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Zackary Johnson

Juli Plant Grainger Associate Professor of Biological Oceanography and Marine Biotechnology
Marine Science and Conservation
135 Duke Marine Lab Rd., Duke Marine Laboratory, Beaufort, NC 28516

Selected Publications


Evidence for Kilometer-Scale Biophysical Features at the Gulf Stream Front

Journal Article Journal of Geophysical Research: Oceans · March 1, 2024 Understanding the interplay of ocean physics and biology at the submesoscale and below (<30 km) is an ongoing challenge in oceanography. While poorly constrained, these scales may be of critical importance for understanding how changing ocean dynamics will ... Full text Cite

Importance of Dense Aquatic Vegetation in Seasonal Phosphate and Particle Transport in an Agricultural Headwater Stream

Journal Article Water Resources Research · September 1, 2023 Agricultural headwater streams and ditches commonly host dense stands of aquatic vegetation that grow and decay over seasons and exert physical and biological controls on the transport of nutrients from cropland to larger rivers. This study examined change ... Full text Cite

Supranutrition of microalgal docosahexaenoic acid and calcidiol improved growth performance, tissue lipid profiles, and tibia characteristics of broiler chickens.

Journal Article Journal of animal science and biotechnology · March 2023 BackgroundDocosahexaenoic acid (DHA) and calcidiol could be enriched in chicken for improving public nutrition and health. It remains unclear if supranutritional levels of DHA and calcidiol impair growth performance or metabolism of broiler chicke ... Full text Cite

A Gulf Stream frontal eddy harbors a distinct microbiome compared to adjacent waters.

Journal Article PloS one · January 2023 Mesoscale oceanographic features, including eddies, have the potential to alter productivity and other biogeochemical rates in the ocean. Here, we examine the microbiome of a cyclonic, Gulf Stream frontal eddy, with a distinct origin and environmental para ... Full text Cite

Robust ocean color from drones: Viewing geometry, sky reflection removal, uncertainty analysis, and a survey of the Gulf Stream front

Journal Article Limnology and Oceanography: Methods · October 1, 2022 Accurate and robust retrieval of ocean color from remote sensing enables critical observations of aquatic natural systems, from open ocean biological oceanography, coastal biodiversity, and water quality for human health. In the last decade, studies have i ... Full text Cite

Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables.

Journal Article Environmental microbiology · September 2022 Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host-associated and engineered systems. In spite of global change both altering environmental averages and increasing extreme events, there ha ... Full text Open Access Cite

Patchy Blooms and Multifarious Ecotypes of Labyrinthulomycetes Protists and Their Implication in Vertical Carbon Export in the Pelagic Eastern Indian Ocean.

Journal Article Microbiology spectrum · June 2022 Labyrinthulomycetes protists are an important heterotrophic component of microeukaryotes in the world's oceans, but their distribution patterns and ecological roles are poorly understood in pelagic waters. This study employed flow cytometry and high-throug ... Full text Cite

Comparative performance and technoeconomic analyses of two microalgae harvesting systems evaluated at a commercially relevant scale

Journal Article Algal Research · May 1, 2022 Using a commercially scalable system designed for processing thousands of liters a day, here we evaluated the factors that affected the performance, energy consumption and capital/operating costs of both flocculation-based and filtration-based algal harves ... Full text Cite

Vertical community patterns of Labyrinthulomycetes protists reveal their potential importance in the oceanic biological pump.

Journal Article Environmental microbiology · April 2022 The biological pump plays a vital role in exporting organic particles into the deep ocean for long-term carbon sequestration. However, much remains unknown about some of its key microbial players. In this study, Labyrinthulomycetes protists (LP) were used ... Full text Cite

Protistan plankton communities in the Galápagos Archipelago respond to changes in deep water masses resulting from the 2015/16 El Niño.

Journal Article Environmental microbiology · April 2022 The Galápagos Archipelago lies within the Eastern Equatorial Pacific Ocean at the convergence of major ocean currents that are subject to changes in circulation. The nutrient-rich Equatorial Undercurrent upwells from the west onto the Galápagos platform, s ... Full text Cite

Niche Partitioning of Labyrinthulomycete Protists Across Sharp Coastal Gradients and Their Putative Relationships With Bacteria and Fungi.

Journal Article Frontiers in microbiology · January 2022 While planktonic microbes play key roles in the coastal oceans, our understanding of heterotrophic microeukaryotes' ecology, particularly their spatiotemporal patterns, drivers, and functions, remains incomplete. In this study, we focus on a ubiquitous mar ... Full text Cite

Transforming the Future of Marine Aquaculture: A Circular Economy Approach

Journal Article Oceanography · 2022 By mid-century, society will need to significantly intensify the output of its food production system while simultaneously reducing that system’s detrimental impacts on climate, land use, freshwater resources, and biodiversity. This will require fi ... Full text Cite

Patchy Distributions and Distinct Niche Partitioning of Mycoplankton Populations across a Nearshore to Open Ocean Gradient.

Journal Article Microbiology spectrum · December 2021 Evidence increasingly suggests planktonic fungi (or mycoplankton) play an important role in marine food webs and biogeochemical cycles. In order to better understand their ecological role and how oceanographic gradients from the coastal to open ocean shape ... Full text Cite

A database of ocean primary productivity from the 14C method

Journal Article Limnology And Oceanography Letters · April 1, 2021 The database on ocean primary productivity comprises over two decades (1985–2008) of data that the authors have participated in collecting, using the assimilation of inorganic 14C through photosynthesis, in incubations carried out in situ. The dataset is p ... Full text Cite

Supplemental dietary full-fatted and defatted Desmodesmus sp. exerted similar effects on growth performance, gut health, and excreta hydrothermal liquefaction of broiler chicks

Journal Article Algal Research · April 1, 2021 This study determined effects of full-fatted (C046, 41% crude protein) and lipid extracted (LEA, 39% crude protein) microalgae Desmodesmus sp. on growth performance, gut health, and excreta hydrothermal liquefaction of broiler chickens. Two experiments wer ... Full text Cite

Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity.

Journal Article The ISME journal · January 2021 Ambient conditions shape microbiome responses to both short- and long-duration environment changes through processes including physiological acclimation, compositional shifts, and evolution. Thus, we predict that microbial communities inhabiting locations ... Full text Cite

Annual Partitioning Patterns of Labyrinthulomycetes Protists Reveal Their Multifaceted Role in Marine Microbial Food Webs.

Journal Article Applied and environmental microbiology · January 2021 Heterotrophic microbes play a key role in remineralizing organic material in the coastal ocean. While there is a significant body of literature examining heterotrophic bacterioplankton and phytoplankton communities, much less is known about the diversity, ... Full text Cite

Evidence for Kilometer-Scale Biophysical Features at the Gulf Stream Front

Journal Article Journal of Geophysical Research: Oceans · March 1, 2024 Understanding the interplay of ocean physics and biology at the submesoscale and below (<30 km) is an ongoing challenge in oceanography. While poorly constrained, these scales may be of critical importance for understanding how changing ocean dynamics will ... Full text Cite

Importance of Dense Aquatic Vegetation in Seasonal Phosphate and Particle Transport in an Agricultural Headwater Stream

Journal Article Water Resources Research · September 1, 2023 Agricultural headwater streams and ditches commonly host dense stands of aquatic vegetation that grow and decay over seasons and exert physical and biological controls on the transport of nutrients from cropland to larger rivers. This study examined change ... Full text Cite

Supranutrition of microalgal docosahexaenoic acid and calcidiol improved growth performance, tissue lipid profiles, and tibia characteristics of broiler chickens.

Journal Article Journal of animal science and biotechnology · March 2023 BackgroundDocosahexaenoic acid (DHA) and calcidiol could be enriched in chicken for improving public nutrition and health. It remains unclear if supranutritional levels of DHA and calcidiol impair growth performance or metabolism of broiler chicke ... Full text Cite

A Gulf Stream frontal eddy harbors a distinct microbiome compared to adjacent waters.

Journal Article PloS one · January 2023 Mesoscale oceanographic features, including eddies, have the potential to alter productivity and other biogeochemical rates in the ocean. Here, we examine the microbiome of a cyclonic, Gulf Stream frontal eddy, with a distinct origin and environmental para ... Full text Cite

Robust ocean color from drones: Viewing geometry, sky reflection removal, uncertainty analysis, and a survey of the Gulf Stream front

Journal Article Limnology and Oceanography: Methods · October 1, 2022 Accurate and robust retrieval of ocean color from remote sensing enables critical observations of aquatic natural systems, from open ocean biological oceanography, coastal biodiversity, and water quality for human health. In the last decade, studies have i ... Full text Cite

Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables.

Journal Article Environmental microbiology · September 2022 Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host-associated and engineered systems. In spite of global change both altering environmental averages and increasing extreme events, there ha ... Full text Open Access Cite

Patchy Blooms and Multifarious Ecotypes of Labyrinthulomycetes Protists and Their Implication in Vertical Carbon Export in the Pelagic Eastern Indian Ocean.

Journal Article Microbiology spectrum · June 2022 Labyrinthulomycetes protists are an important heterotrophic component of microeukaryotes in the world's oceans, but their distribution patterns and ecological roles are poorly understood in pelagic waters. This study employed flow cytometry and high-throug ... Full text Cite

Comparative performance and technoeconomic analyses of two microalgae harvesting systems evaluated at a commercially relevant scale

Journal Article Algal Research · May 1, 2022 Using a commercially scalable system designed for processing thousands of liters a day, here we evaluated the factors that affected the performance, energy consumption and capital/operating costs of both flocculation-based and filtration-based algal harves ... Full text Cite

Vertical community patterns of Labyrinthulomycetes protists reveal their potential importance in the oceanic biological pump.

Journal Article Environmental microbiology · April 2022 The biological pump plays a vital role in exporting organic particles into the deep ocean for long-term carbon sequestration. However, much remains unknown about some of its key microbial players. In this study, Labyrinthulomycetes protists (LP) were used ... Full text Cite

Protistan plankton communities in the Galápagos Archipelago respond to changes in deep water masses resulting from the 2015/16 El Niño.

Journal Article Environmental microbiology · April 2022 The Galápagos Archipelago lies within the Eastern Equatorial Pacific Ocean at the convergence of major ocean currents that are subject to changes in circulation. The nutrient-rich Equatorial Undercurrent upwells from the west onto the Galápagos platform, s ... Full text Cite

Niche Partitioning of Labyrinthulomycete Protists Across Sharp Coastal Gradients and Their Putative Relationships With Bacteria and Fungi.

Journal Article Frontiers in microbiology · January 2022 While planktonic microbes play key roles in the coastal oceans, our understanding of heterotrophic microeukaryotes' ecology, particularly their spatiotemporal patterns, drivers, and functions, remains incomplete. In this study, we focus on a ubiquitous mar ... Full text Cite

Transforming the Future of Marine Aquaculture: A Circular Economy Approach

Journal Article Oceanography · 2022 By mid-century, society will need to significantly intensify the output of its food production system while simultaneously reducing that system’s detrimental impacts on climate, land use, freshwater resources, and biodiversity. This will require fi ... Full text Cite

Patchy Distributions and Distinct Niche Partitioning of Mycoplankton Populations across a Nearshore to Open Ocean Gradient.

Journal Article Microbiology spectrum · December 2021 Evidence increasingly suggests planktonic fungi (or mycoplankton) play an important role in marine food webs and biogeochemical cycles. In order to better understand their ecological role and how oceanographic gradients from the coastal to open ocean shape ... Full text Cite

A database of ocean primary productivity from the 14C method

Journal Article Limnology And Oceanography Letters · April 1, 2021 The database on ocean primary productivity comprises over two decades (1985–2008) of data that the authors have participated in collecting, using the assimilation of inorganic 14C through photosynthesis, in incubations carried out in situ. The dataset is p ... Full text Cite

Supplemental dietary full-fatted and defatted Desmodesmus sp. exerted similar effects on growth performance, gut health, and excreta hydrothermal liquefaction of broiler chicks

Journal Article Algal Research · April 1, 2021 This study determined effects of full-fatted (C046, 41% crude protein) and lipid extracted (LEA, 39% crude protein) microalgae Desmodesmus sp. on growth performance, gut health, and excreta hydrothermal liquefaction of broiler chickens. Two experiments wer ... Full text Cite

Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity.

Journal Article The ISME journal · January 2021 Ambient conditions shape microbiome responses to both short- and long-duration environment changes through processes including physiological acclimation, compositional shifts, and evolution. Thus, we predict that microbial communities inhabiting locations ... Full text Cite

Annual Partitioning Patterns of Labyrinthulomycetes Protists Reveal Their Multifaceted Role in Marine Microbial Food Webs.

Journal Article Applied and environmental microbiology · January 2021 Heterotrophic microbes play a key role in remineralizing organic material in the coastal ocean. While there is a significant body of literature examining heterotrophic bacterioplankton and phytoplankton communities, much less is known about the diversity, ... Full text Cite

The challenges of detecting and attributing ocean acidification impacts on marine ecosystems

Journal Article ICES Journal of Marine Science · December 1, 2020 A substantial body of research now exists demonstrating sensitivities of marine organisms to ocean acidification (OA) in laboratory settings. However, corresponding in situ observations of marine species or ecosystem changes that can be unequivocally attri ... Full text Cite

Water reuse for sustainable microalgae cultivation: Current knowledge and future directions

Journal Article Resources, Conservation and Recycling · October 1, 2020 Microalgae hold great promise as environmentally sustainable sources of food, animal feed, and fuel. However, large amounts of water are used during microalgae cultivation and this negatively impacts economic viability and environmental sustainability. Reu ... Full text Cite

Reused cultivation water from a self-inhibiting alga does not inhibit other algae but alters their microbiomes

Journal Article Algal Research · October 1, 2020 Economical production of algal commodities (food, feed, and fuels) requires reusing cultivation water to reduce operating costs. While some algae strains show growth inhibition in reused water, other strains appear unaffected. Reusing water to grow differe ... Full text Cite

Acidification in the U.S. Southeast: Causes, Potential Consequences and the Role of the Southeast Ocean and Coastal Acidification Network.

Journal Article Frontiers in Marine Science · July 2020 Coastal acidification in southeastern U.S. estuaries and coastal waters is influenced by biological activity, run-off from the land, and increasing carbon dioxide in the atmosphere. Acidification can negatively impact coastal resources such as shellfish, f ... Full text Cite

Decarbonizing agriculture through the conversion of animal manure to dietary protein and ammonia fertilizer.

Journal Article Bioresource technology · February 2020 The decarbonization of agriculture faces many challenges and has received a level of attention insufficient to abate the worst effects of climate change and ensure a sustainable bioeconomy. Agricultural emissions are caused both by fossil-intensive fertili ... Full text Cite

Microbial communities across nearshore to offshore coastal transects are primarily shaped by distance and temperature.

Journal Article Environmental microbiology · October 2019 Recent studies have focused on linking marine microbial communities with environmental factors, yet, relatively little is known about the drivers of microbial community patterns across the complex gradients from the nearshore to open ocean. Here, we examin ... Full text Cite

Microalgae Scenedesmus sp. as a potential ingredient in low fishmeal diets for Atlantic salmon (Salmo salar L.)

Journal Article Aquaculture · February 25, 2019 Salmonid feeds can be formulated with high quality microalgae to maintain sustainability in the aquaculture industry. But, the suitability of different microalgae species as potential feed ingredients needs to be documented to enable ready acceptance by th ... Full text Cite

Reused Cultivation Water Accumulates Dissolved Organic Carbon and Uniquely Influences Different Marine Microalgae.

Journal Article Frontiers in bioengineering and biotechnology · January 2019 Reusing growth medium (water supplemented with nutrients) for microalgae cultivation is required for economical and environmentally sustainable production of algae bioproducts (fuels, feed, and food). However, reused medium often contains microbes and diss ... Full text Open Access Cite

Reused cultivation water accumulates dissolved organic carbon and uniquely influences different marine microalgae

Journal Article Frontiers in Bioengineering and Biotechnology · January 1, 2019 Reusing growth medium (water supplemented with nutrients) for microalgae cultivation is required for economical and environmentally sustainable production of algae bioproducts (fuels, feed, and food). However, reused medium often contains microbes and diss ... Full text Open Access Cite

Pervasive iron limitation at subsurface chlorophyll maxima of the California Current.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · December 2018 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 co ... Full text Cite

A High-Resolution Time Series Reveals Distinct Seasonal Patterns of Planktonic Fungi at a Temperate Coastal Ocean Site (Beaufort, North Carolina, USA).

Journal Article Applied and environmental microbiology · November 2018 There is a growing awareness of the ecological and biogeochemical importance of fungi in coastal marine systems. While highly diverse fungi have been discovered in these marine systems, still, little is known about their seasonality and associated drivers ... Full text Cite

High phylogenetic diversity and abundance pattern of Labyrinthulomycete protists in the coastal waters of the Bohai Sea.

Journal Article Environmental microbiology · August 2018 The unicellular Labyrinthulomycete protists have long been considered to play a significant role in ocean carbon cycling. However, their distribution and biogeochemical function remain poorly understood. We present a large-scale study of their spatiotempor ... Full text Cite

Integrating Algae with Bioenergy Carbon Capture and Storage (ABECCS) Increases Sustainability

Journal Article Earth's Future · March 1, 2018 Bioenergy carbon capture and storage (BECCS) has been proposed to reduce atmospheric CO2 concentrations, but concerns remain about competition for arable land and freshwater. The synergistic integration of algae production, which does not require arable la ... Full text Cite

Degradation of hydrogen peroxide at the ocean's surface: the influence of the microbial community on the realized thermal niche of Prochlorococcus.

Journal Article The ISME journal · February 2018 Prochlorococcus, the smallest and most abundant phytoplankter in the ocean, is highly sensitive to hydrogen peroxide (HOOH), and co-occurring heterotrophs such as Alteromonas facilitate the growth of Prochlorococcus by scavenging HOOH. Temperature is also ... Full text Cite

Ephemeral aggregate layers in the water column leave lasting footprints in the carbon cycle

Journal Article Limnology And Oceanography Letters · December 1, 2017 Marine aggregates play a critical role in the biological pump, both as a dominant component of carbon flux and as hotspots for organic matter remineralization by microbial communities. In this study, we used laboratory experiments to investigate how aggreg ... Full text Cite

Seasonal influence of scallop culture on nutrient flux, bacterial pathogens and bacterioplankton diversity across estuaries off the Bohai Sea Coast of Northern China.

Journal Article Marine pollution bulletin · November 2017 In this study, we investigated the environmental impacts of scallop culture on two coastal estuaries adjacent the Bohai Sea including developing a quantitative PCR assay to assess the abundance of the bacterial pathogens Escherichia coli and Vibrio parahae ... Full text Cite

Annual community patterns are driven by seasonal switching between closely related marine bacteria.

Journal Article The ISME journal · November 2017 This corrects the article DOI: 10.1038/ismej.2017.4. ... Full text Cite

Iron and vitamin interactions in marine diatom isolates and natural assemblages of the Northeast Pacific Ocean

Journal Article Limnology and Oceanography · September 1, 2017 Trace metals and B-vitamins play critical roles in regulating marine phytoplankton growth and composition. While some microorganisms are capable of producing certain B-vitamins, others cannot synthesize them and depend on an exogenous supply. Therefore, ex ... Full text Cite

Annual community patterns are driven by seasonal switching between closely related marine bacteria.

Journal Article The ISME journal · June 2017 Marine microbes exhibit seasonal cycles in community composition, yet the key drivers of these patterns and microbial population fidelity to specific environmental conditions remain to be determined. To begin addressing these questions, we characterized mi ... Full text Cite

Cross-study analysis of factors affecting algae cultivation in recycled medium for biofuel production

Journal Article Algal Research · June 1, 2017 Current high costs of commercial-scale algal biofuel production prevent the widespread use of this renewable fuel source. One cost-saving approach is the reuse of algae cultivation water after biomass harvesting, which reduces water pumping and treatment c ... Full text Cite

Abundance and molecular diversity of thraustochytrids in coastal waters of southern China.

Journal Article FEMS microbiology ecology · June 2017 Thraustochytrids are unicellular fungi-like (heterotrophic) marine protists that have long been considered to play an important role in the biogeochemical cycles of the coastal oceans. However, the significance of their ecological functions and their diver ... Full text Cite

Contrasting seasonal drivers of virus abundance and production in the North Pacific Ocean.

Journal Article PloS one · January 2017 The North Pacific Ocean (between approximately 0°N and 50°N) contains the largest continuous ecosystem on Earth. This region plays a vital role in the cycling of globally important nutrients as well as carbon. Although the microbial communities in this reg ... Full text Open Access Cite

Marine microalgae: Climate, energy, and food security from the sea

Journal Article Oceanography · December 1, 2016 Climate, energy, and food security are three of the greatest challenges society faces this century. Solutions for mitigating the effects of climate change often conflict with solutions for ensuring society’s future energy and food requirements. For example ... Full text Cite

Algal food and fuel coproduction can mitigate greenhouse gas emissions while improving land and water-use efficiency

Journal Article Environmental Research Letters · October 28, 2016 The goals of ensuring energy, water, food, and climate security can often conflict. Microalgae (algae) are being pursued as a feedstock for both food and fuels - primarily due to algae's high areal yield and ability to grow on non-arable land, thus avoidin ... Full text Cite

Diel regulation of hydrogen peroxide defenses by open ocean microbial communities

Journal Article Journal of Plankton Research · August 1, 2016 Hydrogen peroxide (HOOH) is omnipresent in natural waters. Given that sunlight is the primary source of HOOH, we investigated the relationship between time of day and microbial HOOH degradation. Genes encoding HOOHdegrading enzymes were significantly more ... Full text Cite

Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific.

Journal Article The ISME journal · July 2016 The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. W ... Full text Cite

Selective feeding by the giant barrel sponge enhances foraging efficiency

Journal Article Limnology and Oceanography · July 1, 2016 Foraging theory predicts the evolution of feeding behaviors that increase consumer fitness. Sponges were among the earliest metazoans on earth and developed a unique filter-feeding mechanism that does not rely on a nervous system. Once thought indiscrimina ... Full text Cite

Insensitivity of Diverse and Temporally Variable Particle-Associated Microbial Communities to Bulk Seawater Environmental Parameters.

Journal Article Applied and environmental microbiology · June 2016 UnlabelledThere is a growing recognition of the roles of marine microenvironments as reservoirs of biodiversity and as sites of enhanced biological activity and in facilitating biological interactions. Here, we examine the bacterial community inha ... Full text Cite

Variable but persistent coexistence of Prochlorococcus ecotypes along temperature gradients in the ocean's surface mixed layer.

Journal Article Environmental microbiology reports · April 2016 The vast majority of the phytoplankton communities in surface mixed layer of the oligotrophic ocean are numerically dominated by one of two ecotypes of Prochlorococcus, eMIT9312 or eMED4. In this study, we surveyed large latitudinal transects in the Atlant ... Full text Cite

Thermally adaptive tradeoffs in closely related marine bacterial strains.

Journal Article Environ Microbiol · July 2015 Time series studies have shown that some bacterial taxa occur only at specific times of the year while others are ubiquitous in spite of seasonal shifts in environmental variables. Here, we ask if these ubiquitous clades are generalists that grow over a wi ... Full text Link to item Cite

Demonstrated large-scale production of marine microalgae for fuels and feed

Journal Article Algal Research · July 1, 2015 We present the results from sustained tonne-quantity production of two novel strains of marine microalgae, the diatom Staurosira and the chlorophyte Desmodesmus, cultivated in a hybrid system of 25-m3 photobioreactors and 400-m2 open ponds at a large-scale ... Full text Cite

Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · June 2015 Theoretical studies predict that competition for limited resources reduces biodiversity to the point of ecological instability, whereas strong predator/prey interactions enhance the number of coexisting species and limit fluctuations in abundances. In open ... Full text Cite

Transdisciplinary science a path to understanding the interactions among ocean  acidification, ecosystems, and society

Journal Article Oceanography · June 1, 2015 The global nature of ocean acidification (OA) transcends habitats, ecosystems, regions, and science disciplines. The scientific community recognizes that the biggest challenge in improving understanding of how changing OA conditions affect ecosystems, and ... Full text Cite

Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities.

Journal Article The ISME journal · May 2015 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 ... Full text Cite

Techniques for quantifying phytoplankton biodiversity.

Journal Article Annual review of marine science · January 2015 The biodiversity of phytoplankton is a core measurement of the state and activity of marine ecosystems. In the context of historical approaches, we review recent major advances in the technologies that have enabled deeper characterization of the biodiversi ... Full text Cite

The ocean sampling day consortium.

Journal Article GigaScience · January 2015 Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega ... Full text Open Access Cite

Presence of Prochlorococcus in the aphotic waters of the western Pacific Ocean

Journal Article Biogeosciences · April 29, 2014 Prochlorococcus, the smallest but most abundant marine primary producer, plays an important role in carbon cycling of the global ocean. As a phototroph, Prochlorococcus is thought to be confined to the euphotic zone, with commonly observed maximum depths o ... Full text Cite

Distribution and diversity of planktonic fungi in the West Pacific Warm Pool.

Journal Article PloS one · January 2014 Fungi contribute substantially to biogeochemical cycles of terrestrial and marine habitats by decomposing matter and recycling nutrients. Yet, the diversity of their planktonic forms in the open ocean is poorly described. In this study, culture-independent ... Full text Cite

Smartphones: Powerful tools for geoscience education

Journal Article Eos · November 19, 2013 Full text Cite

In situ activity of a dominant Prochlorococcus ecotype (eHL-II) from rRNA content and cell size.

Journal Article Environmental microbiology · October 2013 In the open ocean genetically diverse clades of the unicellular cyanobacteria Prochlorococcus are biogeographically structured along environmental gradients, yet little is known about their in situ activity. To address this gap, here we use the numerically ... Full text Cite

Carbon allocation under light and nitrogen resource gradients in two model marine phytoplankton(1).

Journal Article Journal of phycology · June 2013 Marine phytoplankton have conserved elemental stoichiometry, but there can be significant deviations from this Redfield ratio. Moreover, phytoplankton allocate reduced carbon (C) to different biochemical pools based on nutritional status and light availabi ... Full text Cite

Dramatic variability of the carbonate system at a temperate coastal ocean site (Beaufort, North Carolina, USA) is regulated by physical and biogeochemical processes on multiple timescales.

Journal Article PloS one · January 2013 Increasing atmospheric carbon dioxide (CO2) from anthropogenic sources is acidifying marine environments resulting in potentially dramatic consequences for the physical, chemical and biological functioning of these ecosystems. If current trends continue, m ... Full text Open Access Cite

Relationship between abundance and specific activity of bacterioplankton in open ocean surface waters.

Journal Article Applied and environmental microbiology · January 2013 Marine microbial communities are complex and dynamic, and their ecology impacts biogeochemical cycles in pelagic ecosystems. Yet, little is known about the relative activities of different microbial populations within genetically diverse communities. We us ... Full text Cite

Air-water fluxes of N₂O and CH₄ during microalgae (Staurosira sp.) cultivation in an open raceway pond.

Journal Article Environmental science & technology · October 2012 The industrial-scale production of biofuels from cultivated microalgae has gained considerable interest in the last several decades. While the climate benefits of microalgae cultivation that result from the capture of atmospheric CO(2) are known, the count ... Full text Cite

Abundance and genetic diversity of aerobic anoxygenic phototrophic bacteria of coastal regions of the pacific ocean.

Journal Article Applied and environmental microbiology · April 2012 Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophic microbes that are found in a broad range of aquatic environments. Although potentially significant to the microbial ecology and biogeochemistry of marine ecosystems, their abundance and ... Full text Cite

Viral and bacterial abundance and production in the Western Pacific Ocean and the relation to other oceanic realms.

Journal Article FEMS microbiology ecology · February 2012 We completed a transect through the Western Pacific Warm Pool to examine how environmental variables may influence viral and bacterial abundance and production rates in this globally important oceanic region. Of the variables analyzed, viral abundance and ... Full text Cite

A suite of microplate reader-based colorimetric methods to quantify ammonium, nitrate, orthophosphate and silicate concentrations for aquatic nutrient monitoring.

Journal Article Journal of environmental monitoring : JEM · February 2011 A sensitive, accurate and rapid analysis of major nutrients in aquatic systems is essential for monitoring and maintaining healthy aquatic environments. In particular, monitoring ammonium (NH(4)(+)) concentrations is necessary for maintenance of many fish ... Full text Cite

Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean's surface.

Journal Article PloS one · February 2011 The phytoplankton community in the oligotrophic open ocean is numerically dominated by the cyanobacterium Prochlorococcus, accounting for approximately half of all photosynthesis. In the illuminated euphotic zone where Prochlorococcus grows, reactive oxyge ... Full text Cite

Impact of parasitic fungi on the diversity and functional ecology of marine phytoplankton

Journal Article · January 1, 2011 The population structure and dynamics of phytoplankton are governed by complexinteractions between several biotic and abiotic factors. The importance of physical andchemical conditions and predation has been well-documented in the ecology ofphytoplankton. ... Cite

Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean's surface

Journal Article PLoS ONE · 2011 The phytoplankton community in the oligotrophic open ocean is numerically dominated by the cyanobacterium Prochlorococcus, accounting for approximately half of all photosynthesis. In the illuminated euphotic zone where Prochlorococcus grows, reactive oxyge ... Full text Cite

The effect of iron-and light-limitation on phytoplankton communities of deep chlorophyll maxima of the western Pacific Ocean

Journal Article Journal of Marine Research · March 1, 2010 The deep chlorophyll maximum (DCM) is a widespread feature in most stratified, oligotrophic waters. In addition to their well-established importance for many surface phytoplankton communities, more recent evidence suggests that iron, light or co-limitation ... Full text Cite

Iron and silic acid controls on phytoplankton composition and productivity assessed by Si, C, and N utilization in the central equatorial Pacific Ocean

Journal Article Limnology and Oceanography · 2010 A microcosm nutrient-amendment experiment using central equatorial Pacific Ocean (0°, 140°W) mixed-layer waters was conducted to determine biogeochemical controls on phytoplankton with an emphasis on post-iron enrichment nutrient uptake dynamics and specie ... Link to item Cite

Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters.

Journal Article The ISME journal · January 2010 Microbial community diversity and composition have critical biogeochemical roles in the functioning of marine ecosystems. Large populations of planktonic fungi exist in coastal ocean waters, yet their diversity and role in carbon and nutrient cycling remai ... Full text Cite

Iron and silicic acid effects on phytoplankton productivity, diversity, and chemical composition in the central equatorial Pacific Ocean

Journal Article Limnology and Oceanography · January 1, 2010 A microcosm nutrient-amendment experiment using central equatorial Pacific Ocean (0°, 140°W) mixed-layer waters was conducted to determine biogeochemical controls on phytoplankton with an emphasis on post-iron enrichment nutrient uptake dynamics and specie ... Full text Cite

Prochlorococcus: approved for export.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · June 2009 Full text Cite

Impact of parasitic fungi on the diversity and functional ecology of marine phytoplankton

Chapter · January 1, 2009 The population structure and dynamics of phytoplankton are governed by complex interactions between several biotic and abiotic factors. The importance of physical and chemical conditions and predation has been well-documented in the ecology of phytoplankto ... Cite

Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, prochlorococcus.

Journal Article PloS one · January 2009 The marine cyanobacterium Prochlorococcus MED4 has the smallest genome and cell size of all known photosynthetic organisms. Like all phototrophs at temperate latitudes, it experiences predictable daily variation in available light energy which leads to tem ... Full text Cite

Facilitation of robust growth of Prochlorococcus colonies and dilute liquid cultures by "helper" heterotrophic bacteria.

Journal Article Applied and environmental microbiology · July 2008 Axenic (pure) cultures of marine unicellular cyanobacteria of the Prochlorococcus genus grow efficiently only if the inoculation concentration is large; colonies form on semisolid medium at low efficiencies. In this work, we describe a novel method for gro ... Full text Cite

Photosynthetic maximum quantum yield increases are an essential component of the Southern Ocean phytoplankton response to iron

Journal Article PNAS · 2008 It is well established that an increase in iron supply causes an increase in total oceanic primary production in many regions, but the physiological mechanism driving the observed increases has not been clearly identified. The Southern Ocean iron enrichmen ... Link to item Cite

A high-throughput method to measure photosynthesis-irradiance curves of phytoplankton

Journal Article Limnology and Oceanography: Methods · November 1, 2007 Photosynthesis-irradiance (P-E) curves are an important tool used to characterize the physiology of phytoplankton. In most marine environments, low biomass and photosynthetic rates make the carbon-14 tracer technique, used in conjunction with photosynthetr ... Full text Cite

A high-throughput method to measure photosynthesis-irradiance curves of phytoplankton

Journal Article Limnology and Oceanography: Methods · 2007 Photosynthesis-irradiance (P-E) curves are an important tool used to characterize the physiology of phytoplankton. In most marine environments, low biomass and photosynthetic rates make the carbon-14 tracer technique, used in conjunction with photosynthetr ... Cite

Influence of light and temperature on Prochlorococcus ecotype distributions in the Atlantic Ocean

Journal Article Limnology and Oceanography · January 1, 2007 In a focused analysis of Prochlorococcus population structure in the western North Atlantic, we found that the relative abundances of ecotypes varied significantly with depth and, at seasonally stratified locations, with degree of vertical mixing. More lim ... Full text Cite

Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients.

Journal Article Science (New York, N.Y.) · March 2006 Prochlorococcus is the numerically dominant phytoplankter in the oligotrophic oceans, accounting for up to half of the photosynthetic biomass and production in some regions. Here, we describe how the abundance of six known ecotypes, which have small subuni ... Full text Cite

Prochlorococcus ecotype abundances in the North Atlantic Ocean as revealed by an improved quantitative PCR method.

Journal Article Applied and environmental microbiology · January 2006 The cyanobacterium Prochlorococcus numerically dominates the photosynthetic community in the tropical and subtropical regions of the world's oceans. Six evolutionary lineages of Prochlorococcus have been described, and their distinctive physiologies and ge ... Full text Cite

Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability.

Journal Article Molecular systems biology · January 2006 Nitrogen (N) often limits biological productivity in the oceanic gyres where Prochlorococcus is the most abundant photosynthetic organism. The Prochlorococcus community is composed of strains, such as MED4 and MIT9313, that have different N utilization cap ... Full text Cite

Photosynthesis genes in marine viruses yield proteins during host infection.

Journal Article Nature · November 2005 Cyanobacteria, and the viruses (phages) that infect them, are significant contributors to the oceanic 'gene pool'. This pool is dynamic, and the transfer of genetic material between hosts and their phages probably influences the genetic and functional dive ... Full text Cite

Observed variability of sea surface salinity and thermal inversions in the Lakshadweep Sea during contrast monsoons

Journal Article Geophysical Research Letters · September 28, 2005 The sea surface salinity (SSS) of the Lakshadweep Sea (LS) shows large seasonal variability due to horizontal advection of low (high) salinity waters from south (north) during winter (summer) monsoon. The measurements made in the LS during the Arabian Sea ... Full text Cite

Description and application of the background irradiance gradient-single turnover fluorometer (BIG-STf)

Journal Article Marine Ecology Progress Series · November 30, 2004 Based on previous single turnover, pulse amplitude modulated, and fast repetition rate fluorometers, I describe a novel, bench top, single turnover fluorometer (BIG-STf) that quantifies multiple biophysical properties of Photosystem II (PSII) of phytoplank ... Full text Cite

Properties of overlapping genes are conserved across microbial genomes.

Journal Article Genome research · November 2004 There are numerous examples from the genomes of viruses, mitochondria, and chromosomes that adjacent genes can overlap, sharing at least one nucleotide. Overlaps have been hypothesized to be involved in genome size minimization and as a regulatory mechanis ... Full text Cite

Transfer of photosynthesis genes to and from Prochlorococcus viruses.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · July 2004 Comparative genomics gives us a new window into phage-host interactions and their evolutionary implications. Here we report the presence of genes central to oxygenic photosynthesis in the genomes of three phages from two viral families (Myoviridae and Podo ... Full text Cite

Development and application of the Background Irradiance Gradient - Single Turnover Fluorometer (BIG-STf)

Journal Article Marine Ecology Progress Series · 2004 Based on previous single turnover, pulse amplitude modulated, and fast repetition rate fluorometers, I describe a novel, bench top, single turnover fluorometer (BIG–STf) that quantifies multiple biophysical properties of Photosystem II (PSII) of phytoplank ... Link to item Cite

Properties of overlapping genes are conserved across microbial genomes

Journal Article Genome Research · 2004 There are numerous examples from the genomes of viruses, mitochondria, and chromosomes that adjacent genes can overlap, sharing at least one nucleotide. Overlaps have been hypothesized to be involved in genome size minimization and as a regulatory mechanis ... Full text Link to item Cite

Southern Ocean Iron Enrichment Experiment: Carbon Cycling in High- and Low-Si Waters

Journal Article Science · 2004 The availability of iron is known to exert a controlling influence on biological productivity in surface waters over large areas of the ocean and may have been an important factor in the variation of the concentration of atmospheric carbon dioxide over gla ... Full text Link to item Cite

Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation.

Journal Article Nature · August 2003 The marine unicellular cyanobacterium Prochlorococcus is the smallest-known oxygen-evolving autotroph. It numerically dominates the phytoplankton in the tropical and subtropical oceans, and is responsible for a significant fraction of global photosynthesis ... Full text Cite

The low-light reduction in the quantum yield of photosynthesis: potential errors and biases when calculating the maximum quantum yield.

Journal Article Photosynthesis research · January 2003 Photosynthesis-irradiance (P-E) curves are widely used to describe photosynthetic efficiency and potential. Contemporary models assume maximal photosynthetic quantum yield (phi) at low irradiances. But P-E observations made with both oxygen evolution and c ... Full text Cite

Photosynthetic physiology and physicochemical forcing in the Arabian Sea, 1995

Journal Article Deep-Sea Research I · 2002 The Arabian Sea, characterized by strong seasonal monsoonal forcing as well as prolific mesoscale features, is a complex hydrographic environment for phytoplankton photosynthesis. Previous studies have demonstrated seasonal cycles in both primary productio ... Full text Link to item Cite

Primary productivity and its regulation in the Arabian Sea during 1995

Journal Article Deep-Sea Research II · 2001 The annual cycle of monsoon-driven variability in primary productivity was studied in 1995 during the Arabian Sea Expedition as part of the United States Joint Global Ocean Flux Studies (US JGOFS). This paper describes the seasonal progression of productiv ... Full text Link to item Cite

Marine photosynthetic performance forcing and periodicity for the Bermuda Atlantic Time Series, 1989-1995

Journal Article Deep-Sea Research Part I: Oceanographic Research Papers · August 1, 2000 We use the first seven years of the Bermuda Atlantic Time Series (BATS) core data set (1989-1995) to examine periodicity of and correlations between potential forcing and photosynthetic performance (P(b)opt). This analysis, which focuses on seasonal to ann ... Full text Cite

Energetics and growth kinetics of a deep Prochlorococcus spp. population in the Arabian Sea

Journal Article Deep-Sea Research Part II: Topical Studies in Oceanography · August 1, 1999 During the US JGOFS process studies in the Arabian Sea (1995), secondary fluorescence maxima (SFM) were observed frequently at the oxic-anoxic interface at the extreme base of the euphotic zone. These secondary peaks were most prominent during the early NE ... Full text Cite

Modeled inherent scattering properties of small light-limited phytoplankton: Implications for deep phytoplankton size class distributions

Journal Article Proceedings of SPIE - The International Society for Optical Engineering · December 1, 1997 Small phytoplankton (<2μm), ubiquitous throughout the world's oceans, numerically dominate many open ocean ecosystems with increasing importance towards the base of the euphotic zone. As an example, light-limited deep secondary chlorophyll maxima are usual ... Full text Cite

Ground truthing modeled kPAR and on-deck primary productivity incubations with in-situ observations

Journal Article Proceedings of SPIE - The International Society for Optical Engineering · December 1, 1997 The Arabian Sea Process Study carried out on six cruises in 1995 provided observations that make possible the ground truthing of model estimates of k PAR and on deck productivity incubations with direct kPAR observations and in situ productivity incubation ... Full text Cite

Primary production and irradiance during an intermonsoon cruise to the Arabian Sea (November, 1995)

Journal Article SPIE Ocean Optics XII · 1997 The Process-6 cruise, of the Arabian Sea Expedition of the Joint Global Ocean Flux Study (JGOFS), occurred curing an intermonsoon, in October-November 1995. A variety of water column conditions were sampled in terms of euphotic zone depths, autotrophic bio ... Cite

Observations of a Synechococcus-dominated cyclonic eddy in open-oceanic waters of the Arabian Sea

Journal Article Proceedings SPIE Ocean Optics. XIII · 1997 The optical, chemical and biological characteristics of a cyclonic eddy were investigated in the Arabian Sea during November 1995. This eddy was 3,000 km(2) in area and located 350 km offshore of the coast of Oman. The mixed layer of this feature extended ... Cite