Mak A. Saito

The bioinorganic chemistry of the ancient ocean: the co-evolution of cyanobacterial metal requirements and biogeochemical cycles at the Archean-Proterozoic boundary?

Abstract Recent evidence from the sulfur isotopic record indicates a transition ∼2.5 billion years ago from an ocean chemistry first dominated by iron and then by sulfide. It has been hypothesized that the selection of metal centers in metalloenzymes has been influenced by the availability of metals through geological time, in particular as a result of large differences in the solubility of metals-sulfides. In this study, we examine the trace metal requirements and sensitivities of marine cyanobacteria and use recent stability constants to model the abundance and chemical speciation of metals across this chemical transition ∼2.5 billion years ago. Two major results are reported here: (1) the marine cyanobacterial species studied thus far show trace metal preferences and sensitivities that are consistent with their evolution in a sulfidic marine environment, and (2) in an ancient ocean dominated by high fluxes and concentrations of iron, the relative availability of trace metals would have been similar to that of a sulfidic system—Fe>Mn, Ni, Co≫Cd, Zn, Cu—as a result of the formation of dissolved sulfide complexes. Thus, the formation of strong aqueous metal-sulfide complexes was likely as important as the precipitation of minerals in influencing the selection of metals in biology. These results suggest that marine biogeochemical cycles and marine bioinorganic chemistry have co-evolved, and that the evidence for this co-evolution has been preserved in the physiology and genomes of modern descendants of the early cyanobacteria.

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics.

Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium- and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.

The Transcriptome and Proteome of the Diatom Thalassiosira pseudonana Reveal a Diverse Phosphorus Stress Response

Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem function in the ocean. Diatoms are an abundant class of marine phytoplankton that are responsible for significant amounts of primary production. With the control they exert on the oceanic carbon cycle, there have been a number of studies focused on how diatoms respond to limiting macro and micronutrients such as iron and nitrogen. However, diatom physiological responses to P deficiency are poorly understood. Here, we couple deep sequencing of transcript tags and quantitative proteomics to analyze the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. A total of 318 transcripts were differentially regulated with a false discovery rate of <0.05, and a total of 136 proteins were differentially abundant (p<0.05). Significant changes in the abundance of transcripts and proteins were observed and coordinated for multiple biochemical pathways, including glycolysis and translation. Patterns in transcript and protein abundance were also linked to physiological changes in cellular P distributions, and enzyme activities. These data demonstrate that diatom P deficiency results in changes in cellular P allocation through polyphosphate production, increased P transport, a switch to utilization of dissolved organic P through increased production of metalloenzymes, and a remodeling of the cell surface through production of sulfolipids. Together, these findings reveal that T. pseudonana has evolved a sophisticated response to P deficiency involving multiple biochemical strategies that are likely critical to its ability to respond to variations in environmental P availability.

Complexation of cobalt by natural organic ligands in the Sargasso Sea as determined by a new high-sensitivity electrochemical cobalt speciation method suitable for open ocean work

A high-sensitivity cobalt speciation method was developed and applied to a profile in the North Atlantic. Method development included examining the redox chemistry of the analytical system and calibrating the electroactive cobalt ligand dimethylglyoxime (DMG) using EDTA as a model ligand. The method was applied to a depth profile at the Bermuda Atlantic Time Series Station (BATS) during a September 1999 cruise. Total dissolved cobalt, measured using adsorptive cathodic stripping voltammetry (ACSV) on ultraviolet light irradiated samples, revealed a nutrient-like profile for cobalt. Co speciation, measured using CLE–ACSV (competitive ligand exchange), showed a cobalt binding ligand concentration that was similar to that of total cobalt throughout the profile. An excess of ligand was observed in the chlorophyll maximum where Prochlorococcus and Synechococcus numbers were highest. A conditional stability constant for CoHDMG2 was measured to be logKCoHDMG2cond=11.5±0.3 at pH 8.0. A pH dependence for KCoHDMG2cond was observed and is consistent with model calculations based on the protonation constants for H2DMG. The conditional stability constant for CoL was determined to be logKCoLcond=16.3±0.9 and total ligand concentrations varied from 9 to 83 pM as calculated by a one-ligand non-linear fit using the Levenberg–Marquardt algorithm. Alternate interpretations of the data are discussed, including the possibility for an underestimation of ligand concentrations and stability constants caused by the existence of Co(III) ligands, and kinetic and thermodynamic competition for natural ligands by Ni and Co(II).

Iron conservation by reduction of metalloenzyme inventories in the marine diazotroph Crocosphaera watsonii

The marine nitrogen fixing microorganisms (diazotrophs) are a major source of nitrogen to open ocean ecosystems and are predicted to be limited by iron in most marine environments. Here we use global and targeted proteomic analyses on a key unicellular marine diazotroph Crocosphaera watsonii to reveal large scale diel changes in its proteome, including substantial variations in concentrations of iron metalloproteins involved in nitrogen fixation and photosynthesis, as well as nocturnal flavodoxin production. The daily synthesis and degradation of enzymes in coordination with their utilization results in a lowered cellular metalloenzyme inventory that requires ∼40% less iron than if these enzymes were maintained throughout the diel cycle. This strategy is energetically expensive, but appears to serve as an important adaptation for confronting the iron scarcity of the open oceans. A global numerical model of ocean circulation, biogeochemistry and ecosystems suggests that Crocosphaera’s ability to reduce its iron-metalloenzyme inventory provides two advantages: It allows Crocosphaera to inhabit regions lower in iron and allows the same iron supply to support higher Crocosphaera biomass and nitrogen fixation than if they did not have this reduced iron requirement.

8.5 – Marine Bioinorganic Chemistry: The Role of Trace Metals in the Oceanic Cycles of Major Nutrients

The bulk of living biomass is chiefly made up of only a dozen ‘major’ elements whose proportions vary within a relatively narrow range in most organisms. A number of trace elements, particularly first row transition metals are also ‘essential’ for the growth of organisms. We begin this chapter by discussing what we know of the concentrations of trace elements in marine microorganisms and of the relevant mechanisms and kinetics of trace-metal uptake. We then review the biochemical role of trace elements in the marine cycles of carbon, nitrogen, phosphorus, and silicon. Using this information, we examine the evidence, emanating from both laboratory cultures and field measurements, relevant to the mechanisms and the extent of control by trace metals of marine biogeochemical cycles. Before concluding with a wistful glimpse of the future of marine bioinorganic chemistry we discuss briefly some paleoceanographic aspects of this new field: how the chemistry of the planet ‘Earth’ – particularly the concentrations of trace elements in the oceans – has evolved since its origin, chiefly as a result of biological processes and how the evolution of life has, in turn, been affected by the availability of essential trace elements.

Temporal and spatial variability of cobalt in the Atlantic Ocean

Abstract The spatial and temporal variability of cobalt in the Atlantic Ocean was investigated by means of adsorptive cathodic stripping voltammetry. A vertical profile of total dissolved cobalt at the Bermuda Atlantic Time Series station ranged from 17 to 73 pM and displayed surface depletion indicative of biological utilization. This profile when compared with a cobalt profile from the northeast Pacific shows no increase in deep-water concentrations with thermohaline circulation through the deep ocean basins. Moreover, the middepth maximum observed in northeast Pacific profiles is not present in the Sargasso Sea, perhaps because of the lack of cobalt scavenging by particulate manganese oxides in surface waters and to the absence of a suboxic oxygen minimum zone, which, if present, could dissolve the manganese oxides. Total dissolved cobalt measurements were also made on a surface transect from the Sargasso Sea to coastal Massachusetts, USA, and on time-series samples from the Moored In Situ Trace Element Serial Sampler. Dissolved cobalt on this transect correlated strongly with salinity ( r 2 = 0.93) and ranged from 19 to 133 pM, indicating mixing of cobalt from shelf waters into the Sargasso Sea. Time-series samples near Bermuda did not show an obvious response to the summer maximum in aeolian dust deposition, with an annual average of 20 ± 10 pM at 40- to 47-m depths. By use of this annual value and particulate cobalt data from the literature, 100-m surface-water residence times were calculated to be as low as 0.32 yr for cobalt. Several sharp decreases in cobalt were observed in the time series that occurred simultaneously with a shallowing of the thermocline depth. These decreases could be caused by nutrient drawdown associated with higher productivity mesoscale eddy events. A west-east surface transect across the South Atlantic showed high cobalt concentrations at the boundaries of the transect and low concentrations in the center despite the high precipitation rates in the intertropical convergence zone. Phosphate measurements showed the similar trends as the total cobalt transect. A regression of cobalt vs. phosphate reveals a slope that is an order of magnitude higher than that of the northeast Pacific and that is similar to the slopes observed for zinc vs. phosphate in the Pacific.

Cobalt and nickel in the Peru upwelling region: A major flux of labile cobalt utilized as a micronutrient

behaved as a micronutrient with correlations with major nutrients (nitrate, phosphate; r 2 = 0.90, 0.96) until depleted to � 50 pM of strongly complexed cobalt. Co:P utilization ratios were an order of magnitude higher than in the North Pacific, comparable to utilization rates of zinc in other oceanic regions. Cobalt speciation measurements showed that available cobalt decreased over 4 orders of magnitude in this region, with shifts in phytoplankton assemblages occurring at transitions between labile and nonlabile cobalt. Only small changes in total dissolved nickel were observed, and nickel was present in a labile chemical form throughout the region. In the Peru upwelling region, cobalt uptake was highest at the surface and decreased with depth, suggesting phytoplankton uptake was a more important removal mechanism than co-oxidation with microbial manganese oxidation. These findings show the importance of cobalt as a micronutrient and that cobalt scarcity and speciation may be important in influencing phytoplankton species composition in this economically important environment. INDEX TERMS: 1030 Geochemistry: Geochemical cycles (0330); 1050 Geochemistry: Marine geochemistry (4835, 4850); 1065 Geochemistry: Trace elements (3670); 4279 Oceanography: General: Upwelling and convergences;

Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability

Prochlorococcus contributes significantly to ocean primary productivity. The link between primary productivity and iron in specific ocean regions is well established and iron limitation of Prochlorococcus cell division rates in these regions has been shown. However, the extent of ecotypic variation in iron metabolism among Prochlorococcus and the molecular basis for differences is not understood. Here, we examine the growth and transcriptional response of Prochlorococcus strains, MED4 and MIT9313, to changing iron concentrations. During steady state, MIT9313 sustains growth at an order-of-magnitude lower iron concentration than MED4. To explore this difference, we measured the whole-genome transcriptional response of each strain to abrupt iron starvation and rescue. Only four of the 1159 orthologs of MED4 and MIT9313 were differentially expressed in response to iron in both strains. However, in each strain, the expression of over a hundred additional genes changed, many of which are in labile genomic regions, suggesting a role for lateral gene transfer in establishing diversity of iron metabolism among Prochlorococcus. Furthermore, we found that MED4 lacks three genes near the iron-deficiency-induced gene (idiA) that are present and induced by iron stress in MIT9313. These genes are interesting targets for studying the adaptation of natural Prochlorococcus assemblages to local iron conditions as they show more diversity than other genomic regions in environmental metagenomic databases.

Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

Significance Thaumarchaeota are among the most abundant microbial cells in the ocean, but to date, complete genome sequences for marine Thaumarchaeota are lacking. Here, we report the 1.23-Mbp genome of the pelagic ammonia-oxidizing thaumarchaeon “Candidatus Nitrosopelagicus brevis” str. CN25. We present the first proteomic data, to our knowledge, from this phylum, which show a high proportion of proteins translated in oligotrophic conditions. Metagenomic fragment recruitment using data from the open ocean indicate the ubiquitous presence of Ca. N. brevis-like sequences in the surface ocean and suggest Ca. N. brevis as a model system for understanding the ecology and evolution of pelagic marine Thaumarchaeota. Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name “Candidatus Nitrosopelagicus brevis” str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.