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Papers by Kelly Roe

Research paper thumbnail of Marine Alphaproteobacteria in the Utilization of Heme as an Iron Source by

The bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microor... more The bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microorganisms have rarely been examined. This study used Ruegeria sp. strain TrichCH4B as a model organism to study heme acquisition by a member of the Roseobacter clade. Analogs of known heme transporter proteins were found within the Ruegeria sp. TrichCH4B genome. The identified heme uptake and utilization system appears to be functional, as the heme genes were upregulated under iron stress, the bacterium could grow on ferricporphyrin complexes as the sole iron source, and internalization of 55 Fe from ferric protoporphyrin IX was observed. The potential ability to utilize heme in the Roseobacter clade appears to be common, as half of the isolates in the RoseoBase database were found to have a complete heme uptake system. A degenerate primer set was designed and successfully used to identify the putative heme oxygenase gene (hmus) in the roseobacter heme uptake system from diverse nonenriched marine environments. This study found that members of the Roseobacter clade are capable of utilizing heme as an iron source and that this capability may be present in all types of marine environments. The results of this study add a new perspective to the current picture of iron cycling in marine systems, whereby relatively refractory intracellular pools of heme-bound iron may be taken up quickly and directly reincorporated into living bacteria without previous degradation or the necessity of a siderophore intermediate.

Research paper thumbnail of Utilization of Heme as an Iron Source by Marine Alphaproteobacteria in the Roseobacter Clade

Applied and Environmental Microbiology, Sep 15, 2013

The bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microor... more The bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microorganisms have rarely been examined. This study used Ruegeria sp. strain TrichCH4B as a model organism to study heme acquisition by a member of the Roseobacter clade. Analogs of known heme transporter proteins were found within the Ruegeria sp. TrichCH4B genome. The identified heme uptake and utilization system appears to be functional, as the heme genes were upregulated under iron stress, the bacterium could grow on ferricporphyrin complexes as the sole iron source, and internalization of 55 Fe from ferric protoporphyrin IX was observed. The potential ability to utilize heme in the Roseobacter clade appears to be common, as half of the isolates in the RoseoBase database were found to have a complete heme uptake system. A degenerate primer set was designed and successfully used to identify the putative heme oxygenase gene (hmus) in the roseobacter heme uptake system from diverse nonenriched marine environments. This study found that members of the Roseobacter clade are capable of utilizing heme as an iron source and that this capability may be present in all types of marine environments. The results of this study add a new perspective to the current picture of iron cycling in marine systems, whereby relatively refractory intracellular pools of heme-bound iron may be taken up quickly and directly reincorporated into living bacteria without previous degradation or the necessity of a siderophore intermediate.

Research paper thumbnail of Detection of Non-Photochemical Superoxide in Coastal and Open Ocean Seawater: Particulate Versus Dissolved Sources

Research paper thumbnail of Extracellular Production of Reactive Oxygen Species by Marine Microbiota

The reactive oxygen species (ROS) superoxide (O2-) and hydrogen peroxide (H2O2) are important to ... more The reactive oxygen species (ROS) superoxide (O2-) and hydrogen peroxide (H2O2) are important to the cycling of trace metals and carbon in marine systems. Previous studies have shown that biological ROS production in the ocean may be significant. We examined the ability of five common species of diatoms to produce and break down ROS in the presence and absence of light by suspending cells on filters and measuring downstream ROS concentrations using chemiluminescence probes. Results show a wide range of rates (undetectable to 7.3 x 10-16 mol cell-1 hr-1) and suggest that extracellular ROS production occurs through a variety of pathways. H2O2 decay appears to be mediated primarily by active cell processes, while O2- appears to occur through a combination of active and passive cell processes. Extracellular H2O2 production and decay were also determined for twelve species of heterotrophic bacteria using two different methodologies. Measured decay rates were consistent despite methodological differences. By contrast, large variability of production rates was observed even between replicates of the same species measured using the same methodology. Although production rates cannot be stated with certainty, it is likely that extracellular H2O2 production occurs in most bacterial species.

Research paper thumbnail of Measurement of dark, particle-generated superoxide and hydrogen peroxide production and decay in the subtropical and temperate North Pacific Ocean

Deep Sea Research Part I: Oceanographic Research Papers, 2016

Reactive oxygen species (ROS), which include the superoxide radical (O 2-) and hydrogen peroxide ... more Reactive oxygen species (ROS), which include the superoxide radical (O 2-) and hydrogen peroxide (H 2 O 2), are thought to be generated mostly through photochemical reactions and biological activity in seawater and can influence trace metal speciation in the ocean. This study reports the results of an intercomparison of two methods to measure particle-generated [O 2-concentrations that ranged from undetectable to 0.02 nM, with production rates less than 0.6 nM hr-1 and decay rate coefficients from 0.003 to 0.014 s-1. The southern California Current Ecosystem had particle-generated O 2 concentrations that ranged from undetectable to 0.05 nM, with production rates up to 4.7 nM hr-1 and decay rate coefficients from 0.006 to 0.017 s-1. H 2 O 2 concentrations were measured by chemiluminescence detection, using dark incubations of unfiltered water samples to simultaneously determine production and decay rates. H 2 O 2 concentrations at Station ALOHA ranged from 7 to 88 nM. Dark production rates and decay rate coefficients were low (mostly <1.5 nM hr-1 and <0.03 hr-1 , respectively); higher values were detected when biota were pre-concentrated with net tows. These rates of ROS production are lower than those reported by previous studies in other regions of the Pacific Ocean, but could still be significant compared to photochemical production.

Research paper thumbnail of Biological Production of Hydrogen Peroxide in Prochlorococcus-Dominated Oligotrophic Waters

Hydrogen peroxide, which can serve as both an oxidant and a reductant, is important to trace meta... more Hydrogen peroxide, which can serve as both an oxidant and a reductant, is important to trace metal cycling in marine environments. Hydrogen peroxide production is of particular interest in waters dominated by Prochlorococcus since these cyanobacteria have been shown to lack peroxide-destroying enzymes. We measured biological production of hydrogen peroxide in the Prochlorococcus-dominated oligotrophic waters of the North Pacific Subtropical Gyre. Samples, some of which were spiked with additional hydrogen peroxide, were incubated either in the dark or under a grow light over several hours, and total hydrogen peroxide concentration was measured at regular intervals. This allowed for simultaneous determination of production and decay rates. Both samples concentrated by filtration and samples of organisms concentrated by a net tow were also incubated and measured by the same methods. We will present rates of biological production and decay of hydrogen peroxide and compare them with rat...

Research paper thumbnail of Superoxide production and decay in the subtropical North Pacific

Research paper thumbnail of Acquisition of iron by Trichodesmium and associated bacteria in culture

Environmental Microbiology, 2011

Trichodesmium colonies contain an abundant microbial consortium that is likely to play a role in ... more Trichodesmium colonies contain an abundant microbial consortium that is likely to play a role in nutrient cycling within the colony. This study used laboratory cultures of Trichodesmium and two genome-sequenced strains of bacteria typical of Trichodesmium-associated microbes to develop an understanding of the cycling of iron, a potentially limiting micronutrient, within Trichodesmium colonies. We found that the ferric siderophores desferrioxamine B and aerobactin were not readily bioavailable to Trichodesmium, relative to ferric chloride or citrate-associated iron. In contrast, the representative bacterial strains we studied were able to acquire iron from all of the iron sources, implying that naturally occurring Trichodesmium-associated bacteria may be capable of utilizing a more diverse array of iron sources than Trichodesmium. From the organism-specific uptake data collected in this study, a theoretical Trichodesmium colony was designed to model whole colony iron uptake. The bacteria accounted for most (&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; 70%) of the iron acquired by the colony, highlighting the importance of determining organism-specific uptake in a complex environment. Our findings suggest that, although they may share the same micro-environment, Trichodesmium and its colony-associated microbial cohort may differ substantially in terms of iron acquisition strategy.

Research paper thumbnail of Uptake mechanisms for inorganic iron and ferric citrate in Trichodesmium erythraeum IMS101

Metallomics, 2014

Trichodesmium erythraeumIMS101 utilizes two different iron uptake systems to acquire iron from Fe... more Trichodesmium erythraeumIMS101 utilizes two different iron uptake systems to acquire iron from FeCl3and ferric citrate, potentially allowingTrichodesmiumto have a competitive advantage in its bacteria-rich colony environment.

Research paper thumbnail of Heme Uptake by Microscilla marina and Evidence for Heme Uptake Systems in the Genomes of Diverse Marine Bacteria

Applied and Environmental Microbiology, 2008

The ability to acquire diverse and abundant forms of iron would be expected to confer a survival ... more The ability to acquire diverse and abundant forms of iron would be expected to confer a survival advantage in the marine environment, where iron is scarce. Marine bacteria are known to use siderophores and inorganic iron, but their ability to use heme, an abundant intracellular iron form, has only been examined preliminarily. Microscilla marina , a cultured relative of a bacterial group frequently found on marine particulates, was used as a model organism to examine heme uptake. Searches of the genome revealed analogs to known heme transport proteins, and reverse transcription-quantitative PCR analysis of these genes showed that they were expressed and upregulated under iron stress and during growth on heme. M. marina was found to take up heme-bound iron and could grow on heme as a sole iron source, supporting the genetic evidence for heme transport. Similar putative heme transport components were identified in the genomes of diverse marine bacteria. These systems were found in the ...

Research paper thumbnail of Utilization of Heme as an Iron Source by Marine Alphaproteobacteria in the Roseobacter Clade

Applied and Environmental Microbiology, 2013

ABSTRACTThe bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine... more ABSTRACTThe bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microorganisms have rarely been examined. This study usedRuegeriasp. strain TrichCH4B as a model organism to study heme acquisition by a member of theRoseobacterclade. Analogs of known heme transporter proteins were found within theRuegeriasp. TrichCH4B genome. The identified heme uptake and utilization system appears to be functional, as the heme genes were upregulated under iron stress, the bacterium could grow on ferric-porphyrin complexes as the sole iron source, and internalization of55Fe from ferric protoporphyrin IX was observed. The potential ability to utilize heme in theRoseobacterclade appears to be common, as half of the isolates in the RoseoBase database were found to have a complete heme uptake system. A degenerate primer set was designed and successfully used to identify the putative heme oxygenase gene (hmus) in the roseobacter heme uptake system from diverse nonenriched...

Research paper thumbnail of Microbial iron cycling on Trichodesmium colonies : laboratory culture studies of Trichodesmium and associated model organisms

Research paper thumbnail of Pervasive iron limitation at subsurface chlorophyll maxima of the California Current

Subsurface chlorophyll maximum layers (SCMLs) are nearly ubiquitous in stratified water columns a... more 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. Here we present multiple lines of evidence demonstrating that iron (Fe) limits or with light co-limits 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, biogeochemical proxies for Fe limitation peaked in SCML waters, and transcripts of diatom and picoeukaryote Fe stress genes were strikingly abundant in SCML metatranscriptomes. A 40-year time-series indicates that SCMLs in ...

Research paper thumbnail of Species-Level Variability in Extracellular Production Rates of Reactive Oxygen Species by Diatoms

Frontiers in Chemistry, 2016

Biological production and decay of the reactive oxygen species (ROS) hydrogen peroxide (H 2 O 2) ... more Biological production and decay of the reactive oxygen species (ROS) hydrogen peroxide (H 2 O 2) and superoxide (O −) likely have significant effects on the cycling of trace metals 2 and carbon in marine systems. In this study, extracellular production rates of H 2 O 2 and O − were determined for five species of marine diatoms in the presence and absence 2 of light. Production of both ROS was measured in parallel by suspending cells on filters and measuring the ROS downstream using chemiluminescence probes. In addition, the ability of these organisms to break down O − and H 2 O 2 was examined by measuring 2 recovery of O − and H 2 O 2 added to the influent medium. O − production rates ranged 2 2 from undetectable to 7.3 × 10 −16 mol cell −1 h −1 , while H 2 O 2 production rates ranged from undetectable to 3.4 × 10 −16 mol cell −1 h −1. Results suggest that extracellular ROS production occurs through a variety of pathways even amongst organisms of the same genus. Thalassiosira spp. produced more O − in light than dark, even when the organisms 2 were killed, indicating that O − is produced via a passive photochemical process on the 2 cell surface. The ratio of H 2 O 2 to O − production rates was consistent with production 2 of H 2 O 2 solely through dismutation of O − for T. oceanica, while T. pseudonana made 2 much more H 2 O 2 than O −. T. weissflogii only produced H 2 O 2 when stressed or killed. 2 P. tricornutum cells did not make cell-associated ROS, but did secrete H 2 O 2-producing substances into the growth medium. In all organisms, recovery rates for killed cultures (94-100% H 2 O 2 ; 10-80% O −) were consistently higher than those for live cultures 2 (65-95% H 2 O 2 ; 10-50% O −). While recovery rates for killed cultures in H 2 O 2 indicate that 2 nearly all H 2 O 2 was degraded by active cell processes, O − decay appeared to occur via 2 a combination of active and passive processes. Overall, this study shows that the rates and pathways for ROS production and decay vary greatly among diatom species, even between those that are closely related, and as a function of light conditions.

Research paper thumbnail of Measurement of dark, particle-generated superoxide and hydrogen peroxide production and decay in the subtropical and temperate North Pacific Ocean

Reactive oxygen species (ROS), which include the superoxide radical (O2-) and hydrogen peroxide (... more Reactive oxygen species (ROS), which include the superoxide radical (O2-) and hydrogen peroxide (H2O2), are thought to be generated mostly through photochemical reactions and biological activity in seawater and can influence trace metal speciation in the ocean. This study reports the results of an intercomparison of two methods to measure particle-generated [O2-] in seawater samples, as well as measurements of particle-generated O2- and H2O2 concentrations, decay kinetics, and dark production rates in seawater samples at Station ALOHA and (O2- only) in the southern California Current Ecosystem. O2- was measured using two different methods relying on chemiluminescence detection. The first method measured the difference between steady-state [O2-] in filtered and unfiltered seawater, while the second method (standard method) measured O2- decay to baseline in freshly filtered seawater. Because both methods detected [O2-] relative to the background signal from filtered seawater, both should have measured [O2-] generated by particles (presumably biota). However, the O2- concentrations determined by the first method were always much smaller than those obtained from the second (standard) method. Follow-up laboratory and field experiments showed that the increased signal in the standard method was due to a filtration artifact that could neither be eliminated nor consistently accounted for under the tested conditions. We therefore recommend the first method for measuring particle-generated [O2-]. Measured by this method, Station ALOHA had particle-generated O2- concentrations that ranged from undetectable to 0.03 nM, with production rates less than 0.6 nM hr-1 and decay rate coefficients from 0.003 to 0.014 s-1. The southern California Current Ecosystem had particle-generated O2- concentrations that ranged from undetectable to 0.05 nM, with production rates up to 3.1 nM hr-1 and decay rate coefficients from 0.006 to 0.017 s-1. H2O2 concentrations were measured by chemiluminescence detection, using dark incubations of unfiltered water samples to simultaneously determine production and decay rates. H2O2 concentrations at Station ALOHA ranged from 7 to 88 nM. Dark production rates and decay rate coefficients were low (mostly <1.5 nM hr-1 and <0.03 hr-1, respectively); higher values were detected when biota were pre-concentrated with net tows. These rates of ROS production are lower than those reported by previous studies in other regions of the Pacific Ocean, but could still be significant compared to photochemical production.

Research paper thumbnail of Marine Alphaproteobacteria in the Utilization of Heme as an Iron Source by

The bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microor... more The bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microorganisms have rarely been examined. This study used Ruegeria sp. strain TrichCH4B as a model organism to study heme acquisition by a member of the Roseobacter clade. Analogs of known heme transporter proteins were found within the Ruegeria sp. TrichCH4B genome. The identified heme uptake and utilization system appears to be functional, as the heme genes were upregulated under iron stress, the bacterium could grow on ferricporphyrin complexes as the sole iron source, and internalization of 55 Fe from ferric protoporphyrin IX was observed. The potential ability to utilize heme in the Roseobacter clade appears to be common, as half of the isolates in the RoseoBase database were found to have a complete heme uptake system. A degenerate primer set was designed and successfully used to identify the putative heme oxygenase gene (hmus) in the roseobacter heme uptake system from diverse nonenriched marine environments. This study found that members of the Roseobacter clade are capable of utilizing heme as an iron source and that this capability may be present in all types of marine environments. The results of this study add a new perspective to the current picture of iron cycling in marine systems, whereby relatively refractory intracellular pools of heme-bound iron may be taken up quickly and directly reincorporated into living bacteria without previous degradation or the necessity of a siderophore intermediate.

Research paper thumbnail of Utilization of Heme as an Iron Source by Marine Alphaproteobacteria in the Roseobacter Clade

Applied and Environmental Microbiology, Sep 15, 2013

The bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microor... more The bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microorganisms have rarely been examined. This study used Ruegeria sp. strain TrichCH4B as a model organism to study heme acquisition by a member of the Roseobacter clade. Analogs of known heme transporter proteins were found within the Ruegeria sp. TrichCH4B genome. The identified heme uptake and utilization system appears to be functional, as the heme genes were upregulated under iron stress, the bacterium could grow on ferricporphyrin complexes as the sole iron source, and internalization of 55 Fe from ferric protoporphyrin IX was observed. The potential ability to utilize heme in the Roseobacter clade appears to be common, as half of the isolates in the RoseoBase database were found to have a complete heme uptake system. A degenerate primer set was designed and successfully used to identify the putative heme oxygenase gene (hmus) in the roseobacter heme uptake system from diverse nonenriched marine environments. This study found that members of the Roseobacter clade are capable of utilizing heme as an iron source and that this capability may be present in all types of marine environments. The results of this study add a new perspective to the current picture of iron cycling in marine systems, whereby relatively refractory intracellular pools of heme-bound iron may be taken up quickly and directly reincorporated into living bacteria without previous degradation or the necessity of a siderophore intermediate.

Research paper thumbnail of Detection of Non-Photochemical Superoxide in Coastal and Open Ocean Seawater: Particulate Versus Dissolved Sources

Research paper thumbnail of Extracellular Production of Reactive Oxygen Species by Marine Microbiota

The reactive oxygen species (ROS) superoxide (O2-) and hydrogen peroxide (H2O2) are important to ... more The reactive oxygen species (ROS) superoxide (O2-) and hydrogen peroxide (H2O2) are important to the cycling of trace metals and carbon in marine systems. Previous studies have shown that biological ROS production in the ocean may be significant. We examined the ability of five common species of diatoms to produce and break down ROS in the presence and absence of light by suspending cells on filters and measuring downstream ROS concentrations using chemiluminescence probes. Results show a wide range of rates (undetectable to 7.3 x 10-16 mol cell-1 hr-1) and suggest that extracellular ROS production occurs through a variety of pathways. H2O2 decay appears to be mediated primarily by active cell processes, while O2- appears to occur through a combination of active and passive cell processes. Extracellular H2O2 production and decay were also determined for twelve species of heterotrophic bacteria using two different methodologies. Measured decay rates were consistent despite methodological differences. By contrast, large variability of production rates was observed even between replicates of the same species measured using the same methodology. Although production rates cannot be stated with certainty, it is likely that extracellular H2O2 production occurs in most bacterial species.

Research paper thumbnail of Measurement of dark, particle-generated superoxide and hydrogen peroxide production and decay in the subtropical and temperate North Pacific Ocean

Deep Sea Research Part I: Oceanographic Research Papers, 2016

Reactive oxygen species (ROS), which include the superoxide radical (O 2-) and hydrogen peroxide ... more Reactive oxygen species (ROS), which include the superoxide radical (O 2-) and hydrogen peroxide (H 2 O 2), are thought to be generated mostly through photochemical reactions and biological activity in seawater and can influence trace metal speciation in the ocean. This study reports the results of an intercomparison of two methods to measure particle-generated [O 2-concentrations that ranged from undetectable to 0.02 nM, with production rates less than 0.6 nM hr-1 and decay rate coefficients from 0.003 to 0.014 s-1. The southern California Current Ecosystem had particle-generated O 2 concentrations that ranged from undetectable to 0.05 nM, with production rates up to 4.7 nM hr-1 and decay rate coefficients from 0.006 to 0.017 s-1. H 2 O 2 concentrations were measured by chemiluminescence detection, using dark incubations of unfiltered water samples to simultaneously determine production and decay rates. H 2 O 2 concentrations at Station ALOHA ranged from 7 to 88 nM. Dark production rates and decay rate coefficients were low (mostly <1.5 nM hr-1 and <0.03 hr-1 , respectively); higher values were detected when biota were pre-concentrated with net tows. These rates of ROS production are lower than those reported by previous studies in other regions of the Pacific Ocean, but could still be significant compared to photochemical production.

Research paper thumbnail of Biological Production of Hydrogen Peroxide in Prochlorococcus-Dominated Oligotrophic Waters

Hydrogen peroxide, which can serve as both an oxidant and a reductant, is important to trace meta... more Hydrogen peroxide, which can serve as both an oxidant and a reductant, is important to trace metal cycling in marine environments. Hydrogen peroxide production is of particular interest in waters dominated by Prochlorococcus since these cyanobacteria have been shown to lack peroxide-destroying enzymes. We measured biological production of hydrogen peroxide in the Prochlorococcus-dominated oligotrophic waters of the North Pacific Subtropical Gyre. Samples, some of which were spiked with additional hydrogen peroxide, were incubated either in the dark or under a grow light over several hours, and total hydrogen peroxide concentration was measured at regular intervals. This allowed for simultaneous determination of production and decay rates. Both samples concentrated by filtration and samples of organisms concentrated by a net tow were also incubated and measured by the same methods. We will present rates of biological production and decay of hydrogen peroxide and compare them with rat...

Research paper thumbnail of Superoxide production and decay in the subtropical North Pacific

Research paper thumbnail of Acquisition of iron by Trichodesmium and associated bacteria in culture

Environmental Microbiology, 2011

Trichodesmium colonies contain an abundant microbial consortium that is likely to play a role in ... more Trichodesmium colonies contain an abundant microbial consortium that is likely to play a role in nutrient cycling within the colony. This study used laboratory cultures of Trichodesmium and two genome-sequenced strains of bacteria typical of Trichodesmium-associated microbes to develop an understanding of the cycling of iron, a potentially limiting micronutrient, within Trichodesmium colonies. We found that the ferric siderophores desferrioxamine B and aerobactin were not readily bioavailable to Trichodesmium, relative to ferric chloride or citrate-associated iron. In contrast, the representative bacterial strains we studied were able to acquire iron from all of the iron sources, implying that naturally occurring Trichodesmium-associated bacteria may be capable of utilizing a more diverse array of iron sources than Trichodesmium. From the organism-specific uptake data collected in this study, a theoretical Trichodesmium colony was designed to model whole colony iron uptake. The bacteria accounted for most (&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; 70%) of the iron acquired by the colony, highlighting the importance of determining organism-specific uptake in a complex environment. Our findings suggest that, although they may share the same micro-environment, Trichodesmium and its colony-associated microbial cohort may differ substantially in terms of iron acquisition strategy.

Research paper thumbnail of Uptake mechanisms for inorganic iron and ferric citrate in Trichodesmium erythraeum IMS101

Metallomics, 2014

Trichodesmium erythraeumIMS101 utilizes two different iron uptake systems to acquire iron from Fe... more Trichodesmium erythraeumIMS101 utilizes two different iron uptake systems to acquire iron from FeCl3and ferric citrate, potentially allowingTrichodesmiumto have a competitive advantage in its bacteria-rich colony environment.

Research paper thumbnail of Heme Uptake by Microscilla marina and Evidence for Heme Uptake Systems in the Genomes of Diverse Marine Bacteria

Applied and Environmental Microbiology, 2008

The ability to acquire diverse and abundant forms of iron would be expected to confer a survival ... more The ability to acquire diverse and abundant forms of iron would be expected to confer a survival advantage in the marine environment, where iron is scarce. Marine bacteria are known to use siderophores and inorganic iron, but their ability to use heme, an abundant intracellular iron form, has only been examined preliminarily. Microscilla marina , a cultured relative of a bacterial group frequently found on marine particulates, was used as a model organism to examine heme uptake. Searches of the genome revealed analogs to known heme transport proteins, and reverse transcription-quantitative PCR analysis of these genes showed that they were expressed and upregulated under iron stress and during growth on heme. M. marina was found to take up heme-bound iron and could grow on heme as a sole iron source, supporting the genetic evidence for heme transport. Similar putative heme transport components were identified in the genomes of diverse marine bacteria. These systems were found in the ...

Research paper thumbnail of Utilization of Heme as an Iron Source by Marine Alphaproteobacteria in the Roseobacter Clade

Applied and Environmental Microbiology, 2013

ABSTRACTThe bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine... more ABSTRACTThe bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microorganisms have rarely been examined. This study usedRuegeriasp. strain TrichCH4B as a model organism to study heme acquisition by a member of theRoseobacterclade. Analogs of known heme transporter proteins were found within theRuegeriasp. TrichCH4B genome. The identified heme uptake and utilization system appears to be functional, as the heme genes were upregulated under iron stress, the bacterium could grow on ferric-porphyrin complexes as the sole iron source, and internalization of55Fe from ferric protoporphyrin IX was observed. The potential ability to utilize heme in theRoseobacterclade appears to be common, as half of the isolates in the RoseoBase database were found to have a complete heme uptake system. A degenerate primer set was designed and successfully used to identify the putative heme oxygenase gene (hmus) in the roseobacter heme uptake system from diverse nonenriched...

Research paper thumbnail of Microbial iron cycling on Trichodesmium colonies : laboratory culture studies of Trichodesmium and associated model organisms

Research paper thumbnail of Pervasive iron limitation at subsurface chlorophyll maxima of the California Current

Subsurface chlorophyll maximum layers (SCMLs) are nearly ubiquitous in stratified water columns a... more 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. Here we present multiple lines of evidence demonstrating that iron (Fe) limits or with light co-limits 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, biogeochemical proxies for Fe limitation peaked in SCML waters, and transcripts of diatom and picoeukaryote Fe stress genes were strikingly abundant in SCML metatranscriptomes. A 40-year time-series indicates that SCMLs in ...

Research paper thumbnail of Species-Level Variability in Extracellular Production Rates of Reactive Oxygen Species by Diatoms

Frontiers in Chemistry, 2016

Biological production and decay of the reactive oxygen species (ROS) hydrogen peroxide (H 2 O 2) ... more Biological production and decay of the reactive oxygen species (ROS) hydrogen peroxide (H 2 O 2) and superoxide (O −) likely have significant effects on the cycling of trace metals 2 and carbon in marine systems. In this study, extracellular production rates of H 2 O 2 and O − were determined for five species of marine diatoms in the presence and absence 2 of light. Production of both ROS was measured in parallel by suspending cells on filters and measuring the ROS downstream using chemiluminescence probes. In addition, the ability of these organisms to break down O − and H 2 O 2 was examined by measuring 2 recovery of O − and H 2 O 2 added to the influent medium. O − production rates ranged 2 2 from undetectable to 7.3 × 10 −16 mol cell −1 h −1 , while H 2 O 2 production rates ranged from undetectable to 3.4 × 10 −16 mol cell −1 h −1. Results suggest that extracellular ROS production occurs through a variety of pathways even amongst organisms of the same genus. Thalassiosira spp. produced more O − in light than dark, even when the organisms 2 were killed, indicating that O − is produced via a passive photochemical process on the 2 cell surface. The ratio of H 2 O 2 to O − production rates was consistent with production 2 of H 2 O 2 solely through dismutation of O − for T. oceanica, while T. pseudonana made 2 much more H 2 O 2 than O −. T. weissflogii only produced H 2 O 2 when stressed or killed. 2 P. tricornutum cells did not make cell-associated ROS, but did secrete H 2 O 2-producing substances into the growth medium. In all organisms, recovery rates for killed cultures (94-100% H 2 O 2 ; 10-80% O −) were consistently higher than those for live cultures 2 (65-95% H 2 O 2 ; 10-50% O −). While recovery rates for killed cultures in H 2 O 2 indicate that 2 nearly all H 2 O 2 was degraded by active cell processes, O − decay appeared to occur via 2 a combination of active and passive processes. Overall, this study shows that the rates and pathways for ROS production and decay vary greatly among diatom species, even between those that are closely related, and as a function of light conditions.

Research paper thumbnail of Measurement of dark, particle-generated superoxide and hydrogen peroxide production and decay in the subtropical and temperate North Pacific Ocean

Reactive oxygen species (ROS), which include the superoxide radical (O2-) and hydrogen peroxide (... more Reactive oxygen species (ROS), which include the superoxide radical (O2-) and hydrogen peroxide (H2O2), are thought to be generated mostly through photochemical reactions and biological activity in seawater and can influence trace metal speciation in the ocean. This study reports the results of an intercomparison of two methods to measure particle-generated [O2-] in seawater samples, as well as measurements of particle-generated O2- and H2O2 concentrations, decay kinetics, and dark production rates in seawater samples at Station ALOHA and (O2- only) in the southern California Current Ecosystem. O2- was measured using two different methods relying on chemiluminescence detection. The first method measured the difference between steady-state [O2-] in filtered and unfiltered seawater, while the second method (standard method) measured O2- decay to baseline in freshly filtered seawater. Because both methods detected [O2-] relative to the background signal from filtered seawater, both should have measured [O2-] generated by particles (presumably biota). However, the O2- concentrations determined by the first method were always much smaller than those obtained from the second (standard) method. Follow-up laboratory and field experiments showed that the increased signal in the standard method was due to a filtration artifact that could neither be eliminated nor consistently accounted for under the tested conditions. We therefore recommend the first method for measuring particle-generated [O2-]. Measured by this method, Station ALOHA had particle-generated O2- concentrations that ranged from undetectable to 0.03 nM, with production rates less than 0.6 nM hr-1 and decay rate coefficients from 0.003 to 0.014 s-1. The southern California Current Ecosystem had particle-generated O2- concentrations that ranged from undetectable to 0.05 nM, with production rates up to 3.1 nM hr-1 and decay rate coefficients from 0.006 to 0.017 s-1. H2O2 concentrations were measured by chemiluminescence detection, using dark incubations of unfiltered water samples to simultaneously determine production and decay rates. H2O2 concentrations at Station ALOHA ranged from 7 to 88 nM. Dark production rates and decay rate coefficients were low (mostly <1.5 nM hr-1 and <0.03 hr-1, respectively); higher values were detected when biota were pre-concentrated with net tows. These rates of ROS production are lower than those reported by previous studies in other regions of the Pacific Ocean, but could still be significant compared to photochemical production.