@article{paerl_curtis_bittner_cohn_gifford_bannon_rowland_bertrand_2023, title={Use and detection of a vitamin B1 degradation product yields new views of the marine B1 cycle and plankton metabolite exchange}, volume={6}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.00061-23}, abstractNote={ABSTRACT}, journal={MBIO}, author={Paerl, Ryan W. and Curtis, Nathaniel P. and Bittner, Meriel J. and Cohn, Melanie R. and Gifford, Scott M. and Bannon, Catherine C. and Rowland, Elden and Bertrand, Erin M.}, year={2023}, month={Jun} }
 @article{sathe_paerl_hazra_2022, title={Exchange of Vitamin B-1 and Its Biosynthesis Intermediates Shapes the Composition of Synthetic Microbial Cocultures and Reveals Complexities of Nutrient Sharing}, volume={204}, ISSN={["1098-5530"]}, DOI={10.1128/jb.00503-21}, abstractNote={
            Vitamin B
            1
            (thiamin) is an essential nutrient for cellular metabolism. Microorganisms that are unable to synthesize thiamin either fully or in part exogenously obtain it from their environment or via exchanges with other microbial members in their community.
          }, number={4}, journal={JOURNAL OF BACTERIOLOGY}, author={Sathe, Rupali R. M. and Paerl, Ryan W. and Hazra, Amrita B.}, year={2022}, month={Apr} }
 @article{plaas_paerl_baumann_karl_popendorf_barnard_chang_curtis_huang_mathieson_et al._2022, title={Harmful cyanobacterial aerosolization dynamics in the airshed of a eutrophic estuary}, volume={852}, ISSN={["1879-1026"]}, DOI={10.1016/j.scitotenv.2022.158383}, abstractNote={In addition to obvious negative effects on water quality in eutrophic aquatic ecosystems, recent work suggests that cyanobacterial harmful algal blooms (CHABs) also impact air quality via emissions carrying cyanobacterial cells and cyanotoxins. However, the environmental controls on CHAB-derived aerosol and its potential public health impacts remain largely unknown. Accordingly, the aims of this study were to 1) investigate the occurrence of microcystins (MC) and putatively toxic cyanobacterial communities in particulate matter ≤ 2.5 μm in diameter (PM2.5), 2) elucidate environmental conditions promoting their aerosolization, and 3) identify associations between CHABs and PM2.5 concentrations in the airshed of the Chowan River-Albemarle Sound, an oligohaline, eutrophic estuary in eastern North Carolina, USA. In summer 2020, during peak CHAB season, continuous PM2.5 samples and interval water samples were collected at two distinctive sites for targeted analyses of cyanobacterial community composition and MC concentration. Supporting air and water quality measurements were made in parallel to contextualize findings and permit statistical analyses of environmental factors driving changes in CHAB-derived aerosol. MC concentrations were low throughout the study, but a CHAB dominated by Dolichospermum occurred from late June to early August. Several aquatic CHAB genera recovered from Chowan River surface water were identified in PM2.5 during multiple time points, including Anabaena, Aphanizomenon, Dolichospermum, Microcystis, and Pseudanabaena. Cyanobacterial enrichment in PM2.5 was indistinctive between subspecies, but at one site during the early bloom, we observed the simultaneous enrichment of several cyanobacterial genera in PM2.5. In association with the CHAB, the median PM2.5 mass concentration increased to 8.97 μg m−3 (IQR = 5.15), significantly above the non-bloom background of 5.35 μg m−3 (IQR = 3.70) (W = 1835, p < 0.001). Results underscore the need for highly resolved temporal measurements to conclusively investigate the role that CHABs play in regional air quality and respiratory health risk.}, journal={SCIENCE OF THE TOTAL ENVIRONMENT}, author={Plaas, Haley E. and Paerl, Ryan W. and Baumann, Karsten and Karl, Colleen and Popendorf, Kimberly J. and Barnard, Malcolm A. and Chang, Naomi Y. and Curtis, Nathaniel P. and Huang, Hwa and Mathieson, Olivia L. and et al.}, year={2022}, month={Dec} }
 @article{wienhausen_bittner_paerl_2022, title={Key Knowledge Gaps to Fill at the Cell-To-Ecosystem Level in Marine B-Vitamin Cycling}, volume={9}, ISSN={["2296-7745"]}, DOI={10.3389/fmars.2022.876726}, abstractNote={B-vitamins are essential micronutrients for marine plankton. Additionally, we now know many marine plankton cannot synthesize B-vitamins de novo (from scratch) and thus are reliant on external supplies. Details of B-vitamin exchange, whether ‘active’ or ‘passive’ (i.e. through cell secretion or mortality), are lacking and as a result we struggle to predict microbial physiology, community composition and biogeochemistry. We argue that significant advances in understanding of the impact of B-vitamin exchange and cycling on marine community structure and biogeochemistry can be made by focusing on unknowns related to the ‘in’s and out’s’ of B-vitamin transport, exchange between plankton, and ecosystem scale processing/transformation of B-vitamins. We point out that it is particularly necessary to reach beyond traditional categorization of populations as B-vitamin auxotrophs (requiring supplied vitamin) or prototrophs (de novo vitamin synthesizers) and begin addressing which populations are net ‘providers’ and/or ‘consumers’. This is a particularly interesting problem as organisms cannot be confidently categorized as net ‘providers’ and/or ‘consumers’ based on genome-based prediction, and it is possible the two roles may change over time and environmental conditions. We posit that greater knowledge of B-vitamin exchange, e.g. cross-feeding, acquisition and secretion systems, environmental triggers of ‘provision’ and ‘consumption’, will reveal unforeseen networking and novel niches across marine planktonic communities. Last, we advocate for further experiments tracking the responses of isolates or natural communities relative to vitamin availability, tracing flow of B-vitamins between cells using novel approaches (e.g. isotopic, fluorometric), and greater consideration of altered B-vitamin exchange and cycling under future climate scenarios.}, journal={FRONTIERS IN MARINE SCIENCE}, author={Wienhausen, Gerrit and Bittner, Meriel J. and Paerl, Ryan W.}, year={2022}, month={May} }
 @article{asmala_osburn_paerl_paerl_2021, title={Elevated organic carbon pulses persist in estuarine environment after major storm events}, volume={6}, ISSN={["2378-2242"]}, url={https://doi.org/10.1002/lol2.10169}, DOI={10.1002/lol2.10169}, abstractNote={Abstract}, number={1}, journal={LIMNOLOGY AND OCEANOGRAPHY LETTERS}, publisher={Wiley}, author={Asmala, Eero and Osburn, Christopher L. and Paerl, Ryan W. and Paerl, Hans W.}, year={2021}, month={Feb}, pages={43–50} }
 @article{paerl_venezia_sanchez_paerl_2020, title={Picophytoplankton dynamics in a large temperate estuary and impacts of extreme storm events}, volume={10}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-020-79157-6}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Paerl, Ryan W. and Venezia, Rebecca E. and Sanchez, Joel J. and Paerl, Hans W.}, year={2020}, month={Dec} }
 @article{yadav_venezia_paerl_petters_2019, title={Characterization of Ice‐Nucleating Particles Over Northern India}, volume={124}, ISSN={2169-897X 2169-8996}, url={http://dx.doi.org/10.1029/2019jd030702}, DOI={10.1029/2019JD030702}, abstractNote={Abstract}, number={19}, journal={Journal of Geophysical Research: Atmospheres}, publisher={American Geophysical Union (AGU)}, author={Yadav, S. and Venezia, R. E. and Paerl, R. W. and Petters, M. D.}, year={2019}, month={Oct}, pages={10467–10482} }
 @article{paerl_bertrand_rowland_schatt_mehiri_niehaus_hanson_riemann_bouget_2018, title={Author Correction: Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis}, volume={8}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/S41598-018-27042-8}, DOI={10.1038/S41598-018-27042-8}, abstractNote={A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Paerl, Ryan W. and Bertrand, Erin M. and Rowland, Elden and Schatt, Phillippe and Mehiri, Mohamed and Niehaus, Thomas D. and Hanson, Andrew D. and Riemann, Lasse and Bouget, Francois-Yves}, year={2018}, month={Jun} }
 @article{paerl_bertrand_rowland_schatt_mehiri_niehaus_hanson_riemann_bouget_2018, title={Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis}, volume={8}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-018-24321-2}, DOI={10.1038/s41598-018-24321-2}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Paerl, Ryan W. and Bertrand, Erin M. and Rowland, Elden and Schatt, Phillippe and Mehiri, Mohamed and Niehaus, Thomas D. and Hanson, Andrew D. and Riemann, Lasse and Bouget, Francois-Yves}, year={2018}, month={Apr} }
 @article{pedersen_bombar_paerl_riemann_2018, title={Diazotrophs and N-2-Fixation Associated With Particles in Coastal Estuarine Waters}, volume={9}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2018.02759}, abstractNote={Putative heterotrophic bacteria carrying out N2-fixation, so-called non-cyanobacterial diazotrophs (NCDs), are widely distributed in marine waters, but details of how the O2-inhibited N2-fixation process is promoted in the oxic water column remains ambiguous. Here we carried out two experiments with water from a eutrophic temperate fjord to examine whether low-oxygen microenvironments within particulate organic matter could be loci suitable for N2-fixation. First, water enriched with natural particles or sediment showed higher N2-fixation rates than bulk water, and nitrogenase genes (nifH) revealed that specific diazotrophs were affiliated with the particulate matter. Second, pristine artificial surfaces were rapidly colonized by diverse bacteria, while putative diazotrophs emerged relatively late (after 80 h) during the colonization, and phylotypes related to Pseudomonas and to anaerobic bacteria became dominant with time. Our study pinpoints natural particles as sites of N2-fixation, and indicates that resuspension of sediment material can elevate pelagic N2-fixation. Moreover, we show that diverse natural diazotrophs can colonize artificial surfaces, but colonization by “pioneer” bacterioplankton that more rapidly associate with surfaces appears to be a prerequisite. Whereas our experimental study supports the idea of pelagic particles as sites of N2-fixation by heterotrophic bacteria, future in situ studies are needed in order to establish identity, activity and ecology of particle associated NCDs as a function of individual particle characteristics.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Pedersen, Jeppe N. and Bombar, Deniz and Paerl, Ryan W. and Riemann, Lasse}, year={2018}, month={Nov} }
 @article{bombar_paerl_anderson_riemann_2018, title={Filtration via Conventional Glass Fiber Filters in 15N2 Tracer Assays Fails to Capture All Nitrogen-Fixing Prokaryotes}, volume={5}, ISSN={2296-7745}, url={http://dx.doi.org/10.3389/fmars.2018.00006}, DOI={10.3389/fmars.2018.00006}, abstractNote={Biological dinitrogen fixation (BNF) represents a major input of reduced nitrogen (N) to the oceans. Accurate direct measurements of BNF rates are crucial for reliably determining the biogeochemical significance of diazotrophy at local and global scales. Traditionally, borosilicate glass fiber filters (GF/F, Whatman) with a nominal pore size of 0.7 µm are used to collect suspended particles by filtration after incubations with added 15N2 tracer. We carried out BNF experiments in the Baltic Sea, Danish coastal waters, and the Pacific Ocean comparing the retentive characteristics of precombusted GF/F filters with newer Advantec glass fiber filters which have a smaller nominal pore size of 0.3 µm. Where BNF was detected, rates were nearly always higher, and sometimes even exclusively detectable, when using Advantec filters. In the majority of samples across tested habitats, significantly more cells were lost to GF/F filtrate (average = 51 %, range = 10 – 70 % of cells) than to Advantec filtrate (average = 40 %, range = 10 – 54 %). Using Illumina sequencing of nitrogenase (nifH) gene amplicons, we show that diazotroph communities can markedly differ between bulk water and filtrates from GF/F and Advantec filtrations, suggesting that different diazotrophs can pass through the filter types. In order to reduce the potential underestimations of BNF due to filtration loss of diazotrophs, we recommend using Advantec filters or alternatively silver membranes with 0.2 µm pore size, especially in waters expected to be inhabited by relatively small, unicellular diazotrophs.}, journal={Frontiers in Marine Science}, publisher={Frontiers Media SA}, author={Bombar, Deniz and Paerl, Ryan W. and Anderson, Ruth and Riemann, Lasse}, year={2018}, month={Jan} }
 @article{paerl_hansen_henriksen_olesen_riemann_2018, title={N-fixation and related O2 constraints on model marine diazotroph Pseudomonas stutzeri BAL361}, volume={81}, ISSN={0948-3055 1616-1564}, url={http://dx.doi.org/10.3354/ame01867}, DOI={10.3354/ame01867}, abstractNote={AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 81:125-136 (2018) - DOI: https://doi.org/10.3354/ame01867 N-fixation and related O2 constraints on model marine diazotroph Pseudomonas stutzeri BAL361 Ryan W. Paerl*, Tobias N. G. Hansen, Nathalie N. S. E. Henriksen, Asmus K. Olesen, Lasse Riemann Marine Biological Section, University of Copenhagen, 3000 Helsingør, Denmark *Corresponding author: rpaerl@ncsu.edu ABSTRACT: Marine non-cyanobacterial diazotrophs are widespread in the ocean and can be the dominant nitrogen (N) fixers in certain regions. Lagging behind distribution and diversity data for these diazotrophs is a fundamental understanding of their physiologies—particularly in regards to dealing with oxygen, a potential inhibitor of N-fixation present in most of the ocean. To address this constraint, we conducted multiple experiments with Pseudomonas stutzeri BAL361, a model marine planktonic non-cyanobacterial diazotroph previously isolated from the Baltic Sea. Here, we confirm that BAL361 uses nitrogenase to convert N2 gas into biomass via N-fixation, reaching N-fixation rates upwards of 0.046 fmol N cell-1 h-1. Planktonic BAL361 cells exhibited nitrogenase activity at ~54 µM O2 or less—an O2 threshold notably lower than that recently reported (~160 µM O2) in experiments with BAL361 where large aggregates were observed. Provision of hydrophobic or hydrophilic particles or surfaces, used previously to stimulate N-fixation by aerobic natural communities, did not enhance N-fixation by aerobic BAL361 cultures. We empirically show that bulk N-fixation under aerobic conditions by BAL361 alone is possible by aggregation; however, it remains elusive how low numbers of solitary planktonic BAL361 cells in nature accomplish this same feat. Our findings draw new attention to the possibility that nutrient-rich conditions (including N-rich conditions) may be key to ultimately enable diazotrophs like BAL361 to overcome the ‘O2 problem’ and perform N-fixation via microoxic zones within aerobic marine bulk waters. KEY WORDS: Diazotrophs · N-fixation · Pseudomonas · Oxygen · Marine particles Full text in pdf format Supplementary material PreviousNextCite this article as: Paerl RW, Hansen TNG, Henriksen NNSE, Olesen AK, Riemann L (2018) N-fixation and related O2 constraints on model marine diazotroph Pseudomonas stutzeri BAL361. Aquat Microb Ecol 81:125-136. https://doi.org/10.3354/ame01867 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 81, No. 2. Online publication date: March 21, 2018 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2018 Inter-Research.}, number={2}, journal={Aquatic Microbial Ecology}, publisher={Inter-Research Science Center}, author={Paerl, RW and Hansen, TNG and Henriksen, NNSE and Olesen, AK and Riemann, L}, year={2018}, month={Mar}, pages={125–136} }
 @article{paerl_sundh_tan_svenningsen_hylander_pinhassi_andersson_riemann_2018, title={Prevalent reliance of bacterioplankton on exogenous vitamin B1 and precursor availability}, volume={115}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1806425115}, abstractNote={Significance}, number={44}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Paerl, Ryan W. and Sundh, John and Tan, Demeng and Svenningsen, Sine L. and Hylander, Samuel and Pinhassi, Jarone and Andersson, Anders F. and Riemann, Lasse}, year={2018}, month={Oct}, pages={E10447–E10456} }
 @article{paerl_bouget_lozano_vergé_schatt_allen_palenik_azam_2017, title={Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton}, volume={11}, ISSN={1751-7362 1751-7370}, url={http://dx.doi.org/10.1038/ISMEJ.2016.145}, DOI={10.1038/ismej.2016.145}, abstractNote={Abstract}, number={3}, journal={The ISME journal}, publisher={Springer Nature}, author={Paerl, R.W. and Bouget, F.Y. and Lozano, J.C. and Vergé, V. and Schatt, P. and Allen, E.E. and Palenik, B. and Azam, F.}, year={2017}, pages={753–765} }
 @article{bombar_paerl_riemann_2016, title={Marine Non-Cyanobacterial Diazotrophs: Moving beyond Molecular Detection}, volume={24}, ISSN={0966-842X}, url={http://dx.doi.org/10.1016/j.tim.2016.07.002}, DOI={10.1016/j.tim.2016.07.002}, abstractNote={The nitrogen input through biological N2 fixation is essential for life in vast areas of the global ocean. The belief is that cyanobacteria are the only relevant N2-fixing (diazotrophic) organisms. It has, however, now become evident that non-cyanobacterial diazotrophs, bacteria and archaea with ecologies fundamentally distinct from those of cyanobacteria, are widespread and occasionally fix N2 at significant rates. The documentation of a globally relevant nitrogen input from these diazotrophs would constitute a new paradigm for research on oceanic nitrogen cycling. Here we highlight the need for combining rate measurements and molecular analyses of field samples with cultivation studies in order to clarify the ecology of non-cyanobacteria and their contribution to marine N2 fixation on local and global scales.}, number={11}, journal={Trends in Microbiology}, publisher={Elsevier BV}, author={Bombar, Deniz and Paerl, Ryan W. and Riemann, Lasse}, year={2016}, month={Nov}, pages={916–927} }
 @article{paerl_bertrand_allen_palenik_azam_2015, title={Vitamin B1 ecophysiology of marine picoeukaryotic algae: Strain-specific differences and a new role for bacteria in vitamin cycling}, volume={60}, ISSN={0024-3590}, url={http://dx.doi.org/10.1002/LNO.10009}, DOI={10.1002/LNO.10009}, abstractNote={We confirmed multiple picoeukaryotic algae, Ostreococcus, Micromonas, and Pelagomonas spp., as thiamine (vitamin B1) auxotrophs in laboratory experiments with axenic cultures. Examined strains have half saturation growth constants (Ks) for B1 between 1.26 and 6.22 pmol B1 L−1, which is higher than reported seawater concentrations. Minimum B1 cell quotas for Ostreococcus and Micromonas spp. are high (2.20 × 10−8–4.46 × 10−8 pmol B1 cell−1) relative to other B1 auxotrophic phytoplankton, potentially making them B1 rich prey for zooplankton and significant B1 reservoirs in oligotrophic marine habitats. Ostreococcus and Micromonas genomes are nonuniformly missing portions of the B1 biosynthesis pathway. Given their gene repertoires, Ostreococcus lucimarinus CCE9901 and Ostreococcus tauri OTH95 are expected to salvage B1 from externally provided 4‐methyl‐5‐thiazoleethanol (HET) and 4‐amino‐5‐hydroxymethyl‐2‐methylpyrimidine (HMP). However, in culture, neither could use HET plus HMP instead of B1, highlighting current limitations of genome‐based prediction of B1 salvaging by picoeukaryotic algae. HMP and phosphorylated B1 use varied amongst tested strains and notably all Prasinophytes tested could not use HMP. B1‐limited O. lucimarinus CCE9901 could not grow on added thiamine diphosphate (TDP), a phosophorylated B1 form. However, in co‐culture with Pseudoalteromonas sp. TW7, a bacterium known to exhibit phosphatase activity, O. lucimarinus CCE9901 exhibited increased growth following TDP additions. This demonstrates that bacteria influence vitamin B1 availability beyond de novo synthesis and consumption; they can also serve as conduits that chemically alter, but not completely degrade or retain B1 analogs (e.g., TDP), and make them accessible to a broader range of microbes.}, number={1}, journal={Limnology and Oceanography}, publisher={Wiley}, author={Paerl, R. W. and Bertrand, E. M. and Allen, A. E. and Palenik, B. and Azam, F.}, year={2015}, month={Jan}, pages={215–228} }
 @article{shilova_robidart_james tripp_turk-kubo_wawrik_post_thompson_ward_hollibaugh_millard_et al._2014, title={A microarray for assessing transcription from pelagic marine microbial taxa}, volume={8}, ISSN={1751-7362 1751-7370}, url={http://dx.doi.org/10.1038/ismej.2014.1}, DOI={10.1038/ismej.2014.1}, abstractNote={Abstract}, number={7}, journal={The ISME Journal}, publisher={Springer Science and Business Media LLC}, author={Shilova, Irina N and Robidart, Julie C and James Tripp, H and Turk-Kubo, Kendra and Wawrik, Boris and Post, Anton F and Thompson, Anne W and Ward, Bess and Hollibaugh, James T and Millard, Andy and et al.}, year={2014}, month={Jan}, pages={1476–1491} }
 @article{moisander_serros_paerl_beinart_zehr_2014, title={Gammaproteobacterial diazotrophs and nifH gene expression in surface waters of the South Pacific Ocean}, volume={8}, ISSN={1751-7362 1751-7370}, url={http://dx.doi.org/10.1038/ismej.2014.49}, DOI={10.1038/ismej.2014.49}, abstractNote={Abstract}, number={10}, journal={The ISME Journal}, publisher={Springer Science and Business Media LLC}, author={Moisander, Pia H and Serros, Tracy and Paerl, Ryan W and Beinart, Roxanne A and Zehr, Jonathan P}, year={2014}, month={Apr}, pages={1962–1973} }
 @article{robidart_preston_paerl_turk_mosier_francis_scholin_zehr_2012, title={Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation}, volume={6}, ISSN={1751-7362 1751-7370}, url={http://dx.doi.org/10.1038/ismej.2011.127}, DOI={10.1038/ismej.2011.127}, abstractNote={Abstract}, number={3}, journal={The ISME journal}, publisher={Springer Science and Business Media LLC}, author={Robidart, J.C. and Preston, C.M. and Paerl, R.W. and Turk, K.A. and Mosier, A.C. and Francis, C.A. and Scholin, C.A. and Zehr, J.P}, year={2012}, pages={513–523} }
 @article{paerl_tozzi_kolber_zehr_2012, title={Variation in Synechococcus sp. CC9311 narB mRNA abundance relative to changes in light, nitrogen growth conditions and nitrate assimilation.}, volume={48}, ISSN={0022-3646}, url={http://dx.doi.org/10.1111/j.1529-8817.2012.01197.x}, DOI={10.1111/j.1529-8817.2012.01197.x}, abstractNote={Synechococcus‐ and Prochlorococcus‐specific narB genes that encode for an assimilatory nitrate reductase are found in coastal to open‐ocean waters. However, it remains uncertain if these picocyanobacteria assimilate nitrate in situ. This unknown can potentially be addressed by examining narB mRNA from the environment, but this requires a better understanding of the influence of environmental factors on narB gene transcription. In laboratory experiments with Synechococcus sp. CC9311 cultures exposed to diel light fluctuations and grown on nitrate or ammonium, there was periodic change in narB transcript abundance. This periodicity was broken in cultures subjected to a doubling of irradiance (40–80 μmol photons · m−2 · s−1) during the mid‐light period. Therefore, the irradiance level, not circadian rhythm, was the dominant factor controlling narB transcription. In nitrate‐grown cultures, diel change in narB transcript abundance and nitrate assimilation rate did not correlate; suggesting narB mRNA levels better indicate nitrate assimilation activity than assimilation rate. Growth history also affected narB transcription, as changes in narB mRNA levels in nitrogen‐deprived CC9311 cultures following nitrate amendment were distinct from cultures grown solely on nitrate. Environmental sampling for narB transcripts should consider time, irradiance, and the growth status of cells to ecologically interpret narB transcript abundances.}, number={4}, journal={Journal of Phycology}, publisher={Wiley}, author={Paerl, Ryan W. and Tozzi, Sasha and Kolber, Zbigniew S. and Zehr, Jonathan P.}, year={2012}, month={Jul}, pages={1028–1039} }
 @article{paerl_johnson_welsh_worden_chavez_zehr_2011, title={Differential Distributions of Synechococcus Subgroups Across the California Current System}, volume={2}, ISSN={1664-302X}, url={http://dx.doi.org/10.3389/fmicb.2011.00059}, DOI={10.3389/fmicb.2011.00059}, abstractNote={Synechococcus is an abundant marine cyanobacterial genus composed of different populations that vary physiologically. Synechococcus narB gene sequences (encoding for nitrate reductase in cyanobacteria) obtained previously from isolates and the environment (e.g., North Pacific Gyre Station ALOHA, Hawaii or Monterey Bay, CA, USA) were used to develop quantitative PCR (qPCR) assays. These qPCR assays were used to quantify populations from specific narB phylogenetic clades across the California Current System (CCS), a region composed of dynamic zones between a coastal-upwelling zone and the oligotrophic Pacific Ocean. Targeted populations (narB subgroups) had different biogeographic patterns across the CCS, which appear to be driven by environmental conditions. Subgroups C_C1, D_C1, and D_C2 were abundant in coastal-upwelling to coastal-transition zone waters with relatively high to intermediate ammonium, nitrate, and chl. a concentrations. Subgroups A_C1 and F_C1 were most abundant in coastal-transition zone waters with intermediate nutrient concentrations. E_O1 and G_O1 were most abundant at different depths of oligotrophic open-ocean waters (either in the upper mixed layer or just below). E_O1, A_C1, and F_C1 distributions differed from other narB subgroups and likely possess unique ecologies enabling them to be most abundant in waters between coastal and open-ocean waters. Different CCS zones possessed distinct Synechococcus communities. Core California current water possessed low numbers of narB subgroups relative to counted Synechococcus cells, and coastal-transition waters contained high abundances of Synechococcus cells and total number of narB subgroups. The presented biogeographic data provides insight on the distributions and ecologies of Synechococcus present in an eastern boundary current system.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Paerl, Ryan W. and Johnson, Kenneth S. and Welsh, Rory M. and Worden, Alexandra Z. and Chavez, Francisco P. and Zehr, Jonathan P.}, year={2011} }
 @article{foster_kuypers_vagner_paerl_musat_zehr_2011, title={Nitrogen fixation and transfer in open ocean diatom–cyanobacterial symbioses}, volume={5}, ISSN={1751-7362 1751-7370}, url={http://dx.doi.org/10.1038/ismej.2011.26}, DOI={10.1038/ismej.2011.26}, abstractNote={Abstract}, number={9}, journal={The ISME Journal}, publisher={Springer Science and Business Media LLC}, author={Foster, Rachel A and Kuypers, Marcel M M and Vagner, Tomas and Paerl, Ryan W and Musat, Niculina and Zehr, Jonathan P}, year={2011}, month={Mar}, pages={1484–1493} }
 @article{paerl_turk_beinart_chavez_zehr_2011, title={Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes in Monterey Bay determined by rbcL and narB quantitative PCR}, volume={14}, ISSN={1462-2912}, url={http://dx.doi.org/10.1111/j.1462-2920.2011.02594.x}, DOI={10.1111/j.1462-2920.2011.02594.x}, abstractNote={Summary}, number={3}, journal={Environmental Microbiology}, publisher={Wiley}, author={Paerl, Ryan W. and Turk, Kendra A. and Beinart, Roxanne A. and Chavez, Francisco P. and Zehr, Jonathan P.}, year={2011}, month={Sep}, pages={580–593} }
 @article{goebel_turk_achilles_paerl_hewson_morrison_montoya_edwards_zehr_2010, title={Abundance and distribution of major groups of diazotrophic cyanobacteria and their potential contribution to N2 fixation in the tropical Atlantic Ocean}, volume={12}, DOI={10.1111/j.1462-2920.2010.02303.x}, abstractNote={Summary}, journal={Environmental Microbiology}, author={Goebel, N.L. and Turk, K.A. and Achilles, K.M. and Paerl, R.W. and Hewson, I. and Morrison, A.E. and Montoya, J.P. and Edwards, C.A. and Zehr, J.P.}, year={2010}, pages={3272–3289} }
 @article{boyd_barham_hall_schumann_paerl_osburn_2010, title={Variation in ultrafiltered and LMW organic matter fluorescence properties under simulated estuarine mixing transects: 2. Mixing with photoexposure}, volume={115}, ISSN={0148-0227}, url={http://dx.doi.org/10.1029/2009JG000994}, DOI={10.1029/2009JG000994}, abstractNote={Ultrafiltered and low molecular weight dissolved organic matter (UDOM and LMW‐DOM, respectively) fluorescence was studied under simulated estuarine mixing along with moderate photoexposure using Delaware, Chesapeake, and San Francisco Bays (USA) natural organic matter. UDOM was produced by tangential flow ultrafiltration (TFF) from the marine (>33 PSU), mid‐estuarine (∼16 PSU), and freshwater (<1 PSU) members. TFF permeates (<1 kDa) were used to create artificial salinity transects nominally ranging from ∼0 to ∼36, with 4 PSU increments. UDOM or permeate (as control) from freshwater and mid‐estuary was added to each salinity mix in the artificial transect to determine the impact of mixing behavior on optical properties. Three‐dimensional fluorescence excitation‐emission matrix (EEMs) spectra were generated for each end‐member permeate (LMW fraction) and UDOM through the full artificial mixing transect. Fluorescent properties representing standard‐identified peaks, fluorescence ratios and excitation‐emission characteristics were assayed as previously reported. However, in this study, each sample was additionally photobleached for three days (nominally) to determine the coupled effect of estuarine mixing and photobleaching on LMW and UDOM fluorescence. Permeates, except Delaware Bay samples, were more bleached at lower salinities (<16). This effect was especially noticeable for mid‐estuarine LMW organic material which was highly bleached at low salinities. Humic‐type UDOM was generally bleached less at low salinities, maximally at mid‐salinities, and less as it mixed toward the ocean end‐member. As with mixing alone experiments, the B peak showed virtually no variability in the LMW and UDOMs fraction and was not significantly bleached. The N and T peak behaved similarly to one another and were significantly bleached. PCA and PARAFAC models confirmed trends for individual peaks. A four‐dimensional PARAFAC model with pre‐ and post‐bleached as the fourth dimension showed increases in the T peak fluorescence after photobleaching (with some overlap of the B and N peak). Results from this study indicate that coupled mixing and photobleaching can alter CDOM fluorescence in ways which might increase the difficulty in using CDOM as a proxy for DOM in regional carbon cycling biogeochemical models.}, journal={Journal of Geophysical Research}, publisher={American Geophysical Union (AGU)}, author={Boyd, Thomas J. and Barham, Bethany P. and Hall, Gregory J. and Schumann, Brandon S. and Paerl, Ryan W. and Osburn, Christopher L.}, year={2010}, month={Sep} }
 @article{hewson_poretsky_beinart_white_shi_bench_moisander_paerl_tripp_montoya_et al._2009, title={In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii}, volume={3}, ISSN={1751-7362 1751-7370}, url={http://dx.doi.org/10.1038/ismej.2009.8}, DOI={10.1038/ismej.2009.8}, abstractNote={Abstract}, number={5}, journal={The ISME Journal}, publisher={Springer Science and Business Media LLC}, author={Hewson, Ian and Poretsky, Rachel S and Beinart, Roxanne A and White, Angelicque E and Shi, Tuo and Bench, Shellie R and Moisander, Pia H and Paerl, Ryan W and Tripp, H James and Montoya, Joseph P and et al.}, year={2009}, month={Feb}, pages={618–631} }
 @article{hewson_paerl_tripp_zehr_karl_2009, title={Metagenomic potential of microbial assemblages in the surface waters of the central Pacific Ocean tracks variability in oceanic habitat}, volume={54}, ISSN={0024-3590}, url={http://dx.doi.org/10.4319/lo.2009.54.6.1981}, DOI={10.4319/lo.2009.54.6.1981}, abstractNote={Oceanic habitats may select for different organisms, thereby tuning genomic capabilities to local environmental conditions. To understand the relationship between microbial assemblage composition, functional capability, and habitat, a random genome shotgun sequencing (metagenomic) survey was conducted with surface‐water microbial assemblages (0.2–5‐µm size fraction) collected at seven locations along a meridional transect from the northern edge of the South Pacific subtropical gyre to the southern edge of the North Pacific subtropical gyre (16°S–13.5°N). A total of 1.1 million unique sequence reads were obtained, of which ~45% could be annotated to metabolic category. Microbial assemblages in equatorial divergence and countercurrent habitats were distinct phylogenetically from those in gyre waters. Ecotypes of dominant Cyanobacteria (Prochlorococcus and Synechococcus) had distinct distributions congruent with their physiological characteristics in cultivation. The metagenomic distribution of genes among metabolic pathways was very similar at all stations despite phylogenetic differences, but was unrelated to physicochemical habitat, suggesting that dominant microorganisms have a core suite of genes necessary for life in the open ocean. Among metabolic genes that varied across the transect, several patterns were observed. For example, phosphate (PO43‐) stress response genes were more common in gyre waters than at the equator. The variability in frequency of several metabolic pathways (e.g., chlorophyll biosynthesis, PO43‐ metabolism, and transcription initiation bacterial sigma factors) was related to physicochemical conditions, most of which were related to taxonomic differences among habitats. Microbial communities in the central Pacific Ocean are phylogenetically distinct to the oceanic provinces which they inhabit.}, number={6}, journal={Limnology and Oceanography}, publisher={Wiley}, author={Hewson, Ian and Paerl, Ryan W. and Tripp, H. James and Zehr, Jonathan P. and Karl, David M.}, year={2009}, month={Aug}, pages={1981–1994} }
 @article{paerl_foster_jenkins_montoya_zehr_2008, title={Phylogenetic diversity of cyanobacterial narB genes from various marine habitats}, volume={10}, ISSN={1462-2912 1462-2920}, url={http://dx.doi.org/10.1111/j.1462-2920.2008.01741.x}, DOI={10.1111/j.1462-2920.2008.01741.x}, abstractNote={Summary}, number={12}, journal={Environmental Microbiology}, publisher={Wiley}, author={Paerl, Ryan W. and Foster, Rachel A. and Jenkins, Bethany D. and Montoya, Joseph P. and Zehr, Jonathan P.}, year={2008}, month={Dec}, pages={3377–3387} }