@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
          Vitamin B1 (thiamin) is a vital nutrient for most cells in nature, including marine plankton. Early and recent experiments show that B1 degradation products instead of B1 can support the growth of marine bacterioplankton and phytoplankton. However, the use and occurrence of some degradation products remains uninvestigated, namely N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine (FAMP), which has been a focus of plant oxidative stress research. We investigated the relevance of FAMP in the ocean. Experiments and global ocean meta-omic data indicate that eukaryotic phytoplankton, including picoeukaryotes and harmful algal bloom species, use FAMP while bacterioplankton appear more likely to use deformylated FAMP, 4-amino-5-aminomethyl-2-methylpyrimidine. Measurements of FAMP in seawater and biomass revealed that it occurs at picomolar concentrations in the surface ocean, heterotrophic bacterial cultures produce FAMP in the dark—indicating non-photodegradation of B1 by cells, and B1-requiring (auxotrophic) picoeukaryotic phytoplankton produce intracellular FAMP. Our results require an expansion of thinking about vitamin degradation in the sea, but also the marine B1 cycle where it is now crucial to consider a new B1-related compound pool (FAMP), as well as generation (dark degradation—likely via oxidation), turnover (plankton uptake), and exchange of the compound within the networks of plankton.
          
            IMPORTANCE
            Results of this collaborative study newly show that a vitamin B1 degradation product, N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine (FAMP), can be used by diverse marine microbes (bacteria and phytoplankton) to meet their vitamin B1 demands instead of B1 and that FAMP occurs in the surface ocean. FAMP has not yet been accounted for in the ocean and its use likely enables cells to avoid B1 growth deficiency. Additionally, we show FAMP is formed in and out of cells without solar irradiance—a commonly considered route of vitamin degradation in the sea and nature. Altogether, the results expand thinking about oceanic vitamin degradation, but also the marine B1 cycle where it is now crucial to consider a new B1-related compound pool (FAMP), as well as its generation (dark degradation—likely via oxidation), turnover (plankton uptake), and exchange within networks of plankton.
          }, 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={AbstractEstuaries regulate transport of dissolved organic carbon (DOC) from land to ocean. Export of terrestrial DOC from coastal watersheds is exacerbated by increasing major rainfall and storm events and human activities, leading to pulses of DOC that are shunted through rivers downstream to estuaries. Despite an upward trend of extreme events, the fate of the pulsed terrestrial DOC in estuaries remains unclear. We analyzed the effects of seven major tropical cyclones (TC) from 1999 to 2017 on the quantity and fate of DOC in the Neuse River Estuary (NC, USA). Significant TC‐induced increases in DOC were observed throughout the estuary; the increase lasting from around 50 d at head‐of‐tide to over 6 months in lower estuary. Our results suggest that pulsed terrestrial DOC associated with TCs temporarily overwhelms the estuarine filter's abiotic and biotic degradation capacity under such high flow events, enhancing the shunt of terrestrial carbon to the coastal ocean.}, 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={AbstractPicophytoplankton (PicoP) are increasingly recognized as significant contributors to primary productivity and phytoplankton biomass in coastal and estuarine systems. Remarkably though, PicoP composition is unknown or not well-resolved in several large estuaries including the semi-lagoonal Neuse River Estuary (NRE), a tributary of the second largest estuary-system in the lower USA, the Pamlico-Albemarle Sound. The NRE is impacted by extreme weather events, including recent increases in precipitation and flooding associated with tropical cyclones. Here we examined the impacts of moderate to extreme (Hurricane Florence, September 2018) precipitation events on NRE PicoP abundances and composition using flow cytometry, over a 1.5 year period. Phycocyanin-richSynechococcus-like cells were the most dominant PicoP, reaching ~ 106cells mL−1, which highlights their importance as key primary producers in this relatively long residence-time estuary. Ephemeral “blooms” of picoeukaryotic phytoplankton (PEUK) during spring and after spikes in river flow were also detected, making PEUK periodically major contributors to PicoP biomass (up to ~ 80%). About half of the variation in PicoP abundance was explained by measured environmental variables. Temperature explained the most variation (24.5%). Change in total dissolved nitrogen concentration, an indication of increased river discharge, explained the second-most variation in PicoP abundance (15.9%). The short-term impacts of extreme river discharge from Hurricane Florence were particularly evident as PicoP biomass was reduced by ~ 100-fold for more than 2 weeks. We conclude that precipitation is a highly influential factor on estuarine PicoP biomass and composition, and show how ‘wetter’ future climate conditions will have ecosystem impacts down to the smallest of phytoplankton.}, 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={AbstractThe sources and concentrations of ice‐nucleating particles (INPs) over India are not well known. Here, INP concentrations in rainwater from Northern India and a dust sample from the Thar Desert are characterized. Rainwater INP concentrations ranged between 104 and 3 × 107 L−1 water, spanning temperatures between −4 and −28 °C. During the monsoon season, INP concentrations were low and approached those in remote marine air mass. During the winter season, INPs active between −4 to −10 °C were occasionally observed. An increase in INP activity sometimes occurred after the initial onset of rain. The onset freezing temperature of samples active at warmer temperatures was shifted to colder temperature after heat treatment, suggesting that the INP activity stemmed from biological influence. Plating was used to isolate and sequence INP active bacterial strains from some of the rainwater samples, specifically strains of close taxonomic affiliation with the ice nucleating genera Pantoea. The size‐resolved ice nucleation active site density for 200–600‐nm particles of Thar Desert Dust ranged between 107 and 109 m−2 at −20 °C, values similar to dusts from other regions of the world. The data reported herein may help constrain models that seek to predict the impact of INP on the properties of mixed‐phased clouds over the Indian subcontinent.}, 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={AbstractAlmost all cells require thiamin, vitamin B1 (B1), which is synthesized via the coupling of thiazole and pyrimidine precursors. Here we demonstrate that 5-(2-hydroxyethyl)-4-methyl-1,3-thiazole-2-carboxylic acid (cHET) is a useful in vivo B1 precursor for representatives of ubiquitous marine picoeukaryotic phytoplankton and Escherichia coli – drawing attention to cHET as a valuable exogenous micronutrient for microorganisms with ecological, industrial, and biomedical value. Comparative utilization experiments with the terrestrial plant Arabidopsis thaliana revealed that it can also use exogenous cHET, but notably, picoeukaryotic marine phytoplankton and E. coli were adapted to grow on low (picomolar) concentrations of exogenous cHET. Our results call for the modification of the conventional B1 biosynthesis model to incorporate cHET as a key precursor for B1 biosynthesis in two domains of life, and for consideration of cHET as a microbial micronutrient currency modulating marine primary productivity and community interactions in human gut-hosted microbiomes.}, 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
          Virtually all organisms require vitamin B1, including bacterioplankton that impact nutrient cycling and productivity in aquatic systems and Earth’s climate. Here, we show that B1 auxotrophy, the need for exogenous B1 or precursors for survival, is widespread among wild bacterioplankton. Genetic analyses of wild bacterioplankton revealed that most are B1 auxotrophs and the abundance of several B1-related genotypes changes temporally at an estuarine monitoring station, suggesting that B1/precursor availability influences bacterioplankton succession. Complementarily, in-field nutrient-amendment experiments and bioassays indicate that B1/precursor bioavailability periodically limits bulk growth of bacterioplankton. Together the presented data highlight the prevalent reliance of bacterioplankton upon exogenous B1/precursors and suggest a hitherto overlooked influence of B1/precursor availability on aquatic biochemical cycling.}, 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{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_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
               Several cosmopolitan marine picoeukaryotic phytoplankton are B1 auxotrophs requiring exogenous vitamin B1 or precursor to survive. From genomic evidence, representatives of picoeukaryotic phytoplankton (Ostreococcus and Micromonas spp.) were predicted to use known thiazole and pyrimidine B1 precursors to meet their B1 demands, however, recent culture-based experiments could not confirm this assumption. We hypothesized these phytoplankton strains could grow on precursors alone, but required a thiazole-related precursor other the well-known and extensively tested 4-methyl-5-thiazoleethanol. This hypothesis was tested using bioassays and co-cultures of picoeukaryotic phytoplankton and bacteria. We found that specific B1-synthesizing proteobacteria and phytoplankton are sources of a yet-to-be chemically identified thiazole-related precursor(s) that, along with pyrimidine B1 precursor 4-amino-5-hydroxymethyl-2-methylpyrimidine, can support growth of Ostreococcus spp. (also Micromonas spp.) without B1. We additionally found that the B1-synthesizing plankton do not require contact with picoeukaryotic phytoplankton cells to produce thiazole-related precursor(s). Experiments with wild-type and genetically engineered Ostreococcus lines revealed that the thiazole kinase, ThiM, is required for growth on precursors, and that thiazole-related precursor(s) accumulate to appreciable levels in the euphotic ocean. Overall, our results point to thiazole-related B1 precursors as important micronutrients promoting the survival of abundant phytoplankton influencing surface ocean production and biogeochemical cycling.}, 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{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
               Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world’s oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.}, 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
               In addition to the cyanobacterial N2-fixers (diazotrophs), there is a high nifH gene diversity of non-cyanobacterial groups present in marine environments, yet quantitative information about these groups is scarce. N2 fixation potential (nifH gene expression), diversity and distributions of the uncultivated diazotroph phylotype γ-24774A11, a putative gammaproteobacterium, were investigated in the western South Pacific Ocean. γ-24774A11 gene copies correlated positively with diazotrophic cyanobacteria, temperature, dissolved organic carbon and ambient O2 saturation, and negatively with depth, chlorophyll a and nutrients, suggesting that carbon supply, access to light or inhibitory effects of DIN may control γ-24774A11 abundances. Maximum nifH gene-copy abundance was 2 × 104 l−1, two orders of magnitude less than that for diazotrophic cyanobacteria, while the median γ-24774A11 abundance, 8 × 102 l−1, was greater than that for the UCYN-A cyanobacteria, suggesting a more homogeneous distribution in surface waters. The abundance of nifH transcripts by γ-24774A11 was greater during the night than during the day, and the transcripts generally ranged from 0–7%, but were up to 26% of all nifH transcripts at each station. The ubiquitous presence and low variability of γ-24774A11 abundances across tropical and subtropical oceans, combined with the consistent nifH expression reported in this study, suggest that γ-24774A11 could be one of the most important heterotrophic (or photoheterotrophic) diazotrophs and may need to be considered in future N budget estimates and models.}, 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{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
               Many diatoms that inhabit low-nutrient waters of the open ocean live in close association with cyanobacteria. Some of these associations are believed to be mutualistic, where N2-fixing cyanobacterial symbionts provide N for the diatoms. Rates of N2 fixation by symbiotic cyanobacteria and the N transfer to their diatom partners were measured using a high-resolution nanometer scale secondary ion mass spectrometry approach in natural populations. Cell-specific rates of N2 fixation (1.15–71.5 fmol N per cell h−1) were similar amongst the symbioses and rapid transfer (within 30 min) of fixed N was also measured. Similar growth rates for the diatoms and their symbionts were determined and the symbiotic growth rates were higher than those estimated for free-living cells. The N2 fixation rates estimated for Richelia and Calothrix symbionts were 171–420 times higher when the cells were symbiotic compared with the rates estimated for the cells living freely. When combined, the latter two results suggest that the diatom partners influence the growth and metabolism of their cyanobacterial symbionts. We estimated that Richelia fix 81–744% more N than needed for their own growth and up to 97.3% of the fixed N is transferred to the diatom partners. This study provides new information on the mechanisms controlling N input into the open ocean by symbiotic microorganisms, which are widespread and important for oceanic primary production. Further, this is the first demonstration of N transfer from an N2 fixer to a unicellular partner. These symbioses are important models for molecular regulation and nutrient exchange in symbiotic systems.}, 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{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
               Monterey Bay, CA is an Eastern boundary upwelling system that is nitrogen limited much of the year. In order to resolve population dynamics of microorganisms important for nutrient cycling in this region, we deployed the Environmental Sample Processor with quantitative PCR assays targeting both ribosomal RNA genes and functional genes for subclades of cyanobacteria (Synechococcus) and ammonia-oxidizing Archaea (Thaumarchaeota) populations. Results showed a strong correlation between Thaumarchaea abundances and nitrate during the spring upwelling but not the fall sampling period. In relatively stratified fall waters, the Thaumarchaeota community reached higher numbers than in the spring, and an unexpected positive correlation with chlorophyll concentration was observed. Further, we detected drops in Synechococcus abundance that occurred on short (that is, daily) time scales. Upwelling intensity and blooms of eukaryotic phytoplankton strongly influenced Synechococcus distributions in the spring and fall, revealing what appear to be the environmental limitations of Synechococcus populations in this region. Each of these findings has implications for Monterey Bay biogeochemistry. High-resolution sampling provides a better-resolved framework within which to observe changes in the plankton community. We conclude that controls on these ecosystems change on smaller scales than are routinely assessed, and that more predictable trends will be uncovered if they are evaluated within seasonal (monthly), rather than on annual or interannual scales.}, 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_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={SummarySynechococcus is a cosmopolitan marine cyanobacterial genus, and is often the most abundant picocyanobacterial genus in coastal waters. Little is known about Synechococcus seasonal dynamics in coastal zones highly impacted by upwelling. This was investigated by collecting seasonal samples from an upwelling‐impacted Monterey Bay (MB) monitoring station M0, in parallel with measurements of oceanographic conditions during 2006–2008. Synechococcus abundances were determined using quantitative PCR (qPCR) assays and flow cytometry (FCM). A new qPCR assay was designed to target dominant Synechococcus in MB using the rbcL gene, while previously designed assays targeted distinct phylotypes (called narB subgroups) with the narB gene. The rbcL qPCR assay successfully tracked abundant Synechococcus in MB, accounting for on average 89% (± 57%) of FCM‐based counts. Annual spring upwelling caused decreases in Synechococcus and narB subgroup abundances. Differences in narB subgroup abundance maxima and abundance patterns support the view that subgroups differ in their ecologies, including subgroup D_C1, which seems to specifically thrive in coastal waters. Correlations between narB subgroup abundances and measured environmental variables were similar among the subgroups. Therefore, non‐measured environmental factors (e.g. metals, mortality) likely had different influences on subgroups, which led to their distinct abundance patterns at M0.}, 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={SummaryThe abundances of six N2‐fixing cyanobacterial phylotypes were profiled at 22 stations across the tropical Atlantic Ocean during June 2006, and used to model the contribution of the diazotrophs to N2 fixation. Diazotroph abundances were measured by targeting the nifH gene of Trichodesmium, unicellular groups A, B, C (UCYN‐A, UCYN‐B and UCYN‐C), and diatom‐cyanobiont symbioses Hemiaulus–Richelia, Rhizosolenia–Richelia and Chaetoceros–Calothrix. West to east gradients in temperature, salinity and nutrients [NO3‐ + NO2‐, PO43−, Si(OH)4] showed the influence of the Amazon River plume and its effect on the distributions of the diazotrophs. Trichodesmium accounted for more than 93% of all nifH genes detected, dominated the warmer waters of the western Atlantic, and was the only diazotroph detected at the equatorial upwelling station. UCYN‐A was the next most abundant (> 5% of all nifH genes) and dominated the cooler waters of the eastern Atlantic near the Cape Verde Islands. UCYN‐C was found at a single depth (200 m) of high salinity and low temperature and nutrients, whereas UCYN‐B cells were widespread but in very low abundance (6.1 × 101 ±  4.6 × 102 gene copies l−1). The diatom‐cyanobionts were observed primarily in the western Atlantic within or near the high Si(OH)4 input of the Amazon River plume. Overall, highest diazotroph abundances were observed at the surface and declined with depth, except for some subsurface peaks in Trichodesmium, UCYN‐B and UCYN‐A. Modelled contributions of Trichodesmium, UCYN‐B and UCYN‐A to total N2 fixation suggested that Trichodesmium had the largest input, except for the potential of UCYN‐A at the Cape Verde Islands.}, 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
               The diazotrophic cyanobacterium Crocosphaera watsonii supplies fixed nitrogen (N) to N-depleted surface waters of the tropical oceans, but the factors that determine its distribution and contribution to global N2 fixation are not well constrained for natural populations. Despite the heterogeneity of the marine environment, the genome of C. watsonii is highly conserved in nucleotide sequence in contrast to sympatric planktonic cyanobacteria. We applied a whole assemblage shotgun transcript sequencing approach to samples collected from a bloom of C. watsonii observed in the South Pacific to understand the genomic mechanisms that may lead to high population densities. We obtained 999 C. watsonii transcript reads from two metatranscriptomes prepared from mixed assemblage RNA collected in the day and at night. The C. watsonii population had unexpectedly high transcription of hypothetical protein genes (31% of protein-encoding genes) and transposases (12%). Furthermore, genes were expressed that are necessary for living in the oligotrophic ocean, including the nitrogenase cluster and the iron-stress-induced protein A (isiA) that functions to protect photosystem I from high-light-induced damage. C. watsonii transcripts retrieved from metatranscriptomes at other locations in the southwest Pacific Ocean, station ALOHA and the equatorial Atlantic Ocean were similar in composition to those recovered in the enriched population. Quantitative PCR and quantitative reverse transcriptase PCR were used to confirm the high expression of these genes within the bloom, but transcription patterns varied at shallower and deeper horizons. These data represent the first transcript study of a rare individual microorganism in situ and provide insight into the mechanisms of genome diversification and the ecophysiology of natural populations of keystone organisms that are important in global nitrogen cycling.}, 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={SummaryNitrate, the most abundant combined, dissolved form of inorganic nitrogen in global oceans, is a common source of nitrogen (N) for phytoplankton including cyanobacteria. Using a nested polymerase chain reaction (PCR) method, the diversity of the cyanobacterial nitrate reductase gene, narB, was examined in plankton samples from a variety of marine habitats. A total of 480 narB gene fragment sequences were obtained from a coastal coral reef (Heron Island, Australia), open‐ocean tropical and subtropical oceanic waters (Atlantic and Pacific Oceans) and a temperate N. Pacific Ocean site (34°N, 129°W). Phylogenetic analyses distinguished eight picocyanobacterial narB clades comprised of DNA sequences derived from the nutrient‐replete coastal, nutrient‐deplete pelagic and tidally influenced coral reef habitats. The phylogeny of recovered narB gene sequences was consistent with 16S rRNA and ITS sequence phylogenies, suggesting minimal horizontal gene transfer of the narB gene. Depending on sampled habitat, environmental narB sequence types segregated into three divisions: non‐picocyanobacterial, coastal picocyanobacterial and open‐ocean picocyanobacterial sequences. Using a reverse transcription PCR method, narB mRNA sequences were amplified from Heron Island samples, indicating that narB expression can be detected in environmental samples.}, 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} }