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Dupont, CL, McCrow JP, Valas R, Moustafa A, Walworth N, Goodenough U, Roth R, Hogle SL, Bai J, Johnson ZI, Mann E, Palenik B, Barbeau KA, Craig Venter J, Allen AE.  2015.  Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. ISME J. 9:1076-1092.: International Society for Microbial Ecology   10.1038/ismej.2014.198   Abstract

Transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteria enriched in the>3.0-[mu]m size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM.

Bundy, RM, Jiang M, Carter M, Barbeau KA.  2016.  Iron-binding ligands in the southern California Current System: Mechanistic studies. Frontiers in Marine Science. 3:27.   10.3389/fmars.2016.00027   Abstract

The distributions of dissolved iron and organic iron-binding ligands were examined in water column profiles and deckboard incubation experiments in the southern California Current System (sCCS) along a transition from coastal to semi-oligotrophic waters. Analysis of the iron-binding ligand pool by competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE-ACSV) using multiple analytical windows (MAWs) revealed three classes of iron-binding ligands present throughout the water column (L1-L3), whose distributions closely matched those of dissolved iron and nitrate. Despite significant biogeochemical gradients, ligand profiles were similar between stations, with surface minima in strong ligands (L1 and L2), and relatively constant concentrations of weaker ligands (L3) down to 500 m. A phytoplankton grow-out incubation, initiated from an iron-limited water mass, showed dynamic temporal cycling of iron-binding ligands. A biological iron model was able to capture the patterns of the strong ligands in the grow-out incubation relatively well with only the microbial community as a biological source. An experiment focused on remineralization of particulate organic matter showed production of both strong and weak iron-binding ligands by the heterotrophic community, supporting a mechanism for in-situ production of both strong and weak iron-binding ligands in the subsurface water column. Photochemical experiments showed a variable influence of sunlight on the degradation of natural iron-binding ligands, providing some evidence to explain differences in surface ligand concentrations between stations. Patterns in ligand distributions between profiles and in the incubation experiments were primarily related to macronutrient concentrations, suggesting microbial remineralization processes might dominate on longer time-scales over short-term changes associated with photochemistry or phytoplankton growth.

Semeniuk, DM, Taylor RL, Bundy RM, Johnson WK, Cullen JT, Robert M, Barbeau KA, Maldonado MT.  2016.  Iron-copper interactions in iron-limited phytoplankton in the northeast subarctic Pacific Ocean. Limnology and Oceanography. 61:279-297.   10.1002/lno.10210   AbstractWebsite

In August 2010, iron (Fe) and Fe and copper (Cu) addition incubation experiments were conducted at two low Fe stations (P20 and P26) along Line P, off the western coast of British Columbia, to investigate Cu physiology in Fe- and Fe-light co-limited phytoplankton. Chlorophyll a concentrations ([Chl a]), maximum variable fluorescence yield (F-v/F-m), and Fe uptake rates by the Cu-dependent high-affinity Fe transport system (HAFeTS) were measured. Additions of Fe resulted in an increase in [Chl a] and F-v/F-m at both stations compared with the controls, regardless of light availability, and confirmed that the phytoplankton communities were Fe-limited. Uptake of Fe by the HAFeTS in both incubations increased with the addition of Fe, and likely reflects luxury Fe uptake and storage. While the in situ inorganic Cu concentrations were similar to those that can induce Cu-limitation in laboratory cultures, increasing Cu availability had no effect on biomass accumulation during both incubations, regardless of Fe availability or light regime. At P26, additions of 1 nmol L-1 CuSO4 resulted in a short-term increase in F-v/F-m of the phytoplankton community, and an increase in Fe uptake rates by large phytoplankton (>5 mu m), but only when light was not limiting. These data confirm a complex interaction between light, Fe and Cu physiology in indigenous phytoplankton communities, and suggest that these interactions may be both spatially heterogeneous and different for different phytoplankton size classes.

Chappell, PD, Armbrust EV, Barbeau KA, Bundy RM, Moffett JW, Vedamati J, Jenkins BD.  2019.  Patterns of diatom diversity correlate with dissolved trace metal concentrations and longitudinal position in the northeast Pacific coastal-offshore transition zone. Marine Ecology Progress Series. 609:69-86.   10.3354/meps12810   AbstractWebsite

Diatoms are important primary producers in the northeast Pacific Ocean, with their productivity closely linked to pulses of trace elements in the western high nitrate, low chlorophyll (HNLC) region of the oceanographic time series transect 'Line P.' Recently, the coastal-HNLC transition zone of the Line P transect was identified as a hotspot of phytoplankton productivity, potentially controlled by a combination of trace element and macronutrient concentrations. Here we describe diatom community composition in the eastern Line P transect, including the coastal- HNLC transition zone, with a method using high-throughput sequencing of diatom 18S gene amplicons. We identified significant correlations between shifting diatom community composition and longitude combined with concentrations of dissolved copper and 2 other dissolved trace metals (dissolved Fe [dFe] and/or dissolved zinc) and/or a physical factor (salinity or density). None of these variables on its own was significantly correlated with shifts in community composition, and 3 of the factors (dFe, salinity, and density) correlated with one another. Longitude could incorporate multiple factors that may influence diatom communities, including distance from shore, proximity of sampling stations, and an integration of previous pulses of macro- and micro-nutrients. We also evaluated in situ Fe limitation of the diatom Thalassiosira oceanica using a quantitative reverse-transcription polymerase chain reaction method, and found biological evidence of Fe stress in samples from the coastal-HNLC transition zone. Combined, our results support a prior hypothesis that dissolved trace metals as well as longitudinal distance may be important to diatom diversity in the coastal-HNLC transition zone of the Line P transect.

Hogle, SL, Dupont CL, Hopkinson BM, King AL, Buck KN, Roe KL, Stuart RK, Allen AE, Mann EL, Johnson ZI, Barbeau KA.  2018.  Pervasive iron limitation at subsurface chlorophyll maxima of the California Current. Proceedings of the National Academy of Sciences of the United States of America. 115:13300-13305.   10.1073/pnas.1813192115   AbstractWebsite

Subsurface chlorophyll maximum layers (SCMLs) are nearly ubiquitous in stratified water columns and exist at horizontal scales ranging from the submesoscale to the extent of oligotrophic gyres. These layers of heightened chlorophyll and/or phytoplankton concentrations are generally thought to be a consequence of a balance between light energy from above and a limiting nutrient flux from below, typically nitrate (NO3). Here we present multiple lines of evidence demonstrating that iron (Fe) limits or with light colimits phytoplankton communities in SCMLs along a primary productivity gradient from coastal to oligotrophic offshore waters in the southern California Current ecosystem. SCML phytoplankton responded markedly to added Fe or Fe/light in experimental incubations and transcripts of diatom and picoeukaryote Fe stress genes were strikingly abundant in SCML metatranscriptomes. Using a biogeochemical proxy with data from a 40-y time series, we find that diatoms growing in California Current SCMLs are persistently Fe deficient during the spring and summer growing season. We also find that the spatial extent of Fe deficiency within California Current SCMLs has significantly increased over the last 25 y in line with a regional climate index. Finally, we show that diatom Fe deficiency may be common in the subsurface of major upwelling zones worldwide. Our results have important implications for our understanding of the biogeochemical consequences of marine SCML formation and maintenance.

Jiang, MS, Barbeau KA, Selph KE, Measures CI, Buck KN, Azam F, Mitchell BG, Zhou M.  2013.  The role of organic ligands in iron cycling and primary productivity in the Antarctic Peninsula: A modeling study. Deep-Sea Research Part Ii-Topical Studies in Oceanography. 90:112-133.   10.1016/j.dsr2.2013.01.029   AbstractWebsite

Iron (Fe) is the limiting nutrient for primary productivity in the Southern Ocean, with much of the dissolved iron (dFe) bound to organic ligands or colloids. A Fe model for the Southern Ocean (SOFe) is developed to understand the role of bacteria and organic ligands in controlling Fe cycling and productivity. The model resolves the classical food web and microbial loop, including three types of nutrients (N, Si, Fe) and two types of Fe ligands. Simulations of the zero-dimensional (0-D) model are calibrated with detailed results of shipboard grow-out incubation experiments conducted with Antarctic Peninsula phytoplankton communities during winter 2006 to provide the best estimate of key biological parameters. Then a one-dimensional (1-D) model is developed by coupling the biological model with the Regional Oceanic Modeling System (ROMS) for a site on the Antarctic Peninsula shelf, and the model parameters are further calibrated with data collected from two surveys (summer 2004 and winter 2006) in the area. The results of the numerical simulations agree reasonably well with observations. An analysis of the 1-D model results suggests that bacteria and organic ligands may play an important role in Fe cycling, which can be categorized into a relatively fast mode within the euphotic zone dominated by photo-reactions (summer d Fe residence time about 600 days) and complexation and a slow mode below with most of the dFe biologically complexed (summer dFe residence time > 10 years). The dFe removal from the euphotic zone is dominated by colloidal formation and further aggregations with additional contribution from biological uptake, and an increase of organic ligands would reduce Fe export. The decrease of Fe removal rate over depth is due to the continuous dissolution and remineralization of particulate Fe. A number of sensitivity experiments are carried out for both O-D and 1-D models to understand the importance of photo-reactive processes in primary productivity, bacterial activity, Fe speciation, and dFe residence time within the euphotic zone. The bio-availability of ligand-bound Fe (FeL) is critical to modeled high primary productivity, which is consistent with both shipboard measurements and field observations. In addition, model productivity is sensitive to photoreaction rates if FeL is not directly available for phytoplankton uptake. (C) 2013 Elsevier Ltd. All rights reserved.