Iron and phosphorus co-limit nitrogen fixation in the eastern tropical North Atlantic

The role of iron in enhancing phytoplankton productivity in high nutrient, low chlorophyll oceanic regions was demonstrated first through iron-addition bioassay experiments1 and subsequently confirmed by large-scale iron fertilization experiments2. Iron supply has been hypothesized to limit nitrogen fixation and hence oceanic primary productivity on geological timescales3, providing an alternative to phosphorus as the ultimate limiting nutrient4. Oceanographic observations have been interpreted both to confirm and refute this hypothesis5, 6, but direct experimental evidence is lacking7. We conducted experiments to test this hypothesis during the Meteor 55 cruise to the tropical North Atlantic. This region is rich in diazotrophs8 and strongly impacted by Saharan dust input9. Here we show that community primary productivity was nitrogen-limited, and that nitrogen fixation was co-limited by iron and phosphorus. Saharan dust addition stimulated nitrogen fixation, presumably by supplying both iron and phosphorus10, 11. Our results support the hypothesis that aeolian mineral dust deposition promotes nitrogen fixation in the eastern tropical North Atlantic

Relative amino acid composition signatures of organisms and environments

BACKGROUND: Identifying organism-environment interactions at the molecular level is crucial to understanding how organisms adapt to and change the chemical and molecular landscape of their habitats. In this work we investigated whether relative amino acid compositions could be used as a molecular signature of an environment and whether such a signature could also be observed at the level of the cellular amino acid composition of the microorganisms that inhabit that environment. METHODOLOGIES/PRINCIPAL FINDINGS: To address these questions we collected and analyzed environmental amino acid determinations from the literature, and estimated from complete genomic sequences the global relative amino acid abundances of organisms that are cognate to the different types of environment. Environmental relative amino acid abundances clustered into broad groups (ocean waters, host-associated environments, grass land environments, sandy soils and sediments, and forest soils), indicating the presence of amino acid signatures specific for each environment. These signatures correlate to those found in organisms. Nevertheless, relative amino acid abundance of organisms was more influenced by GC content than habitat or phylogeny. CONCLUSIONS: Our results suggest that relative amino acid composition can be used as a signature of an environment. In addition, we observed that the relative amino acid composition of organisms is not highly determined by environment, reinforcing previous studies that find GC content to be the major factor correlating to amino acid composition in living organisms.AM was supported by Fundação para a Ciência e a Tecnologia, Portugal, through the postdoctoral grant SFRH/BPD/72256/2010. RA was partially supported by the Ministerio de Ciencia e Innovación (Spain) through grant BFU2010-17704, and by the Generalitat de Catalunya through a grant for research group 2009SGR809. MAS was supported in part by a grant from the US Public Health Service (RO1-GM30054). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Authors wish to thank Albert Sorribas, Enrique Herrero and Ester Vilaprinyo for critical reading of the manuscript and Ester Vilaprinyo for assistance with Wolfram Mathematica software.publishe

Abundances of Iron-Binding Photosynthetic and Nitrogen-Fixing Proteins of Trichodesmium Both in Culture and In Situ from the North Atlantic

Marine cyanobacteria of the genus Trichodesmium occur throughout the oligotrophic tropical and subtropical oceans, where they can dominate the diazotrophic community in regions with high inputs of the trace metal iron (Fe). Iron is necessary for the functionality of enzymes involved in the processes of both photosynthesis and nitrogen fixation. We combined laboratory and field-based quantifications of the absolute concentrations of key enzymes involved in both photosynthesis and nitrogen fixation to determine how Trichodesmium allocates resources to these processes. We determined that protein level responses of Trichodesmium to iron-starvation involve down-regulation of the nitrogen fixation apparatus. In contrast, the photosynthetic apparatus is largely maintained, although re-arrangements do occur, including accumulation of the iron-stress-induced chlorophyll-binding protein IsiA. Data from natural populations of Trichodesmium spp. collected in the North Atlantic demonstrated a protein profile similar to iron-starved Trichodesmium in culture, suggestive of acclimation towards a minimal iron requirement even within an oceanic region receiving a high iron-flux. Estimates of cellular metabolic iron requirements are consistent with the availability of this trace metal playing a major role in restricting the biomass and activity of Trichodesmium throughout much of the subtropical ocean

Alternatives to vitamin B 1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages

Vitamin B 1 (thiamine pyrophosphate, TPP) is essential to all life but scarce in ocean surface waters. In many bacteria and a few eukaryotic groups thiamine biosynthesis genes are controlled by metabolite-sensing mRNA-based gene regulators known as riboswitches. Using available genome sequences and transcriptomes generated from ecologically important marine phytoplankton, we identified 31 new eukaryotic riboswitches. These were found in alveolate, cryptophyte, haptophyte and rhizarian phytoplankton as well as taxa from two lineages previously known to have riboswitches (green algae and stramenopiles). The predicted secondary structures bear hallmarks of TPP-sensing riboswitches. Surprisingly, most of the identified riboswitches are affiliated with genes of unknown function, rather than characterized thiamine biosynthesis genes. Using qPCR and growth experiments involving two prasinophyte algae, we show that expression of these genes increases significantly under vitamin B 1 -deplete conditions relative to controls. Pathway analyses show that several algae harboring the uncharacterized genes lack one or more enzymes in the known TPP biosynthesis pathway. We demonstrate that one such alga, the major primary producer Emiliania huxleyi, grows on 4-amino-5-hydroxymethyl-2-methylpyrimidine (a thiamine precursor moiety) alone, although long thought dependent on exogenous sources of thiamine. Thus, overall, we have identified riboswitches in major eukaryotic lineages not known to undergo this form of gene regulation. In these phytoplankton groups, riboswitches are often affiliated with widespread thiamine-responsive genes with as yet uncertain roles in TPP pathways. Further, taxa with 'incomplete' TPP biosynthesis pathways do not necessarily require exogenous vitamin B 1, making vitamin control of phytoplankton blooms more complex than the current paradigm suggests. © 2014 International Society for Microbial Ecology. All rights reserved

Large-scale distribution of Atlantic nitrogen fixation controlled by iron availability

Oceanic fixed-nitrogen concentrations are controlled by the balance between nitrogen fixation and denitrification1, 2, 3, 4. A number of factors, including iron limitation5, 6, 7, can restrict nitrogen fixation, introducing the potential for decoupling of nitrogen inputs and losses2, 5, 8. Such decoupling could significantly affect the oceanic fixed-nitrogen inventory and consequently the biological component of ocean carbon storage and hence air–sea partitioning of carbon dioxide2, 5, 8, 9. However, the extent to which nutrients limit nitrogen fixation in the global ocean is uncertain. Here, we examined rates of nitrogen fixation and nutrient concentrations in the surface waters of the Atlantic Ocean along a north–south 10,000 km transect during October and November 2005. We show that rates of nitrogen fixation were markedly higher in the North Atlantic compared with the South Atlantic Ocean. Across the two basins, nitrogen fixation was positively correlated with dissolved iron and negatively correlated with dissolved phosphorus concentrations. We conclude that inter-basin differences in nitrogen fixation are controlled by iron supply rather than phosphorus availability. Analysis of the nutrient content of deep waters suggests that the fixed nitrogen enters North Atlantic Deep Water. Our study thus supports the suggestion that iron significantly influences nitrogen fixation5, and that subsequent interactions with ocean circulation patterns contribute to the decoupling of nitrogen fixation and loss2, 4, 8

Distribution and diversity of phytate-mineralizing bacteria

Phytate, the most abundant organic phosphorus compound in soil, dominates the biotic phosphorus input from terrestrial runoffs into aquatic systems. Microbial mineralization of phytate by phytases is a key process for recycling phosphorus in the biosphere. Bioinformatic studies were carried out on microbial genomes and environmental metagenomes in the NCBI and the CAMERA databases to determine the distribution of the four known classes of phytase in the microbial world. The Β-propeller phytase is the only phytase family that can be found in aquatic environments and it is also distributed in soil and plant bacteria. The Β-propeller phytase-like genes can be classified into several subgroups based on their domain structure and the positions of their conserved cysteine residues. Analysis of the genetic contexts of these subgroups showed that Β-propeller phytase genes exist either as an independent gene or are closely associated with a TonB-dependent receptor-like gene in operons, suggesting that these two genes are functionally linked and thus may play an important role in the cycles of phosphorus and iron. Our work suggests that Β-propeller phytases play a major role in phytate-phosphorus cycling in both soil and aquatic microbial communities. © 2007 International Society for Microbial Ecology All rights reserved.link_to_subscribed_fulltex

Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity

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