Robert H Lampe

University of California, San Diego | UCSD · Scripps Institution of Oceanography (SIO)

Environmental DNA (eDNA)-based ecological co-occurrence networks can provide a valuable tool for fisheries and conservation management. In the past, it was nearly impossible to explore the microscopic world of larval fishes in one sampling event. Now, eDNA data and ecological co-occurrence network modeling provide windows into ecosystems that suppo...

In the California Current Ecosystem, upwelled water low in dissolved iron (Fe) can limit phytoplankton growth, altering the elemental stoichiometry of the particulate matter and dissolved macronutrients. Iron-limited diatoms can increase biogenic silica (bSi) content >2-fold relative to that of particulate organic carbon (C) and nitrogen (N), which...

Microeukaryotes (protists) serve fundamental roles in the marine environment as contributors to biogeochemical nutrient cycling and ecosystem function. Their activities can be inferred through metatranscriptomic investigations, which provide a detailed view into cellular processes, chemical-biological interactions in the environment, and ecological...

The ecological and oceanographic processes that drive the response of pelagic ocean microbiomes to environmental changes remain poorly understood, particularly in coastal upwelling ecosystems. Here we show that seasonal and interannual variability in coastal upwelling predicts pelagic ocean microbiome diversity and community structure in the Southe...

The study of micronutrient requirements is essential to understand diatom biology. Some micronutrients are small organic molecules (B-vitamins) with novel enzymatic roles, high biosynthetic costs, and low concentrations in aquatic environments. Despite being abundant in the Earth’s crust, many micronutrient metals are poorly soluble in seawater, an...

Diatom primary productivity is tightly coupled with carbon export through the ballasted nature of the silica-based cell wall, linking the oceanic silicon and carbon cycles. However, despite low productivity, iron (Fe)-limited regimes are considered ‘hot spots’ of diatom silica burial with enhanced carbon export efficiency, raising questions about t...

Wind-driven upwelling followed by relaxation results in cycles of cold nutrient- rich water fueling intense phytoplankton blooms followed by nutrient depletion, bloom decline, and sinking of cells. Surviving cells at depth can then be vertically transported back to the surface with upwelled waters to seed another bloom. As a result of these cycles,...

18S and 16S amplicon library preparation protocol. DNA or RNA is usually extracted with our automated protocols from sterivex but other types of samples are occasionally used. If using RNA, first generate cDNA with Invitrogen's SuperScript III First-Strand Synthesis System. Blanks from the nucleic acid extraction should always be used as negative c...

This protocol describes our sampling strategy and techniques for the NOAA-CalCOFI Ocean Genomics (NCOG) project. In summary, seawater for DNA and RNA from multiple depths is filtered onto Sterivex filters at each station. Although the protocol is specific to this project, it is easily adaptable for other field-based sampling.

Phytoplankton communities in upwelling regions experience a wide range of light and nutrient conditions as a result of upwelling cycles. These cycles can begin with a bloom at the surface followed by cells sinking to depth when nutrients are depleted. Cells can then be transported back to the surface with upwelled waters to seed another bloom. In s...

A mostly automated protocol for extraction of total RNA from seawater filtered onto a Sterivex filter (Cat. No. SVGP0150). Reagents come from the Macherey-Nagel NucleoMag RNA kit (Cat. No. 744350). Automated liquid handling is performed on an eppendorf EpMotion 5075t with multi-channel pipettes. This protocol assumes that the Sterivex is sealed wit...

A mostly automated protocol for extraction of genomic DNA from seawater filtered onto a Sterivex filter (Cat. No. SVGP0150). Reagents come from the Macherey-Nagel NucleoMag Plant Kit for DNA purfication (Cat. No. 744400). Automated liquid handling is performed on an eppendorf EpMotion 5075t with multi-channel pipettes. This protocol assumes that th...

A mostly automated protocol for extraction of genomic DNA from seawater filtered onto a Sterivex filter (Cat. No. SVGP0150). Reagents come from the Macherey-Nagel NucleoMag Plant Kit for DNA purfication (Cat. No. 744400). Automated liquid handling is performed on an eppendorf EpMotion 5075t with multi-channel pipettes. This protocol assumes that th...

Despite generally low primary productivity and diatom abundances in oligotrophic subtropical gyres, the North Atlantic Subtropical Gyre (NASG) exhibits significant diatom-driven carbon export on an annual basis. Subsurface pulses of nutrients likely fuel brief episodes of diatom growth, but the exact mechanisms utilized by diatoms in response to th...

Diatoms are prominent eukaryotic phytoplankton despite being limited by the micronutrient iron in vast expanses of the ocean. As iron inputs are often sporadic, diatoms have evolved mechanisms such as the ability to store iron that enable them to bloom when iron is resupplied and then persist when low iron levels are reinstated. Two iron storage me...

The California Current System is a productive eastern boundary region off the coasts of Washington, Oregon, and California. There is strong seasonality to the region, with high levels of rainfall and river input to the coastal ocean during the winter season, and coastal and Ekman upwelling during the spring and summer. Iron (Fe) input to the coasta...

Frequent blooms of phytoplankton occur in coastal upwelling zones creating hotspots of biological productivity in the ocean. As cold, nutrient-rich water is brought up to sunlit layers from depth, phytoplankton are also transported upwards to seed surface blooms that are often dominated by diatoms. The physiological response of phytoplankton to thi...

Changes in iron (Fe) bioavailability influence diatom physiology and community composition, and thus have a profound impact on primary productivity and ecosystem dynamics. Iron limitation of diatom growth rates has been demonstrated in both oceanic and coastal waters of the Northeast Pacific Ocean and is predicted to become more pervasive in future...

Iron availability limits primary productivity in large areas of the world's oceans. Ascertaining the iron status of phytoplankton is essential for understanding the factors regulating their growth and ecology. We developed an incubation-independent, molecular-based approach to assess the iron nutritional status of specific members of the diatom com...

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, external factors influencing vitamin synthesis, such as micronutrient concentrations, alter the...

The formation of marine snow (MS) by the toxic diatom Pseudo-nitschia australis was simulated using a roller table experiment. Concentrations of particulate and dissolved domoic acid (pDA and dDA) differed significantly among exponential phase and MS formation under simulated near surface conditions (16 °C/12:12-dark:light cycle) and also differed...