Falkowski PG. Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean. Nature. 1997;387:272–5.
Google Scholar
Zehr JP. Nitrogen fixation by marine cyanobacteria. Trends Microbiol. 2011;19:162–73.
Google Scholar
Capone DG, Zehr JP, Paerl HW, Bergman B, Carpenter EJ. Trichodesmium a globally significant marine cyanobacterium. Science (80-). 1997;276:1221–9.
Google Scholar
Bergman B, Sandh G, Lin S, Larsson J, Carpenter EJ. Trichodesmium – a widespread marine cyanobacterium with unusual nitrogen fixation properties. FEMS Microbiol Rev. 2013;37:286–302. 37(3):286–302
Google Scholar
Capone DG, Burns JA, Montoya JP, Subramaniam A, Mahaffey C, Gunderson T, et al. Nitrogen fixation by Trichodesmium spp.: An important source of new nitrogen to the tropical and subtropical North Atlantic Ocean. Glob Biogeochem Cycles. 2005;19:1–17.
Mahaffey C, Michaels AF, Capone DG. The conundrum of marine N2 fixation. Am J Sci. 2005;305:546–95.
Google Scholar
Moore C, Mills MM, Achterberg EP, Geider RJ, Laroche J, Lucas MI, et al. Large-scale distribution of Atlantic nitrogen fixation controlled by iron availability. Nat Geosci. 2009;2:867–71.
Google Scholar
Dyhrman ST, Webb EA, Anderson DM, Moffett JW, Waterbury JB. Cell-specific detection of phosphorus stress in Trichodesmium from the Western North Atlantic. Limnol Oceanogr. 2002;47:1832–6.
Snow JT, Schlosser C, Woodward EMS, Mills MM, Achterberg EP, Mahaffey C, et al. Environmental controls on the biogeography of diazotrophy and Trichodesmium in the Atlantic Ocean. Glob Biogeochem Cycles. 2015;29:865–84.
Google Scholar
Jickells TD, An ZS, Andersen KK, Baker AR, Bergametti C, Brooks N, et al. Global iron connections between desert dust, ocean biogeochemistry, and climate. Science. 2005;308:67–71.
Google Scholar
Schlosser CA, Strzepek K, Gao X, Fant C, Blanc É, Paltsev S, et al. The future of global water stress: an integrated assessment. Earth’s Future. 2014;2:341–61.
Wu J, Sunda W, Boyle EA, Karl DM. Phosphate depletion in the Western North Atlantic. Ocean Sci. 2000;289:759–62.
Google Scholar
Mather RL, Reynolds SE, Wolff GA, Williams RG, Torres-Valdes S, Woodward EMS, et al. Phosphorus cycling in the North and South Atlantic Ocean subtropical gyres. Nat Geosci. 2008;1:439–43.
Google Scholar
Ward BA, Dutkiewicz S, Moore CM, Follows MJ. Iron, phosphorus, and nitrogen supply ratios define the biogeography of nitrogen fixation. Limnol Oceanogr. 2013;58:2059–75.
Google Scholar
Mills MM, Moore CM, Langlois R, Milne A, Achterberg E, Nachtigall K, et al. Nitrogen and phosphorus co-limitation of bacterial productivity and growth in the oligotrophic subtropical North Atlantic. Limnol Oceanogr. 2008;53:824–34.
Google Scholar
Garcia NS, Fu F, Sedwick PN, Hutchins DA. Iron deficiency increases growth and nitrogen-fixation rates of phosphorus-deficient marine cyanobacteria. ISME J. 2015;9:238–45.
Google Scholar
Walworth NG, Fu FX, Webb EA, Saito MA, Moran D, McLlvin MR, et al. Mechanisms of increased Trichodesmium fitness under iron and phosphorus co-limitation in the present and future ocean. Nat Commun. 2016;7:1–11.
Walworth NG, Fu FX, Lee MD, Cai X, Saito MA, Webb EA, et al. Nutrient-colimited Trichodesmium as a nitrogen source or sink in a future ocean. Appl Environ Microbiol. 2018;84:1–14.
Google Scholar
Held NA, Webb EA, McIlvin MM, Hutchins DA, Cohen NR, Moran DM, et al. Co-occurrence of Fe and P stress in natural populations of the marine diazotroph Trichodesmium. Biogeosciences 2020;17:2537–51.
Polyviou D, Baylay AJ, Hitchcock A, Robidart J, Moore CM, Bibby TS. Desert dust as a source of iron to the globally important diazotroph Trichodesmium. Front Microbiol. 2018;8:2683.
Google Scholar
Snow JT, Polyviou D, Skipp P, Chrismas NA, Hitchcock A, Geider R, et al. Quantifying Integrated Proteomic Responses to Iron Stress in the Globally Important Marine Diazotroph Trichodesmium. PLOS ONE 2015;10:e0142626.
Frischkorn KR, Haley ST, Dyhrman ST. Transcriptional and proteomic choreography under phosphorus deficiency and re-supply in the N2 fixing cyanobacterium Trichodesmium erythraeum. Front Microbiol. 2019;10:330. 2012;6:1728–39
Google Scholar
Rouco M, Frischkorn KR, Haley ST, Alexander H, Dyhrman ST. Transcriptional patterns identify resource controls on the diazotroph Trichodesmium in the Atlantic and Pacific oceans. ISME J. 2018;12:1486–95.
Google Scholar
Shi T, Sun Y, Falkowski PG. Effects of iron limitation on the expression of metabolic genes in the marine cyanobacterium Trichodesmium erythraeum IMS101. Environ Microbiol. 2007;9:2945–56.
Google Scholar
Saito MA, Bertrand EM, Dutkiewicz S, Bulygin VV, Moran DM, Monteiro FM, et al. Iron conservation by reduction of metalloenzyme inventories in the marine diazotroph Crocosphaera watsonii. Proc Natl Acad Sci USA 2011;108:2184–9.
Google Scholar
La Roche J, Boyd PW, McKay RML, Geider RJ. Flavodoxin as an in situ marker for iron stress in phytoplankton. Nature. 1996;382:802–5.
De la Cerda B, Castielli O, Durán RV, Navarro JA, Hervás M, De la Rosa MA. A proteomic approach to iron and copper homeostasis in cyanobacteria. Brief Funct Genom Proteom. 2007;6:322–9.
Chappell PD, Webb EA. A molecular assessment of the iron stress response in the two phylogenetic clades of Trichodesmium. Environ Microbiol. 2010;12:13–27.
Google Scholar
Polyviou D, Machelett MM, Hitchcock A, Baylay AJ, MacMillan F, Mark Moore C, et al. Structural and functional characterization of IdiA/FutA (Tery_3377), an iron-binding protein from the ocean diazotroph Trichodesmium erythraeum. J Biol Chem. 2018;293:18099–109.
Google Scholar
Berman-Frank I, Lundgren P, Chen YB, Küpper H, Kolber Z, Bergman B, et al. Segregation of nitrogen fixation and oxygenic photosynthesis in the marine cyanobacterium Trichodesmium. Science. 2001;294:1534–7.
Google Scholar
Berman-Frank I, Lundgren P, Falkowski P. Nitrogen fixation and photosynthetic oxygen evolution in cyanobacteria. Res Microbiol. 2003;154:157–64.
Google Scholar
Sandh G, Ran L, Xu L, Sundqvist G, Bulone V, Bergman B. Comparative proteomic profiles of the marine cyanobacterium Trichodesmium erythraeum IMS101 under different nitrogen regimes. Proteomics. 2011;11:406–19.
Google Scholar
Orchard ED, Webb EA, Dyhrman ST. Molecular analysis of the phosphorus starvation response in Trichodesmium spp. Environ Microbiol. 2009;11:2400–11.
Google Scholar
Dyhrman ST, Ruttenberg KC. Presence and regulation of alkaline phosphatase activity in eukaryotic phytoplankton from the coastal ocean: Implications for dissolved organic phosphorus remineralization. Limnol Oceanogr. 2006;51:1381–90.
Google Scholar
Karl DM. Nutrient dynamics in the deep blue sea. Trends Microbiol. 2002;10:410–8.
Google Scholar
Polyviou D, Hitchcock A, Baylay AJ, Moore CM, Bibby TS. Phosphite utilization by the globally important marine diazotroph Trichodesmium. Environ Microbiol Rep. 2015;7:824–30.
Google Scholar
Obata H, Karatani H, Matsui M, Nakayama E. Fundamental studies for chemical speciation of iron in seawater with an improved analytical method. Marine Chemistry. 1997;56:97–106.
Kunde K, Wyatt NJ, González-Santana D, Tagliabue A, Mahaffey C, Lohan MC. Iron Distribution in the Subtropical North Atlantic: The Pivotal Role of Colloidal Iron. Glob Biogeochem Cycles. 2019;33:1532–47.
Google Scholar
Woodward EMS, Rees AP. Nutrient distributions in an anticyclonic eddy in the northeast Atlantic Ocean, with reference to nanomolar ammonium concentrations. Deep Res Part II Top Stud Oceanogr. 2001;48:775–93.
Google Scholar
Davis CE, Blackbird S, Wolff G, Woodward M, Mahaffey C. Seasonal organic matter dynamics in a temperate shelf sea. Prog Oceanogr. 2019;177:101925.
Lomas MW, Burke AL, Lomas DA, Bell DW, Shen C, Dyhrman ST, et al. Sargasso Sea phosphorus biogeochemistry: an important role for dissolved organic phosphorus (DOP). Biogeosci Discuss. 2009;6:10137–75.
Klawonn I, Lavik G, Böning P, et al. Simple approach for the preparation of 15−15N2-enriched water for nitrogen fixation assessments: evaluation, application and recommendations. Front Microbiol. 2015;6:769.
Google Scholar
Frischkorn KR, Haley ST, Dyhrman ST. Coordinated gene expression between Trichodesmium and its microbiome over day-night cycles in the North Pacific Subtropical Gyre. ISME J. 2018;12:997–1007.
Google Scholar
Tang W, Cerdán-García E, Berthelot H, Polyviou D, Wang S, Baylay A, et al. New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods. ISME J. 2020;14:2514–26.
Google Scholar
Zehr JP, McReynolds LA. Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol. 1989;55:2522–6.
Google Scholar
Zani S, Mellon MT, Collier JL, Zehr JP. Expression of nifH genes in natural microbial assemblages in Lake George, New York, detected by reverse transcriptase PCR. Appl Environ Microbiol. 2000;66:3119–24.
Google Scholar
Turk KA, Rees AP, Zehr JP, Pereira N, Swift P, Shelley R, et al. Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic. ISME J. 2011;5:1201–12.
Google Scholar
Hitchen J, Sooknanan R, Khanna A. ScriptSeq V2 Library Preparation Method: A Rapid and Efficient Method for Preparing Directional RNA-Seq Libraries. J Biomol Tech. 2012;23:S33–S34.
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet J. 2011;17:10–2.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. MetaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Google Scholar
Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using. Microbiome. 2014;2:4904–9.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Google Scholar
Hyatt D, Chen GL, LoCascio PF, Land ML, Frank W, Larimer LJH. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:1–11.
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30:1575–84.
Google Scholar
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42:D206–14.
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. correspondence QIIME allows analysis of high- throughput community sequencing data Intensity normalization improves color calling in SOLiD sequencing. Nat Publ Gr. 2010;7:335–6.
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Google Scholar
Edgar RC. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.
Google Scholar
Westreich ST, Treiber ML, Mills DA, Korf I, Lemay DG. SAMSA2: a standalone metatranscriptome analysis pipeline. BMC Bioinforma. 2018;19:1–11.
Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Google Scholar
Kopylova E, Noé L, Touzet H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 2012;28:3211–7.
Google Scholar
Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: A fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 2014;30:614–20.
Google Scholar
Tatusova T, Ciufo S, Fedorov B, O’Neill K, Tolstoy I. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res. 2014;42:D553–9.
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37:907–15.
Google Scholar
Liao Y, Smyth GK, Shi W. FeatureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics 2014;30:923–30.
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:1–21.
Wu S, Mi T, Zhen Y, Yu K, Wang F, Yu Z. A Rise in ROS and EPS Production: New Insights into the Trichodesmium erythraeum Response to Ocean Acidification. J Phycol. 2021;57:172–82.
Google Scholar
Sedwick PN, Church TM, Bowie AR, Marsay CM, Ussher SJ, Achilles KM, et al. Iron in the Sargasso Sea (Bermuda Atlantic Time-series Study region) during summer: Eolian imprint, spatiotemporal variability, and ecological implications. Global Biogeochem Cycles. 2005;19:GB4006.
Hatta M, Measures CI, Wu J, Roshan S, Fitzsimmons JN, Sedwick P, et al. An overview of dissolved Fe and Mn distributions during the 2010-2011 U.S. GEOTRACES north Atlantic cruises: GEOTRACES GA03. Deep Res Part II Top Stud Oceanogr. 2015;116:117–29.
Google Scholar
Mahaffey C, Reynolds S, Davis CE, Lohan MC. Alkaline phosphatase activity in the subtropical ocean: insights from nutrient, dust and trace metal addition experiments. Front Mar Sci. 2014;1:73.
Church MJ, Mahaffey C, Letelier RM, Lukas R, Zehr JP, Karl DM. Physical forcing of nitrogen fixation and diazotroph community structure in the North Pacific subtropical gyre. Global Biogeochem Cycles. 2009;23:GB2020.
Zehr JP, Capone DG. Changing perspectives in marine nitrogen fixation. Science. 2020;368:eaay9514.
Benavides M, Moisander PH, Daley MC, Bode A, Arístegui J. Longitudinal variability of diazotroph abundances in the subtropical North Atlantic Ocean. J Plankton Res. 2016;38:662–72.
Google Scholar
Luo YW, Doney SC, Anderson LA, Benavides M, Berman-Frank I, Bode A, et al. Database of diazotrophs in global ocean: Abundance, biomass and nitrogen fixation rates. Earth Syst Sci Data. 2012;4:47–73.
Moisander PH, Beinart RA, Voss M, Zehr JP. Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon. ISME J. 2008;2:954–67.
Google Scholar
Moisander PH, Serros T, Paerl RW, Beinart RA, Zehr JP. Gammaproteobacterial diazotrophs and nifH gene expression in surface waters of the South Pacific Ocean. ISME J 2014;8:1962–73.
Google Scholar
Robidart JC, Church MJ, Ryan JP, et al. Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean. ISME J. 2014;8:1175–85.
Google Scholar
Stenegren M, Caputo A, Berg C, Bonnet S, Foster R. Distribution and drivers of symbiotic and free-living diazotrophic cyanobacteria in the western tropical South Pacific. Biogeosciences 2018;15:1559–78.
Google Scholar
Langlois R, Großkopf T, Mills M, Takeda S, LaRoche J. Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, γ-Proteobacterial nifH Phylotype. PLoS ONE. 2015;10:e0128912.
Google Scholar
Ratten J-M, LaRoche J, Desai DK, et al. Sources of iron and phosphate affect the distribution of diazotrophs in the North Atlantic. Deep Sea Res Part II: Topical Stud Oceanogr. 2015;116:332–41.
Google Scholar
Voss, M, Croot, P, Lochte, K, Mills, M, Peeken, I. Patterns of nitrogen fixation along 10°N in the tropical Atlantic. Geophys Res Lett. 2004;31:L23S09.
Bibby TS, Nield J, Barber J. Iron deficiency induces the formation of an antenna ring around trimeric photosystem I in cyanobacteria. Nature. 2001;412:743–5.
Richier S, Macey AI, Pratt NJ, Honey DJ, Moore CM, Bibby TS. Abundances of iron-binding photosynthetic and nitrogen-fixing proteins of Trichodesmium both in culture and in situ from the North Atlantic. PLoS ONE. 2012;7:e35571.
Google Scholar
Keren N, Aurora R, Pakrasi HB. Critical roles of bacterioferritins in iron storage and proliferation of cyanobacteria. Plant Physiol. 2004;135:1666–73.
Google Scholar
González A, Bes MT, Valladares A, Peleato ML, Fillat MF. FurA is the master regulator of iron homeostasis and modulates the expression of tetrapyrrole biosynthesis genes in Anabaena sp. PCC 7120. Environ Microbiol. 2012;14:3175–87.
Google Scholar
Sebastian M, Ammerman JW. The alkaline phosphatase PhoX is more widely distributed in marine bacteria than the classical PhoA. ISME J. 2009;3:563–72.
Google Scholar
Browning TJ, Achterberg EP, Yong JC, Rapp I, Utermann C, Engel A, et al. Iron limitation of microbial phosphorus acquisition in the tropical North Atlantic. Nat Commun. 2017;8:1–7.
Proudfoot M, Kuznetsova E, Brown G, Rao NN, Kitagawa M, Mori H, et al. General enzymatic screens identify three new nucleotidases in Escherichia coli: Biochemical characterization of SurE, YfbR, and YjjG. J Biol Chem. 2004;279:54687–94.
Google Scholar
Orchard ED, Benitez-Nelson CR, Pellechia PJ, Lomas MW, Dyhrman ST. Polyphosphate in Trichodesmium from the low-phosphorus Sargasso Sea. Limnol Oceanogr. 2010;55:2161–9.
Google Scholar
Berman-Frank I, Cullen JT, Shaked Y, Sherrell RM, Falkowski PG. Iron availability, cellular iron quotas, and nitrogen fixation in Trichodesmium. Limnol Oceanogr. 2001;46:1249–60.
Google Scholar
Schoffman H, Keren N. Function of the IsiA pigment–protein complex in vivo. Photosynth Res. 2019;141:343–53.
Google Scholar
Küpper H, Ferimazova N, Šetlík I, Berman-Frank I. Traffic lights in Trichodesmium. Regulation of photosynthesis for nitrogen fixation studied by chlorophyll fluorescence kinetic microscopy. Plant Physiol. 2004;135:2120–33.
Google Scholar
Behrenfeld MJ, Milligan AJ. Photophysiological expressions of iron stress in phytoplankton. Ann Rev Mar Sci. 2013;5:217–46.
Google Scholar
Ho TY. Nickel limitation of nitrogen fixation in Trichodesmium. Limnol Oceanogr. 2013;58:112–20.
Google Scholar
Tilman D. Resources: a graphical‐mechanistic approach to competition and predation. Am Nat. 1980;116:362–3.
Mills MM, Ridame C, Davey M, La Roche J, Geider RJ. Iron and phosphorus co-limit nitrogen fixation in the eastern tropical North Atlantic. Nature 2004;429:292–4.
Google Scholar
Saito MA, McIlvin MR, Moran DM, Goepfert TJ, DiTullio GR, Post AF, et al. Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers. Science 2014;345:1173–7.
Google Scholar
NASA Goddard Space Flight Center, Ocean Ecology Laboratory, Ocean Biology Processing Group. Moderate-resolution Imaging Spectroradiometer (MODIS) Aqua Chlorophyll Data. MODIS-Aqua Level 3 Mapped Chlorophyll Data Version R2018.0. NASA OB.DAAC, Greenbelt, MD, USA. Published online 2017.
Source: Ecology - nature.com
