Iron limitation of a springtime bacterial and phytoplankton community in the Ross Sea : implications for vitamin B12 nutrition

© The Author(s), 2011. This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums. The definitive version was published in Frontiers in Microbiology 2 (2011): 160, doi:10.3389/fmicb.2011.00160.The Ross Sea is home to some of the largest phytoplankton blooms in the Southern Ocean. Primary production in this system has previously been shown to be iron limited in the summer and periodically iron and vitamin B12 colimited. In this study, we examined trace metal limitation of biological activity in the Ross Sea in the austral spring and considered possible implications for vitamin B12 nutrition. Bottle incubation experiments demonstrated that iron limited phytoplankton growth in the austral spring while B12, cobalt, and zinc did not. This is the first demonstration of iron limitation in a Phaeocystis antarctica-dominated, early season Ross Sea phytoplankton community. The lack of B12 limitation in this location is consistent with previous Ross Sea studies in the austral summer, wherein vitamin additions did not stimulate P. antarctica growth and B12 was limiting only when bacterial abundance was low. Bottle incubation experiments and a bacterial regrowth experiment also revealed that iron addition directly enhanced bacterial growth. B12 uptake measurements in natural water samples and in an iron fertilized bottle incubation demonstrated that bacteria serve not only as a source for vitamin B12, but also as a significant sink, and that iron additions enhanced B12 uptake rates in phytoplankton but not bacteria. Additionally, vitamin uptake rates did not become saturated upon the addition of up to 95 pM B12. A rapid B12 uptake rate was observed after 13 min, which then decreased to a slower constant uptake rate over the next 52 h. Results from this study highlight the importance of iron availability in limiting early season Ross Sea phytoplankton growth and suggest that rates of vitamin B12 production and consumption may be impacted by iron availability.This research was supported by NSF grants OCE-0752291, OPP-0440840, OPP-0338097, OPP-0338164, ANT-0732665, OCE-0452883, and OCE-1031271, the Center for Microbial Oceanography Research and Education (CMORE) and a National Science Foundation (NSF) Graduate Research Fellowship (2007037200) and an Environmental Protection Agency STAR Fellowship to EMB (F6E20324)

Methionine synthase interreplacement in diatom cultures and communities : implications for the persistence of B12 use by eukaryotic phytoplankton

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2013. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 58 (2013): 1431–1450, doi:10.4319/lo.2013.58.4.1431.Three proteins related to vitamin B12 metabolism in diatoms were quantified via selected reaction monitoring mass spectrometry: B12-dependent and B12-independent methionine synthase (MetH, MetE) and a B12 acquisition protein (CBA1). B12-mediated interreplacement of MetE and MetH metalloenzymes was observed in Phaeodactylum tricornutum where MetH abundance was highest (0.06 fmol µg−1 protein) under high B12 and MetE abundance increased to 3.25 fmol µg−1 protein under low B12 availability. Maximal MetE abundance was 60-fold greater than MetH, consistent with the expected ∼ 50–100-fold larger turnover number for MetH. MetE expression resulted in 30-fold increase in nitrogen and 40-fold increase in zinc allocated to methionine synthase activity under low B12. CBA1 abundance was 6-fold higher under low-B12 conditions and increased upon B12 resupply to starved cultures. While biochemical pathways that supplant B12 requirements exist and are utilized by organisms such as land plants, B12 use persists in eukaryotic phytoplankton. This study suggests that retention of B12 utilization by phytoplankton results in resource conservation under conditions of high B12 availability. MetE and MetH abundances were also measured in diatom communities from McMurdo Sound, verifying that both these proteins are expressed in natural communities. These protein measurements are consistent with previous studies suggesting that B12 availability influences Antarctic primary productivity. This study illuminates controls on expression of B12-related proteins, quantitatively assesses the metabolic consequences of B12 deprivation, and demonstrates that mass spectrometry–based protein measurements yield insight into the functioning of marine microbial communities.This work was supported by National Science Foundation (NSF) Antarctic Sciences awards 0732665, 1103503, and 0732822; NSF Division of Ocean Science awards 0752291, 0928414, and 1031271; The Gordon and Betty Moore Foundation; Center for Microbial Oceanography Research and Education; an NSF Graduate Research Fellowship (2007037200); and an Environmental Protection Agency Science To Achieve Results (EPA-STAR) Fellowship to E.M.B. (F6E720324)

A seasonal study of dissolved cobalt in the Ross Sea, Antarctica : micronutrient behavior, absence of scavenging, and relationships with Zn, Cd, and P

© The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution 3.0 License. The definitive version was published in Biogeosciences 7 (2010): 4059-4082, doi:10.5194/bg-7-4059-2010.We report the distribution of cobalt (Co) in the Ross Sea polynya during austral summer 2005–2006 and the following austral spring 2006. The vertical distribution of total dissolved Co (dCo) was similar to soluble reactive phosphate (PO43−), with dCo and PO43− showing a significant correlation throughout the water column (r2 = 0.87, 164 samples). A strong seasonal signal for dCo was observed, with most spring samples having concentrations ranging from ~45–85 pM, whereas summer dCo values were depleted below these levels by biological activity. Surface transect data from the summer cruise revealed concentrations at the low range of this seasonal variability (~30 pM dCo), with concentrations as low as 20 pM observed in some regions where PO43− was depleted to ~0.1 μM. Both complexed Co, defined as the fraction of dCo bound by strong organic ligands, and labile Co, defined as the fraction of dCo not bound by these ligands, were typically observed in significant concentrations throughout the water column. This contrasts the depletion of labile Co observed in the euphotic zone of other ocean regions, suggesting a much higher bioavailability for Co in the Ross Sea. An ecological stoichiometry of 37.6 μmol Co:mol−1 PO43− calculated from dissolved concentrations was similar to values observed in the subarctic Pacific, but approximately tenfold lower than values in the Eastern Tropical Pacific and Equatorial Atlantic. The ecological stoichiometries for dissolved Co and Zn suggest a greater overall use of Zn relative to Co in the shallow waters of the Ross Sea, with a Co:PO43−/Zn:PO43− ratio of 1:17. Comparison of these observed stoichiometries with values estimated in culture studies suggests that Zn is a key micronutrient that likely influences phytoplankton diversity in the Ross Sea. In contrast, the observed ecological stoichiometries for Co were below values necessary for the growth of eukaryotic phytoplankton in laboratory culture experiments conducted in the absence of added zinc, implying the need for significant Zn nutrition in the Zn-Co cambialistic enzymes. The lack of an obvious kink in the dissolved Co:PO43− relationship was in contrast to Zn:PO43− and Cd:PO43− kinks previously observed in the Ross Sea. An excess uptake mechanism for kink formation is proposed as a major driver of Cd:PO43− kinks, where Zn and Cd uptake in excess of that needed for optimal growth occurs at the base of the euphotic zone, and no clear Co kink occurs because its abundances are too low for excess uptake. An unusual characteristic of Co geochemistry in the Ross Sea is an apparent lack of Co scavenging processes, as inferred from the absence of dCo removal below the euphotic zone. We hypothesize that this vertical distribution reflects a low rate of Co scavenging by Mn oxidizing bacteria, perhaps due to Mn scarcity, relative to the timescale of the annual deep winter mixing in the Ross Sea. Thus Co exhibits nutrient-like behavior in the Ross Sea, in contrast to its hybrid-type behavior in other ocean regions, with implications for the possibility of increased marine Co inventories and utility as a paleooceanographic proxy.This research was supported by the US National Science Foundation through research grants (OPP-0440840, OPP-0338097, OPP-0732665, OCE-0452883, OCE-0752991, OCE-0928414)

Assessing Sex-Specific Circadian, Metabolic, and Cognitive Phenotypes in the AβPP/PS1 and APPNL-F/NL-F Models of Alzheimer\u27s Disease.

BACKGROUND: Circadian disruption has long been recognized as a symptom of Alzheimer\u27s disease (AD); however, emerging data suggests that circadian dysfunction occurs early on in disease development, potentially preceding any noticeable cognitive deficits. OBJECTIVE: This study compares the onset of AD in male and female wild type (C57BL6/J), transgenic (AβPP/PS1), and knock-in (APPNL-F/NL-F) AD mouse models from the period of plaque initiation (6 months) through 12 months. METHODS: Rhythmic daily activity patterns, glucose sensitivity, cognitive function (Morris water maze, MWM), and AD pathology (plaques formation) were assessed. A comparison was made across sexes. RESULTS: Sex-dependent hyperactivity in AβPP/PS1 mice was observed. In comparison to C57BL/6J animals, 6-month-old male AβPP/PS1 demonstrated nighttime hyperactivity, as did 12-month-old females. Female AβPP/PS1 animals performed significantly worse on a MWM task than AβPP/PS1 males at 12 months and trended toward increased plaque pathology. APPNL-F/NL-F 12-month-old males performed significantly worse on the MWM task compared to 12-month-old females. Significantly greater plaque pathology occurred in AβPP/PS1 animals as compared to APPNL-F/NL-F animals. Female AβPP/PS1 animals performed significantly worse than APPNL-F/NL-F animals in spatial learning and memory tasks, though this was reversed in males. CONCLUSION: Taken together, this study provides novel insights into baseline sex differences, as well as characterizes baseline diurnal activity variations, in the AβPP/PS1 and APPNL-F/NL-F AD mouse models

Alzheimer\u27s disease alters oligodendrocytic glycolytic and ketolytic gene expression

INTRODUCTION: Sporadic Alzheimer\u27s disease (AD) is strongly correlated with impaired brain glucose metabolism, which may affect AD onset and progression. Ketolysis has been suggested as an alternative pathway to fuel the brain. METHODS: RNA-seq profiles of post mortem AD brains were used to determine whether dysfunctional AD brain metabolism can be determined by impairments in glycolytic and ketolytic gene expression. Data were obtained from the Knight Alzheimer\u27s Disease Research Center (62 cases; 13 controls), Mount Sinai Brain Bank (110 cases; 44 controls), and the Mayo Clinic Brain Bank (80 cases; 76 controls), and were normalized to cell type: astrocytes, microglia, neurons, oligodendrocytes. RESULTS: In oligodendrocytes, both glycolytic and ketolytic pathways were significantly impaired in AD brains. Ketolytic gene expression was not significantly altered in neurons, astrocytes, and microglia. DISCUSSION: Oligodendrocytes may contribute to brain hypometabolism observed in AD. These results are suggestive of a potential link between hypometabolism and dysmyelination in disease physiology. Additionally, ketones may be therapeutic in AD due to their ability to fuel neurons despite impaired glycolytic metabolism

The transcriptome and proteome of the diatom Thalassiosira pseudonana reveal a diverse phosphorus stress response

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e33768, doi:10.1371/journal.pone.0033768.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.This research was supported by the National Science Foundation (NSF) Environmental Genomics and NSF Biological Oceanography Program through grant OCE-0723667 to Dr. Dyhrman, Dr. Jenkins, Dr. Saito, and Dr. Rynearson, the NSF Chemical Oceanography Program through grant OCE-0549794 to Dr. Dyhrman and OCE-0526800 to Dr. Jenkins, the G. B. Moore Foundation and OCE-0752291 to Dr. Saito, NSF-EPSCoR (NSF-0554548 & NSF-1004057) to the University of Rhode Island, the Center for Microbial Oceanography: Research and Education, and the Joint Genome Institute/DOE Community Sequencing Program (CSP795793) to Dr. Jenkins, Dr. Dyhrman, Dr. Rynearson and Dr. Saito

The HETDEX Survey: Emission Line Exploration and Source Classification

The Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) is an untargeted spectroscopic survey that aims to measure the expansion rate of the Universe at $z \sim 2.4$ to 1% precision for both $H(z)$ and $D_A(z)$. HETDEX is in the process of mapping in excess of one million Lyman Alpha emitting (LAE) galaxies and a similar number of lower-z galaxies as a tracer of the large-scale structure. The success of the measurement is predicated on the post-observation separation of galaxies with Ly$\alpha$ emission from the lower-$z$ interloping galaxies, primarily [OII], with low contamination and high recovery rates. The Emission Line eXplorer (ELiXer) is the principal classification tool for HETDEX, providing a tunable balance between contamination and completeness as dictated by science needs. By combining multiple selection criteria, ELiXer improves upon the 20 Angstrom rest-frame equivalent width cut commonly used to distinguish LAEs from lower-$z$ [OII] emitting galaxies. Despite a spectral resolving power, R $\sim800$, that cannot resolve the [OII] doublet, we demonstrate the ability to distinguish LAEs from foreground galaxies with 98.1% accuracy. We estimate a contamination rate of Ly$\alpha$ by [OII] of 1.2% and a Ly$\alpha$ recovery rate of 99.1% using the default ELiXer configuration. These rates meet the HETDEX science requirements.Comment: 38 pages, 11 figure

Absorption Troughs of Lyα Emitters in HETDEX

The Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) is designed to detect and measure the redshifts of more than 1 million Lyα emitting galaxies (LAEs) 1.88 < z < 3.52. In addition to its cosmological measurements, these data enable studies of Lyα spectral profiles and the underlying radiative transfer. Using the roughly half a million LAEs in the HETDEX Data Release 3, we stack various subsets to obtain the typical Lyα profile for the z ∼ 2-3 epoch and to understand their physical properties. We find clear absorption wings around Lyα emission, which extend ∼2000 km s−1 both redward and blueward of the central line. Using far-UV spectra of nearby (0.002 < z < 0.182) LAEs in the COS Legacy Archive Spectroscopic Survey treasury and optical/near-IR spectra of 2.8 < z < 6.7 LAEs in the Multi Unit Spectroscopic-Wide survey, we observe absorption profiles in both redshift regimes. Dividing the sample by volume density shows that the troughs increase in higher-density regions. This trend suggests that the depth of the absorption is dependent on the local density of objects near the LAE, a geometry that is similar to damped Lyα systems. Simple simulations of Lyα radiative transfer can produce similar troughs due to absorption of light from background sources by H i gas surrounding the LAEs

HETDEX Public Source Catalog 1 -- Stacking 50K Lyman Alpha Emitters

We describe the ensemble properties of the $1.9 < z < 3.5$ Lyman Alpha Emitters (LAEs) found in the HETDEX survey's first public data release, HETDEX Public Source Catalog 1 (Mentuch Cooper et al. 2023). Stacking the low-resolution ($R \sim$ 800) spectra greatly increases the signal-to-noise ratio, revealing spectral features otherwise hidden by noise, and we show that the stacked spectrum is representative of an average member of the set. The flux limited, Ly$\alpha$ signal-to-noise ratio restricted stack of 50K HETDEX LAEs shows the ensemble biweight ``average" $z \sim 2.6$ LAE to be a blue (UV continuum slope $\sim -2.4$ and E(B-V) $< 0.1$), moderately bright (M$_{\text{UV}} \sim -19.7$) star forming galaxy with strong Ly$\alpha$ emission (log $L_{Ly\alpha}$ $\sim$ 42.8 and $W_{\lambda}$(Ly$\alpha$) $\sim$ 114\AA), and potentially significant leakage of ionizing radiation. The restframe UV light is dominated by a young, metal poor stellar population with an average age 5-15 Myr and metallicity of 0.2-0.3 Z$_{\odot}$.Comment: 17 pages, 11 figures, 2 data files (ApJ Accepted