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  • 1
    Online Resource
    Online Resource
    Nitrogen isotopic constraints on nutrient transport to the upper ocean
    Springer Science and Business Media LLC ; 2021
    In:  Nature Geoscience Vol. 14, No. 11 ( 2021-11), p. 855-861
    Details
    In: Nature Geoscience, Springer Science and Business Media LLC, Vol. 14, No. 11 ( 2021-11), p. 855-861
    Abstract: Ocean circulation supplies the surface ocean with the nutrients that fuel global ocean productivity. However, the mechanisms and rates of water and nutrient transport from the deep ocean to the upper ocean are poorly known. Here, we use the nitrogen isotopic composition of nitrate to place observational constraints on nutrient transport from the Southern Ocean surface into the global pycnocline (roughly the upper 1.2 km), as opposed to directly from the deep ocean. We estimate that 62 ± 5% of the pycnocline nitrate and phosphate originate from the Southern Ocean. Mixing, as opposed to advection, accounts for most of the gross nutrient input to the pycnocline. However, in net, mixing carries nutrients away from the pycnocline. Despite the quantitative dominance of mixing in the gross nutrient transport, the nutrient richness of the pycnocline relies on the large-scale advective flow, through which nutrient-rich water is converted to nutrient-poor surface water that eventually flows to the North Atlantic.
    Type of Medium: Online Resource
    ISSN: 1752-0894 , 1752-0908
    URL: Article
    DOI: 10.1038/s41561-021-00836-8
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
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    detail.hit.zdb_id: 2405323-5
    SSG: 16,13
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  • 2
    Online Resource
    Online Resource
    Enzyme-Specific Coupling of Oxygen and Nitrogen Isotope Fractionation of the Nap and Nar Nitrate Reductases
    American Chemical Society (ACS) ; 2021
    In:  Environmental Science & Technology Vol. 55, No. 8 ( 2021-04-20), p. 5537-5546
    Details
    In: Environmental Science & Technology, American Chemical Society (ACS), Vol. 55, No. 8 ( 2021-04-20), p. 5537-5546
    Type of Medium: Online Resource
    ISSN: 0013-936X , 1520-5851
    URL: Article
    URL: Article
    DOI: 10.1021/acs.est.0c07816
    DOI: 10.1021/acs.est.0c07816.s001
    RVK:
    AR 10100
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2021
    detail.hit.zdb_id: 280653-8
    detail.hit.zdb_id: 1465132-4
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  • 3
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    Online Resource
    Production of diverse brGDGTs by Acidobacterium Solibacter usitatus in response to temperature, pH, and O 2 provides a culturing perspective on br GDGT proxies and biosynthesis
    Wiley ; 2023
    In:  Geobiology Vol. 21, No. 1 ( 2023-01), p. 102-118
    Details
    In: Geobiology, Wiley, Vol. 21, No. 1 ( 2023-01), p. 102-118
    Abstract: Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane lipids that are frequently employed as paleoenvironmental proxies because of the strong empirical correlations between their relative abundances and environmental temperature and pH. Despite the ubiquity of brGDGTs in modern and paleoenvironments, the source organisms of these enigmatic compounds have remained elusive, requiring paleoenvironmental applications to rely solely on observed environmental correlations. Previous laboratory and environmental studies have suggested that the globally abundant bacterial phylum of the Acidobacteria may be an important brGDGT producer in nature. Here, we report on experiments with a cultured Acidobacterium, Solibacter usitatus , that makes a large portion of its cellular membrane (24 ± 9% across all experiments) out of a structurally diverse set of tetraethers including the common brGDGTs Ia, IIa, IIIa, Ib, and IIb. Solibacter usitatus was grown across a range of conditions including temperatures from 15 to 30°C, pH from 5.0 to 6.5, and O 2 from 1% to 21%, and demonstrated pronounced shifts in the degree of brGDGT methylation across these growth conditions. The temperature response in culture was in close agreement with trends observed in published environmental datasets, supporting a physiological basis for the empirical relationship between brGDGT methylation number and temperature. However, brGDGT methylation at lower temperatures (15 and 20°C) was modulated by culture pH with higher pH systematically increasing the degree of methylation. In contrast, pH had little effect on brGDGT cyclization, supporting the hypothesis that changes in bacterial community composition may underlie the link between cyclization number and pH observed in environmental samples. Oxygen concentration likewise affected brGDGT methylation highlighting the potential for this environmental parameter to impact paleotemperature reconstruction. Low O 2 culture conditions further resulted in the production of uncommon brGDGT isomers that could be indicators of O 2 limitation. Finally, the production of brGTGTs (trialkyl tetraethers) in addition to the previously discovered iso‐C15‐based mono‐ and diethers in S. usitatus suggests a potential biosynthetic pathway for brGDGTs that uses homologs of the archaeal tetraether synthase (Tes) enzyme for tetraether synthesis from diethers.
    Type of Medium: Online Resource
    ISSN: 1472-4677 , 1472-4669
    URL: Issue
    URL: Article
    DOI: 10.1111/gbi.v21.1
    DOI: 10.1111/gbi.12525
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2113509-5
    SSG: 12
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  • 4
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    Geochemical, Biological, and Clumped Isotopologue Evidence for Substantial Microbial Methane Production Under Carbon Limitation in Serpentinites of the Samail Ophiolite, Oman
    American Geophysical Union (AGU) ; 2021
    In:  Journal of Geophysical Research: Biogeosciences Vol. 126, No. 10 ( 2021-10)
    Details
    In: Journal of Geophysical Research: Biogeosciences, American Geophysical Union (AGU), Vol. 126, No. 10 ( 2021-10)
    Abstract: 16S rRNA gene sequences affiliated with methanogens and CH 4 clumped isotopologue compositions suggest substantial microbial CH 4 production A second CH 4 source, release of CH 4 from fluid inclusions, is indicated by 13 C‐enriched ethane and propane C availability may influence the apparent C isotope effect of microbial methanogenesis
    Type of Medium: Online Resource
    ISSN: 2169-8953 , 2169-8961
    URL: Article
    DOI: 10.1029/2020JG006025
    Language: English
    Publisher: American Geophysical Union (AGU)
    Publication Date: 2021
    detail.hit.zdb_id: 3094167-2
    detail.hit.zdb_id: 2220777-6
    SSG: 16,13
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  • 5
    Online Resource
    Online Resource
    Interrogating marine virus‐host interactions and elemental transfer with BONCAT and nanoSIMS‐based methods
    Wiley ; 2018
    In:  Environmental Microbiology Vol. 20, No. 2 ( 2018-02), p. 671-692
    Details
    In: Environmental Microbiology, Wiley, Vol. 20, No. 2 ( 2018-02), p. 671-692
    Abstract: While the collective impact of marine viruses has become more apparent over the last decade, a deeper understanding of virus‐host dynamics and the role of viruses in nutrient cycling would benefit from direct observations at the single‐virus level. We describe two new complementary approaches – stable isotope probing coupled with nanoscale secondary ion mass spectrometry (nanoSIMS) and fluorescence‐based biorthogonal non‐canonical amino acid tagging (BONCAT) – for studying the activity and biogeochemical influence of marine viruses. These tools were developed and tested using several ecologically relevant model systems ( Emiliania huxleyi /EhV207, Synechococcus sp . WH8101/Syn1 and Escherichia coli /T7). By resolving carbon and nitrogen enrichment in viral particles, we demonstrate the power of nanoSIMS tracer experiments in obtaining quantitative estimates for the total number of viruses produced directly from a particular production pathway (by isotopically labelling host substrates). Additionally, we show through laboratory experiments and a pilot field study that BONCAT can be used to directly quantify viral production (via epifluorescence microscopy) with minor sample manipulation and no dependency on conversion factors. This technique can also be used to detect newly synthesized viral proteins. Together these tools will help fill critical gaps in our understanding of the biogeochemical impact of viruses in the ocean.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2018.20.issue-2
    DOI: 10.1111/1462-2920.13996
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 6
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    Towards measuring growth rates of pathogens during infections by D 2 O‐labeling lipidomics
    Wiley ; 2018
    In:  Rapid Communications in Mass Spectrometry Vol. 32, No. 24 ( 2018-12-30), p. 2129-2140
    Details
    In: Rapid Communications in Mass Spectrometry, Wiley, Vol. 32, No. 24 ( 2018-12-30), p. 2129-2140
    Abstract: Microbial growth rate is an important physiological parameter that is challenging to measure in situ , partly because microbes grow slowly in many environments. Recently, it has been demonstrated that generation times of S. aureus in cystic fibrosis (CF) infections can be determined by D 2 O‐labeling of actively synthesized fatty acids. To improve species specificity and allow growth rate monitoring for a greater range of pathogens during the treatment of infections, it is desirable to accurately quantify trace incorporation of deuterium into phospholipids. Methods Lipid extracts of D 2 O‐treated E. coli cultures were measured on liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS) instruments equipped with time‐of‐flight (TOF) and orbitrap mass analyzers, and used for comparison with the analysis of fatty acids by isotope‐ratio gas chromatography (GC)/MS. We then developed an approach to enable tracking of lipid labeling, by following the transition from stationary into exponential growth in pure cultures. Lastly, we applied D 2 O‐labeling lipidomics to clinical samples from CF patients with chronic lung infections. Results Lipidomics facilitates deuterium quantification in lipids at levels that are useful for many labeling applications ( 〉 0.03 at% D). In the E. coli cultures, labeling dynamics of phospholipids depend largely on their acyl chains and between phospholipids we notice differences that are not obvious from absolute concentrations alone. For example, cyclopropyl‐containing lipids reflect the regulation of cyclopropane fatty acid synthase, which is predominantly expressed at the beginning of stationary phase. The deuterium incorporation into a lipid that is specific for S. aureus in CF sputum indicates an average generation time of the pathogen on the order of one cell doubling per day. Conclusions This study demonstrates how trace level measurement of stable isotopes in intact lipids can be used to quantify lipid metabolism in pure cultures and provides guidelines that enable growth rate measurements in microbiome samples after incubation with a low percentage of D 2 O.
    Type of Medium: Online Resource
    ISSN: 0951-4198 , 1097-0231
    URL: Issue
    URL: Article
    DOI: 10.1002/rcm.v32.24
    DOI: 10.1002/rcm.8288
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2002158-6
    detail.hit.zdb_id: 58731-X
    SSG: 11
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  • 7
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    Online Resource
    Table_4.XLSX
    Frontiers Media SA ; 2023
    In:  Frontiers in Microbiology Vol. 14 ( 2023-4-21)
    Details
    In: Frontiers in Microbiology, Frontiers Media SA, Vol. 14 ( 2023-4-21)
    Abstract: Nitrogen (N) is an essential element for life. N compounds such as ammonium ( NH 4 + ) may act as electron donors, while nitrate ( NO 3 - ) and nitrite ( NO 2 - ) may serve as electron acceptors to support energy metabolism. However, little is known regarding the availability and forms of N in subsurface ecosystems, particularly in serpentinite-hosted settings where hydrogen (H 2 ) generated through water–rock reactions promotes habitable conditions for microbial life. Here, we analyzed N and oxygen (O) isotope composition to investigate the source, abundance, and cycling of N species within the Samail Ophiolite of Oman. The dominant dissolved N species was dependent on the fluid type, with Mg 2+ - HCO 3 - type fluids comprised mostly of NO 3 - , and Ca 2+ -OH − fluids comprised primarily of ammonia (NH 3 ). We infer that fixed N is introduced to the serpentinite aquifer as NO 3 - . High concentrations of NO 3 - ( & gt;100 μM) with a relict meteoric oxygen isotopic composition (δ 18 O ~ 22‰, Δ 17 O ~ 6‰) were observed in shallow aquifer fluids, indicative of NO 3 - sourced from atmospheric deposition (rainwater NO 3 - : δ 18 O of 53.7‰, Δ 17 O of 16.8‰) mixed with NO 3 - produced in situ through nitrification (estimated endmember δ 18 O and Δ 17 O of ~0‰). Conversely, highly reacted hyperalkaline fluids had high concentrations of NH 3 ( & gt;100 μM) with little NO 3 - detectable. We interpret that NH 3 in hyperalkaline fluids is a product of NO 3 - reduction. The proportionality of the O and N isotope fractionation ( 18 ε / 15 ε) measured in Samail Ophiolite NO 3 - was close to unity ( 18 ε / 15 ε ~ 1), which is consistent with dissimilatory NO 3 - reduction with a membrane-bound reductase (NarG); however, abiotic reduction processes may also be occurring. The presence of genes commonly involved in N reduction processes ( narG, napA, nrfA ) in the metagenomes of biomass sourced from aquifer fluids supports potential biological involvement in the consumption of NO 3 - . Production of NH 4 + as the end-product of NO 3 - reduction via dissimilatory nitrate reduction to ammonium (DNRA) could retain N in the subsurface and fuel nitrification in the oxygenated near surface. Elevated bioavailable N in all sampled fluids indicates that N is not likely limiting as a nutrient in serpentinites of the Samail Ophiolite.
    Type of Medium: Online Resource
    ISSN: 1664-302X
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fmicb.2023.1139633
    DOI: 10.3389/fmicb.2023.1139633.s001
    DOI: 10.3389/fmicb.2023.1139633.s002
    DOI: 10.3389/fmicb.2023.1139633.s003
    DOI: 10.3389/fmicb.2023.1139633.s004
    DOI: 10.3389/fmicb.2023.1139633.s005
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2587354-4
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  • 8
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    Heavy water and 15 N labelling with N ano SIMS analysis reveals growth rate‐dependent metabolic heterogeneity in chemostats
    Wiley ; 2015
    In:  Environmental Microbiology Vol. 17, No. 7 ( 2015-07), p. 2542-2556
    Details
    In: Environmental Microbiology, Wiley, Vol. 17, No. 7 ( 2015-07), p. 2542-2556
    Abstract: To measure single‐cell microbial activity and substrate utilization patterns in environmental systems, we employ a new technique using stable isotope labelling of microbial populations with heavy water (a passive tracer) and 15 N ammonium in combination with multi‐isotope imaging mass spectrometry. We demonstrate simultaneous N ano SIMS analysis of hydrogen, carbon and nitrogen at high spatial and mass resolution, and report calibration data linking single‐cell isotopic compositions to the corresponding bulk isotopic equivalents for P seudomonas aeruginosa and S taphylococcus aureus . Our results show that heavy water is capable of quantifying in situ single‐cell microbial activities ranging from generational time scales of minutes to years, with only light isotopic incorporation (∼0.1 atom % 2 H ). Applying this approach to study the rates of fatty acid biosynthesis by single cells of S . aureus growing at different rates in chemostat culture (∼6 h, 1 day and 2 week generation times), we observe the greatest anabolic activity diversity in the slowest growing populations. By using heavy water to constrain cellular growth activity, we can further infer the relative contributions of ammonium versus amino acid assimilation to the cellular nitrogen pool. The approach described here can be applied to disentangle individual cell activities even in nutritionally complex environments.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2015.17.issue-7
    DOI: 10.1111/1462-2920.12752
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 9
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    Morphological and isotopic changes of heterocystous cyanobacteria in response to N 2 partial pressure
    Wiley ; 2019
    In:  Geobiology Vol. 17, No. 1 ( 2019-01), p. 60-75
    Details
    In: Geobiology, Wiley, Vol. 17, No. 1 ( 2019-01), p. 60-75
    Abstract: Earth's atmospheric composition has changed significantly over geologic time. Many redox active atmospheric constituents have left evidence of their presence, while inert constituents such as dinitrogen gas (N 2 ) are more elusive. In this study, we examine two potential biological indicators of atmospheric N 2 : the morphological and isotopic signatures of heterocystous cyanobacteria. Biological nitrogen fixation constitutes the primary source of fixed nitrogen to the global biosphere and is catalyzed by the oxygen‐sensitive enzyme nitrogenase. To protect this enzyme, some filamentous cyanobacteria restrict nitrogen fixation to microoxic cells (heterocysts) while carrying out oxygenic photosynthesis in vegetative cells. Heterocysts terminally differentiate in a pattern that is maintained as the filaments grow, and nitrogen fixation imparts a measurable isotope effect, creating two biosignatures that have previously been interrogated under modern N 2 partial pressure (pN 2 ) conditions. Here, we examine the effect of variable pN 2 on these biosignatures for two species of the filamentous cyanobacterium Anabaena . We provide the first in vivo estimate of the intrinsic isotope fractionation factor of Mo‐nitrogenase ( ε fix  = −2.71  ±  0.09‰) and show that, with decreasing pN 2 , the net nitrogen isotope fractionation decreases for both species, while the heterocyst spacing decreases for Anabaena cylindrica and remains unchanged for Anabaena variabilis . These results are consistent with the nitrogen fixation mechanisms available in the two species. Application of these quantifiable effects to the geologic record may lead to new paleobarometric measurements for pN 2 , ultimately contributing to a better understanding of Earth's atmospheric evolution.
    Type of Medium: Online Resource
    ISSN: 1472-4677 , 1472-4669
    URL: Issue
    URL: Article
    DOI: 10.1111/gbi.2019.17.issue-1
    DOI: 10.1111/gbi.12312
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2113509-5
    SSG: 12
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  • 10
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    Ligand-Enhanced Abiotic Iron Oxidation and the Effects of Chemical versus Biological Iron Cycling in Anoxic Environments
    American Chemical Society (ACS) ; 2013
    In:  Environmental Science & Technology Vol. 47, No. 6 ( 2013-03-19), p. 2602-2611
    Details
    In: Environmental Science & Technology, American Chemical Society (ACS), Vol. 47, No. 6 ( 2013-03-19), p. 2602-2611
    Type of Medium: Online Resource
    ISSN: 0013-936X , 1520-5851
    URL: Article
    DOI: 10.1021/es3049459
    RVK:
    AR 10100
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2013
    detail.hit.zdb_id: 280653-8
    detail.hit.zdb_id: 1465132-4
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