N2 fixation by subsurface populations of Trichodesmium : an important source of new nitrogen to the North Atlantic Ocean

Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution January 2011Trichodesmium, a genus of diazotrophic cyanobacteria, is an important contributor to the marine nitrogen (N) and carbon (C) cycles. The extent to which Trichodesmium dinitrogen (N2) fixation contributes to the marine N cycle has been modeled based on abundance data and rate estimates from surface populations. However, recent data show that Trichodesmium populations have a broad vertical distribution. The presence of previously unaccounted for subsurface populations suggests that past estimates of the contribution of new N by Trichodesmium to the North Atlantic may be artificially low. Herein, culture and field studies were combined to examine trends in N2 fixation in discrete surface and subsurface Trichodesmium populations in the western North Atlantic. Surface populations were dominated by the raft colony morphology of Trichodesmium and surface N2 fixation rates ranged from (33 to 156 μmol h-1 mol C-1). Subsurface populations were dominated by the puff colony morphology. Subsurface N2 fixation was typically detectable, but consistently lower than surface population rates (9 to 88 μmol h-1 mol C-1). In an analysis of the entire field dataset, N2 fixation rates varied non-linearly as a function of in situ irradiance. This trend in N2 fixation versus in situ irradiance is consistent with field and culture observations in the literature (Bell et al., 2005; Capone et al., 2005), however other models that predict N2 fixation based on light predict higher subsurface N2 fixation than what was detected in this study. In culture, N2 fixation in Trichodesmium was proportional to light level over the range of irradiances tested (10 to 70 μmol quanta m-2 s-1) and over long and short time scales, suggesting subtle changes in the light field could depress subsurface N2 fixation. Since the subsurface samples were dominated by the puff colony morphology, it is unclear if the subsurface N2 fixation rates are the result of the intrinsic responses of different species of Trichodesmium, or light driven population segregation within a single species, among other possibilities including the effects of temperature and nutrient availability. Regardless, the subsurface rates presented herein indicate that N2 fixation by subsurface populations represents an undersampled source of new N to the western north Atlantic. This result is consistent with the findings of Davis and McGillicuddy (2006), who suggest that subsurface populations of Trichodesmium increase the average N2 fixation rate in the North Atlantic by 2.9 to 3.3 times over estimates based solely on surface estimates (Davis and McGillicuddy, 2006).My graduate work has been supported by the Woods Hole Oceanographic Institution Academic Programs Office, the Center for Microbial Oceanography: Research and Education (#CCF-424599), and NSF Biological Oceanography (#OCE-0925284)

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

Nitrogen gas fixation by subsurface populations of Trichodesmium : an important source of new nitrogen to the North Atlantic Ocean

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2011.Cataloged from PDF version of thesis. "February 2011."Includes bibliographical references (leaves 44-48).Trichodesmium, a genus of diazotrophic cyanobacteria, is an important contributor to the marine nitrogen (N) and carbon (C) cycles. The extent to which Trichodesmium dinitrogen (N2) fixation contributes to the marine N cycle has been modeled based on abundance data and rate estimates from surface populations. However, recent data show that Trichodesmium populations have a broad vertical distribution. The presence of previously unaccounted for subsurface populations suggests that past estimates of the contribution of new N by Trichodesmium to the North Atlantic may be artificially low. Herein, culture and field studies were combined to examine trends in N2 fixation in discrete surface and subsurface Trichodesmium populations in the western North Atlantic. Surface populations were dominated by the raft colony morphology of Trichodesmium and surface N2 fixation rates ranged from (33 to 156 μmol h-1 mol C-1). Subsurface populations were dominated by the puff colony morphology. Subsurface N2 fixation was typically detectable, but consistently lower than surface population rates (9 to 88 μmol h-1 mol C-1). In an analysis of the entire field dataset, N2 fixation rates varied non-linearly as a function of in situ irradiance. This trend in N2 fixation versus in situ irradiance is consistent with field and culture observations in the literature (Bell et al., 2005; Capone et al., 2005), however other models that predict N2 fixation based on light predict higher subsurface N2 fixation than what was detected in this study. In culture, N2 fixation in Trichodesmium was proportional to light level over the range of irradiances tested (10 to 70 μmol quanta m-2 s-1) and over long and short time scales, suggesting subtle changes in the light field could depress subsurface N2 fixation. Since the subsurface samples were dominated by the puff colony morphology, it is unclear if the subsurface N2 fixation rates are the result of the inby Abigail Heithoff.S.M

Assessing Cognitive Functioning in People Living With HIV (PLWH): Factor Analytic Results From CHARTER and NNTC Cohorts.

BACKGROUND: Single summary scores, such as the Global Deficit Score, are often used to classify overall performance on neuropsychological batteries. The factor structure of test scores that underlie Global Deficit Score in studies of people living with HIV (PLWH) was assessed to determine whether individual test scores loaded onto a unitary factor to summarize performance. SETTING: Secondary data analysis on baseline data of PLWH from National NeuroAIDS Tissue Consortium and CNS HIV Antiretroviral Therapy Effects Research (CHARTER) Study. METHOD: Primary analyses included testing model structure and fit of neuropsychological test scores with confirmatory and exploratory factor analyses. Secondary analyses involved receiver operating characteristic curves, and associations with psychosocial and medical variables. RESULTS: Participants with confounds were excluded, leading to 798 (National NeuroAIDS Tissue Consortium) and 1222 (CHARTER) cases. When confirmatory factor analysis models were structured to be consistent with theoretically-based cognitive domains, models did not fit adequately. Per exploratory factor analyses, tests assessing speeded information processing, working memory, and executive functions loaded onto a single factor and explained the most variance in both cohorts. This factor tended to be associated with age, estimated premorbid ability, and aspects of substance use history. Its relation to age, in context of demographically corrected neuropsychological scores, suggested accelerated aging. CONCLUSION: Results indicate that individual neuropsychological tests did not load exactly onto expected domains, suggesting another framework for future analyses of cognitive domains. The possibility of a new index, and its use to assess cognitive impairment in PLWH, is suggested for further diagnostic and prognostic purposes

Assessing Cognitive Functioning in People Living With HIV (PLWH): Factor Analytic Results From CHARTER and NNTC Cohorts.

BackgroundSingle summary scores, such as the Global Deficit Score, are often used to classify overall performance on neuropsychological batteries. The factor structure of test scores that underlie Global Deficit Score in studies of people living with HIV (PLWH) was assessed to determine whether individual test scores loaded onto a unitary factor to summarize performance.SettingSecondary data analysis on baseline data of PLWH from National NeuroAIDS Tissue Consortium and CNS HIV Antiretroviral Therapy Effects Research (CHARTER) Study.MethodPrimary analyses included testing model structure and fit of neuropsychological test scores with confirmatory and exploratory factor analyses. Secondary analyses involved receiver operating characteristic curves, and associations with psychosocial and medical variables.ResultsParticipants with confounds were excluded, leading to 798 (National NeuroAIDS Tissue Consortium) and 1222 (CHARTER) cases. When confirmatory factor analysis models were structured to be consistent with theoretically-based cognitive domains, models did not fit adequately. Per exploratory factor analyses, tests assessing speeded information processing, working memory, and executive functions loaded onto a single factor and explained the most variance in both cohorts. This factor tended to be associated with age, estimated premorbid ability, and aspects of substance use history. Its relation to age, in context of demographically corrected neuropsychological scores, suggested accelerated aging.ConclusionResults indicate that individual neuropsychological tests did not load exactly onto expected domains, suggesting another framework for future analyses of cognitive domains. The possibility of a new index, and its use to assess cognitive impairment in PLWH, is suggested for further diagnostic and prognostic purposes

Assessing Cognitive Functioning in People Living With HIV (PLWH): Factor Analytic Results From CHARTER and NNTC Cohorts.

BackgroundSingle summary scores, such as the Global Deficit Score, are often used to classify overall performance on neuropsychological batteries. The factor structure of test scores that underlie Global Deficit Score in studies of people living with HIV (PLWH) was assessed to determine whether individual test scores loaded onto a unitary factor to summarize performance.SettingSecondary data analysis on baseline data of PLWH from National NeuroAIDS Tissue Consortium and CNS HIV Antiretroviral Therapy Effects Research (CHARTER) Study.MethodPrimary analyses included testing model structure and fit of neuropsychological test scores with confirmatory and exploratory factor analyses. Secondary analyses involved receiver operating characteristic curves, and associations with psychosocial and medical variables.ResultsParticipants with confounds were excluded, leading to 798 (National NeuroAIDS Tissue Consortium) and 1222 (CHARTER) cases. When confirmatory factor analysis models were structured to be consistent with theoretically-based cognitive domains, models did not fit adequately. Per exploratory factor analyses, tests assessing speeded information processing, working memory, and executive functions loaded onto a single factor and explained the most variance in both cohorts. This factor tended to be associated with age, estimated premorbid ability, and aspects of substance use history. Its relation to age, in context of demographically corrected neuropsychological scores, suggested accelerated aging.ConclusionResults indicate that individual neuropsychological tests did not load exactly onto expected domains, suggesting another framework for future analyses of cognitive domains. The possibility of a new index, and its use to assess cognitive impairment in PLWH, is suggested for further diagnostic and prognostic purposes

The integrated National NeuroAIDS Tissue Consortium database: a rich platform for neuroHIV research

Herein we present major updates to the National NeuroAIDS Tissue Consortium (NNTC) database. The NNTC's ongoing multisite clinical research study was established to facilitate access to ante-mortem and post-mortem data, tissues and biofluids for the neurohuman immunodeficiency virus (HIV) research community. Recently, the NNTC has expanded to include data from the central nervous system HIV Antiretroviral Therapy Effects Research (CHARTER) study. The data and biospecimens from CHARTER and NNTC cohorts are available to qualified researchers upon request. Data generated by requestors using NNTC biospecimens and tissues are returned to the NNTC upon the conclusion of requestors' work, and this external, experimental data are annotated and curated in the publically accessible NNTC database, thereby extending the utility of each case. A flexible and extensible database ontology allows the integration of disparate data sets, including external experimental data, clinical neuropsychological and neuromedical testing data, tissue pathology and neuroimaging data

Phosphorus supply drives rapid turnover of membrane phospholipids in the diatom Thalassiosira pseudonana

In low-phosphorus (P) marine systems, phytoplankton replace membrane phospholipids with non-phosphorus lipids, but it is not known how rapidly this substitution occurs. Here, when cells of the model diatom Thalassiosira pseudonana were transferred from P-replete medium to P-free medium, the phospholipid content of the cells rapidly declined within 48?h from 45±0.9 to 21±4.5% of the total membrane lipids; the difference was made up by non-phosphorus lipids. Conversely, when P-limited T. pseudonana were resupplied with P, cells reduced the percentage of their total membrane lipids contributed by a non-phosphorus lipid from 43±1.5 to 7.3±0.9% within 24?h, whereas the contribution by phospholipids rose from 2.2±0.1 to 44±3%. This dynamic phospholipid reservoir contained sufficient P to synthesize multiple haploid genomes, suggesting that phospholipid turnover could be an important P source for cells. Field observations of phytoplankton lipid content may thus reflect short-term changes in P supply and cellular physiology, rather than simply long-term adjustment to the environment

Comparison of transcript and protein signals.

<p>Comparison of proteome and transcriptome changes in response to P deficiency. Fold-change presented as the log₂ of the ratio of deficient∶replete conditions. Unity lines are shown in grey solid (fold-change = 1), while a linear regression (log₂[proteins] = 0.49*log₂[transcripts]-0.25) of proteins that are >2-fold in abundance in either treatment against their corresponding transcripts is shown in yellow (r² = 0.53). The dashed line is the 1∶1 line denoting equal fold change between the deficient and replete conditions for the transcriptome and the proteome. Proteins and transcripts of interest that correspond to P-metabolism, glycolysis and ribosomes/translation are highlighted.</p

Transcript, protein, and physiological parameters linked to phosphorus deficiency.

<p>Normalized transcript and protein abundance for significantly differentially regulated signatures and their associated physiological patterns, for polyphosphate metabolism (A), phosphate transport (B), alkaline phosphatase (C, D), phosphodiesterase (E), and sulfolipid synthesis (F) across P-replete (+P) and P-deficient (-P) conditions. Protein data are distinguished with a “p” next to the PID and by the hatched pattern. Polyphosphate abundances as measured by solid state ³¹P NMR (A) and enzyme activities (C, E), were assayed and are reported below each graph. Cell-associated alkaline phosphatase activity (green color) was detected using an enzyme labeled fluorescence substrate. The green fluorescence indicating enzyme activity is present in -P cells (panels 1, 2, 4, 5, and 6) and not present in +P cells (panel 3) (D). Chlorophyll autofluorescence (red) in also visible. Panels 4, 5, and 6 are a Z series through a labeled –P cell. The SQDG:PC ratio is reported from Van Mooy et al. (2009) from replete and P-deficient <i>T. pseudonana</i> cultures <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033768#pone.0033768-VanMooy1" target="_blank">[51]</a>, which were grown similarly to those in this study. SQDG: sulphoquinovosyldiacylglyerol; PG: phosphatidylglycerol.</p