, Osburn CL, Tatters AO. Marine snow formation by the toxin-producing diatom, Pseudo-nitzschia australis. Harmful Algae. 2017;61:23–30.
Google Scholar
Dittmar T, Koch B, Hertkorn N, Kattner G. A simple and efficient method for the solid-phase extraction of dissolved organic matter (SPE-DOM) from seawater. Limnol Oceanogr Methods. 2008;6:230–5.
Google Scholar
Marie D, Partensky F, Jacquet S, Vaulot D. Enumeration and cell cycle analysis of natural populations of marine picoplankton by flow cytometry using the nucleic acid stain SYBR green. Appl Environ Microbiol. 1997;63:186–93.
Google Scholar
Bramucci AR, Focardi A, Rinke C, Hugenholtz P, Tyson GW, Seymour JR, et al. Microvolume DNA extraction methods for microscale amplicon and metagenomic studies. ISME Commun. 2021;1:1–5.
Google Scholar
Rinke C, Low S, Woodcroft BJ, Raina J-B, Skarshewski A, Le XH, et al. Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ. 2016;4:e2486.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv13033997 Q-Bio. 2013.
Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics. 2007;23:1282–8.
Google Scholar
Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.
Google Scholar
Clarke KR, Gorley RN, Somerfield PJ, Warwick RM. Change in marine communities: an approach to statistical analysis and interpretation. 3rd ed. Plymouth: Primer-E Ltd; 2014.
Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2019;20:1160–6.
Google Scholar
Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics. 2019;35:4453–5.
Google Scholar
Edler D, Klein J, Antonelli A, Silvestro D. raxmlGUI 2.0 beta: a graphical interface and toolkit for phylogenetic analyses using RAxML. bioRxiv. 2019. https://doi.org/10.1101/800912.
Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, et al. EPA-ng: massively parallel evolutionary placement of genetic sequences. Syst Biol. 2019;68:365–9.
Google Scholar
Czech L, Barbera P, Stamatakis A. Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data. Bioinformatics. 2020;36:3263–5.
Google Scholar
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2020;36:1925–7.
Google Scholar
Bentzon-Tilia M, Severin I, Hansen LH, Riemann L. Genomics and ecophysiology of heterotrophic nitrogen-fixing bacteria isolated from estuarine surface water. mBio. 2015;6:e00929–15.
Google Scholar
Martínez-Pérez C, Mohr W, Schwedt A, Dürschlag J, Callbeck CM, Schunck H, et al. Metabolic versatility of a novel N2-fixing Alphaproteobacterium isolated from a marine oxygen minimum zone: novel N2-fixer from oxygen minimum zone off Peru. Environ Microbiol. 2018;20:755–68.
Google Scholar
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:119.
Google Scholar
Eschemann A, Kühl M, Cypionka H. Aerotaxis in Desulfovibrio. Environ Microbiol. 1999;1:489–94.
Google Scholar
Zhu S, Kojima S, Homma M. Structure, gene regulation and environmental response of flagella in Vibrio. Front Microbiol. 2013;4:410.
Silva MA, Salgueiro CA. Multistep signaling in nature: a close-up of Geobacter chemotaxis sensing. Int J Mol Sci. 2021;22:9034.
Google Scholar
Taylor BL, Zhulin IB, Johnson MS. Aerotaxis and other energy-sensing behavior in bacteria. Annu Rev Microbiol. 1999;53:103–28.
Google Scholar
Colin R, Sourjik V. Emergent properties of bacterial chemotaxis pathway. Curr Opin Microbiol. 2017;39:24–33.
Google Scholar
Stocker R. Marine microbes see a sea of gradients. Science. 2012;338:628–33.
Google Scholar
Turk‐Kubo KA, Karamchandani M, Capone DG, Zehr JP. The paradox of marine heterotrophic nitrogen fixation: abundances of heterotrophic diazotrophs do not account for nitrogen fixation rates in the Eastern Tropical South Pacific. Environ Microbiol. 2014;16:3095–114.
Google Scholar
Bentzon-Tilia M, Farnelid H, Jürgens K, Riemann L. Cultivation and isolation of N2-fixing bacteria from suboxic waters in the Baltic Sea. FEMS Microbiol Ecol. 2014;88:358–71.
Google Scholar
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