Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean

www.nature.com/ismej ARTICLE OPEN Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean ✉ Shane L. Hogle 1,2 , Thomas Hackl 1,3, Randelle M. Bundy 4, Jiwoon Park4, Brandon Satinsky1, Teppo Hiltunen ✉ 1,5 Steven Biller , Paul M. Berube 1 and Sallie W. Chisholm 1,6 2 , © The Author(s) 2022 1234567890();,: Prochlorococcus and Synechococcus are the most abundant photosynthesizing organisms in the oceans. Gene content variation among picocyanobacterial populations in separate ocean basins often mirrors the selective pressures imposed by the region’s distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread in Synechococcus and low-light adapted Prochlorococcus populations from deep chlorophyll maximum layers of iron-depleted regions of the oligotrophic Pacific and S. Atlantic oceans: Prochlorococcus siderophore consumers were absent in the N. Atlantic ocean (higher new iron flux) but constituted up to half of all Prochlorococcus genomes from metagenomes in the N. Pacific (lower new iron flux). Picocyanobacterial siderophore consumers, like many other bacteria with this trait, also lack siderophore biosynthesis genes indicating that they scavenge exogenous siderophores from seawater. Statistical modeling suggests that the capacity for siderophore uptake is endemic to remote ocean regions where atmospheric iron fluxes are the smallest, especially at deep chlorophyll maximum and primary nitrite maximum layers. We argue that abundant siderophore consumers at these two common oceanographic features could be a symptom of wider community iron stress, consistent with prior hypotheses. Our results provide a clear example of iron as a selective force driving the evolution of marine picocyanobacteria. The ISME Journal; https://doi.org/10.1038/s41396-022-01215-w INTRODUCTION Prochlorococcus and its sister lineage Synechococcus are some of the smallest known photosynthetic organisms and are among the most numerically abundant life forms on the planet. These marine picocyanobacteria are unicellular, free-living, geographically widespread, and highly abundant in the oligotrophic subtropical/ tropical ocean, often comprising half of the total chlorophyll [1]. Prochlorococcus and Synechococcus account for approximately 25% of global marine net primary productivity [2], making the picocyanobacteria key drivers of marine biogeochemical cycles [3]. Light gradients drive the vertical distribution of Prochlorococcus with low-light (LL) adapted clades occupying the deeper parts of the euphotic zone, and high-light (HL) adapted clades near the surface. This broad light-driven ecological and evolutionary division is further partitioned into mostly coherent genomic clusters (clades), each with distinct ecological and physiological properties [4]. Synechococcus clades partition along temperature gradients in the sea, but lack clear association with light and depth [5]. At the finest scale of diversity, picocyanobacterial clades further separate into distinct sympatric subpopulations, which share the majority of their genes but also contain segments of unique genetic material [6]. These variable genomic regions encode functionally adaptive traits that tune each population’s physiology to its local environment. Iron (Fe) is a crucial micronutrient for marine phytoplankton due to its central role as an enzyme cofactor in cellular processes, including respiration and photosynthesis. As a result, the concentrations and chemical forms of Fe influence global carbon cycle dynamics [7]. Dissolved Fe (dFe) is scarce in much of the ocean and is mostly (>99%) complexed with organic chelating ligands that solubilize and stabilize the ions in solution [8]. Concentrations of these ligands quickly increase in response to Fe fertilization events, which implies that they are actively produced by members of the microbial community [9]. It is challenging to determine the chemical structure of these ligands [10], so their abundance and stability coefficients (a measure of how “strongly” the ligand binds Fe) are typically inferred electrochemically [11]. Many electrochemical studies operationally partition the ligand pool into weak (L2) and strong (L1) binding classes. The weak L2 class includes humic-like substances, exopolysaccharides, and undefined colloids. The strong L1 class includes siderophores, small Fe-binding molecules that microbes produce during periods of Fe starvation, but it is not clear how much of the L1 class are genuine siderophores. Under some conditions, siderophores 1 Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. 2Department of Biology, University of Turku, Turku, Finland. Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands. 4School of Oceanography, University of Washington, Seattle, WA, USA. 5 Department of Biological Sciences, Wellesley College, Wellesley, MA, USA. 6Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. ✉email: shane.hogle@utu.fi; 3 Received: 14 November 2021 Revised: 8 February 2022 Accepted: 14 February 2022 S.L. Hogle et al. 2 appear to account for much of the strong L1 ligand fraction in seawater [12, 13]. There are two primary mechanisms by which marine microbes extract dFe bound to the organic ligands in the ocean. First, dFe can dissociate from organic ligands in the extracellular environment (via kinetic control, photodegradation, or cell surface reductases) and is imported across the outer membrane as an unbound, inorganic ion [14]. Second, whole Fe-ligand complexes can be directly translocated across cell membranes (Supplementary Fig. S1) [15]. Direct uptake pathways are prevalent in fastgrowing copiotrophic marine bacteria with large genomes but absent in free-living marine bacteria with streamlined genomes such as Prochlorococcus, Synechococcus, and SAR11 [16, 17]. In these organisms, selection favors the minimization of genome size and metabolic complexity over the versatility of maintaining multiple direct Fe uptake pathways [16]. A decade ago, it was believed that marine picocyanobacteria fulfilled their Fe requirements only via the dissociation mechanism while relying upon a single inner membrane Fe(III) ATP binding cassette transporter [18, 19]. Prior work also showed that Prochlorococcus and marine Synechococcus isolate genomes lacked the genes necessary for siderophore biosynthesis and uptake [19]. This image changed when putative siderophore uptake gene clusters were identified from a handful of genomes from Prochlorococcus surface clades HLII and HLIV collected from remote, low-Fe regions of the global ocean [17, 20]. This exciting finding suggested that some Prochlorococcus populations had adapted to Fe scarcity by (...truncated)