Primary production in the Ross Sea, one of the most productive areas in the Southern Ocean, has previously been shown to be seasonally limited by iron. In two of three bottle incubation experiments ...conducted in the austral summer, significantly higher chlorophyll a (Chl a) concentrations were measured upon the addition of iron and B12, relative to iron additions alone. Initial bacterial abundances were significantly lower in the two experiments that showed phytoplankton stimulation upon addition of B12 and iron relative to the experiment that did not show this stimulation. This is consistent with the hypothesis that the bacteria and archaea in the upper water column are an important source of B12 to marine phytoplankton. The addition of iron alone increased the growth of Phaeocystis antarctica relative to diatoms, whereas in an experiment where iron and B12 stimulated total phytoplankton growth, the diatom Pseudonitzschia subcurvata went from comprising approximately 70% of the phytoplankton community to over 90%. Cobalt additions, with and without iron, did not alter Chl a biomass relative to controls and iron additions alone in the Ross Sea. Iron and vitamin B12 plus iron treatments caused reductions in the DMSP (dimethyl sulfoniopropionate):Chl a ratio relative to the control and B12 treatments, consistent with the notion of an antioxidant function for DMSP. These results demonstrate the importance of a vitamin to phytoplankton growth and community composition in the marine environment.
Atmospheric deposition is a major source of trace metals in marine surface waters and supplies vital micronutrients to phytoplankton, yet measured aerosol trace metal solubility values are ...operationally defined, and there are relatively few multi-element studies on aerosol-metal solubility in seawater. Here we measure the solubility of aluminum (Al), cadmium (Cd), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) from natural aerosol samples in seawater over a 7 days period to (1) evaluate the role of extraction time in trace metal dissolution behavior and (2) explore how the individual dissolution patterns could influence biota. Dissolution behavior occurs over a continuum ranging from rapid dissolution, in which the majority of soluble metal dissolved immediately upon seawater exposure (Cd and Co in our samples), to gradual dissolution, where metals dissolved slowly over time (Zn, Mn, Cu, and Al in our samples). Additionally, dissolution affected by interactions with particles was observed in which a decline in soluble metal concentration over time occurred (Fe and Pb in our samples). Natural variability in aerosol chemistry between samples can cause metals to display different dissolution kinetics in different samples, and this was particularly evident for Ni, for which samples showed a broad range of dissolution rates. The elemental molar ratio of metals in the bulk aerosols was 23,189Fe: 22,651Al: 445Mn: 348Zn: 71Cu: 48Ni: 23Pb: 9Co: 1Cd, whereas the seawater soluble molar ratio after 7 days of leaching was 11Fe: 620Al: 205Mn: 240Zn: 20Cu: 14Ni: 9Pb: 2Co: 1Cd. The different kinetics and ratios of aerosol metal dissolution have implications for phytoplankton nutrition, and highlight the need for unified extraction protocols that simulate aerosol metal dissolution in the surface ocean.
Ocean microbial communities are important contributors to the global biogeochemical reactions that sustain life on Earth. The factors controlling these communities are being increasingly explored ...using metatranscriptomic and metaproteomic environmental biomarkers. Using published proteomes and transcriptomes from the abundant colony-forming cyanobacterium Trichodesmium (strain IMS101) grown under varying Fe and/or P limitation in low and high CO2, we observed robust correlations of stress-induced proteins and RNAs (i.e., involved in transport and homeostasis) that yield useful information on the nutrient status under low and/or high CO2. Conversely, transcriptional and translational correlations of many other central metabolism pathways exhibit broad discordance. A cellular RNA and protein production/degradation model demonstrates how biomolecules with small initial inventories, such as environmentally responsive proteins, achieve large increases in fold-change units as opposed to those with a higher basal expression and inventory such as metabolic systems. Microbial cells, due to their immersion in the environment, tend to show large adaptive responses in both RNA and protein that result in transcript–protein correlations. These observations and model results demonstrate multi-omic coherence for environmental biomarkers and provide the underlying mechanism for those observations, supporting the promise for global application in detecting responses to environmental stimuli in a changing ocean.
Trichodesmium is a globally important marine microbe that provides fixed
nitrogen (N) to otherwise N-limited ecosystems. In nature, nitrogen fixation
is likely regulated by iron or phosphate ...availability, but the extent and
interaction of these controls are unclear. From metaproteomics analyses
using established protein biomarkers for nutrient stress, we found
that iron–phosphate co-stress is the norm rather than the exception for Trichodesmium colonies in the
North Atlantic Ocean. Counterintuitively, the nitrogenase enzyme was more
abundant under co-stress as opposed to single nutrient stress. This is
consistent with the idea that Trichodesmium has a specific physiological state during
nutrient co-stress. Organic nitrogen uptake was observed and occurred
simultaneously with nitrogen fixation. The quantification of the phosphate ABC
transporter PstA combined with a cellular model of nutrient uptake suggested
that Trichodesmium is generally confronted by the biophysical limits of membrane space
and diffusion rates for iron and phosphate acquisition in the field. Colony
formation may benefit nutrient acquisition from particulate and organic
sources, alleviating these pressures. The results highlight that to
predict the behavior of Trichodesmium, both Fe and P stress must be evaluated
simultaneously.
Prochlorococcus is the numerically dominant primary producer in open ocean ecosystems. Analysis of Prochlorococcus genome sequences from cultured isolates and ocean samples has broadened interest in ...studying this tiny cell, and efforts are underway to develop it into a model system for studying marine microbial ecology. A critical component of these efforts has been the development of systematic culturing methods that will facilitate the distribution of Prochlorococcus to diverse labs that may be interested in studying it. This paper provides detailed methods for maintaining cultures of Prochlorococcus, including a comparison of growth rates of cells on two artificial seawater media and on a standard medium that uses a natural seawater base. Procedures for agar plating, cryopreservation, obtaining new isolates, and issues associated with culture volume and carbon limitation also are described.
is a globally distributed cyanobacterium whose nitrogen-fixing capability fuels primary production in warm oligotrophic oceans. Like many photoautotrophs,
serves as a host to various other ...microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here, we utilized metatranscriptomics to examine gene expression activities of microbial communities associated with
(strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor microbial communities similar to those of natural populations. In enrichments maintained under two distinct CO
concentrations for ∼8 years, the community transcriptional profiles were found to be specific to the treatment, demonstrating a restructuring of overall gene expression had occurred. Some of this restructuring involved significant increases in community respiration-related transcripts under elevated CO
, potentially facilitating the corresponding measured increases in host nitrogen fixation rates. Particularly of note, in both treatments, community transcripts involved in the reduction of nitrate, nitrite, and nitrous oxide were detected, suggesting the associated organisms may play a role in colony-level nitrogen cycling. Lastly, a taxon-specific analysis revealed distinct ecological niches of consistently cooccurring major taxa that may enable, or even encourage, the stable cohabitation of a diverse community within
consortia.
is a genus of globally distributed, nitrogen-fixing marine cyanobacteria. As a source of new nitrogen in otherwise nitrogen-deficient systems, these organisms help fuel carbon fixation carried out by other more abundant photoautotrophs and thereby have significant roles in global nitrogen and carbon cycling. Members of the
genus tend to form large macroscopic colonies that appear to perpetually host an association of diverse interacting microbes distinct from the surrounding seawater, potentially making the entire assemblage a unique miniature ecosystem. Since its first successful cultivation in the early 1990s, there have been questions about the potential interdependencies between
and its associated microbial community and whether the host's seemingly enigmatic nitrogen fixation schema somehow involved or benefited from its epibionts. Here, we revisit these old questions with new technology and investigate gene expression activities of microbial communities living in association with
.
Abstract
Biological dinitrogen fixation is the major source of new nitrogen to marine systems and thus essential to the ocean’s biological pump. Constraining the distribution and global rate of ...dinitrogen fixation has proven challenging owing largely to uncertainty surrounding the controls thereon. Existing South Atlantic dinitrogen fixation rate estimates vary five-fold, with models attributing most dinitrogen fixation to the western basin. From hydrographic properties and nitrate isotope ratios, we show that the Angola Gyre in the eastern tropical South Atlantic supports the fixation of 1.4–5.4 Tg N.a
−1
, 28-108% of the existing (highly uncertain) estimates for the basin. Our observations contradict model diagnoses, revealing a substantial input of newly-fixed nitrogen to the tropical eastern basin and no dinitrogen fixation west of 7.5˚W. We propose that dinitrogen fixation in the South Atlantic occurs in hotspots controlled by the overlapping biogeography of excess phosphorus relative to nitrogen and bioavailable iron from margin sediments. Similar conditions may promote dinitrogen fixation in analogous ocean regions. Our analysis suggests that local iron availability causes the phosphorus-driven coupling of oceanic dinitrogen fixation to nitrogen loss to vary on a regional basis.
Proteins are critical in catalyzing chemical reactions, forming key cellular structures, and in regulating cellular processes. Investigation of marine microbial proteins by metaproteomics methods ...enables the discovery of numerous aspects of microbial biogeochemical processes. However, these datasets present big data challenges as they often involve many samples collected across broad geospatial and temporal scales, resulting in thousands of protein identifications, abundances, and corresponding annotation information. The Ocean Protein Portal (OPP) was created to enable data sharing and discovery among multiple scientific domains and serve both research and education functions. The portal focuses on three use case questions: “Where is my protein of interest?”, “Who makes it?”, and “How much is there?” and provides profile and section visualizations, real-time taxonomic analysis, and links to metadata, sequence analysis, and other external resources to enable connections to be made between biogeochemical and proteomics datasets.
Synechococcus sp. WH 8102 is a motile marine cyanobacterium isolated originally from the Sargasso Sea. To test the response of this organism to cadmium (Cd), generally considered a toxin, cultures ...were grown in a matrix of high and low zinc (Zn) and phosphate (PO4 (3-)) and were then exposed to an addition of 4.4 pM free Cd(2+) at mid-log phase and harvested after 24 h. Whereas Zn and PO4 (3-) had little effect on overall growth rates, in the final 24 h of the experiment three growth effects were noticed: (i) low PO4 (3-) treatments showed increased growth rates relative to high PO4 (3-) treatments, (ii) the Zn/high PO4 (3-) treatment appeared to enter stationary phase, and (iii) Cd increased growth rates further in both the low PO4 (3-) and Zn treatments. Global proteomic analysis revealed that: (i) Zn appeared to be critical to the PO4 (3-) response in this organism, (ii) bacterial metallothionein (SmtA) appears correlated with PO4 (3-) stress-associated proteins, (iii) Cd has the greatest influence on the proteome at low PO4 (3-) and Zn, (iv) Zn buffered the effects of Cd, and (v) in the presence of both replete PO4 (3-) and added Cd the proteome showed little response to the presence of Zn. Similar trends in alkaline phosphate (ALP) and SmtA suggest the possibility of a Zn supply system to provide Zn to ALP that involves SmtA. In addition, proteome results were consistent with a previous transcriptome study of PO4 (3-) stress (with replete Zn) in this organism, including the greater relative abundance of ALP (PhoA), ABC phosphate binding protein (PstS) and other proteins. Yet with no Zn in this proteome experiment the PO4 (3-) response was quite different including the greater relative abundance of five hypothetical proteins with no increase in PhoA or PstS, suggesting that Zn nutritional levels are connected to the PO4 (3-) response in this cyanobacterium. Alternate ALP PhoX (Ca) was found to be a low abundance protein, suggesting that PhoA (Zn, Mg) may be more environmentally relevant than PhoX.
Summary
Marine Synechococcus thrive over a range of light regimes in the ocean. We examined the proteomic, genomic and physiological responses of seven Synechococcus isolates to moderate irradiances ...(5–80 μE m−2 s−1), and show that Synechococcus spans a continuum of light responses ranging from low light optimized (LLO) to high light optimized (HLO). These light responses are linked to phylogeny and pigmentation. Marine sub‐cluster 5.1A isolates with higher phycouribilin: phycoerythrobilin ratios fell toward the LLO end of the continuum, while sub‐cluster 5.1B, 5.2 and estuarine Synechococcus with less phycouribilin fell toward the HLO end of the continuum. Global proteomes were highly responsive to light, with > 50% of abundant proteins varying more than twofold between the lowest and highest irradiance. All strains downregulated phycobilisome proteins with increasing irradiance. Regulation of proteins involved in photosynthetic electron transport, carbon fixation, oxidative stress protection (superoxide dismutases) and iron and nitrogen metabolism varied among strains, as did the number of high light inducible protein (Hlip) and DNA photolyase genes in their genomes. All but one LLO strain possessed the photoprotective orange carotenoid protein (OCP). The unique combinations of light responses in each strain gives rise to distinct photophysiological phenotypes that may affect Synechococcus distributions in the ocean.
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