Dianne I. Greenfield

The Environmental Sample Processor (ESP) - An Autonomous Robotic Device for Detecting Microorganisms Remotely using Molecular Probe Technology

We are developing an instrument to conduct molecular biological analyses below the ocean surface, autonomously. The device is known as the Environmental Sample Processor, or ESP. The system is based on a modular design consisting of a core sample processor (the ESP), analytical modules and sampling modules. The core ESP provides the primary interface between the environment and a set of DNA and antibody-based tests that are carried out onboard the instrument in real-time. In addition, the ESP can be used to archive samples for a variety of analyses after the instrument is returned to a laboratory. Sampling modules are devices external to the core ESP that can be added to meet specialized needs, such as operating in the deep-sea (etc). Analytical modules are conceived of as stand-alone devices that can be added to the core ESP to impart different suites of analytical functions downstream of common sample processing operations. At the time of this writing we have worked most extensively on the core ESP and detection chemistries that involve DNA probe and protein arrays. The ESP has been deployed successfully in coastal ocean surface waters. We are also developing a sample collection module and pressure housing suitable for deploying the ESP at depths to 1000m. This version of the instrument is known as the deep-sea ESP, or D-ESP. The long-term objective of the D-ESP program is to provide a molecular analytical capability at deep-sea hot vents and cold seeps. The D-ESP will be deployed using an ROV and later transitioned to benthic moorings and a cabled observatory. Finally, we are just starting work to incorporate a microfluidic analytical module to support assays that require DNA purification and amplification

Controlling a Robotic Marine Environmental Sampler with the Ruby Scripting Language

The Environmental Sample Processor (ESP) is an autonomous robotic instrument developed at the Monterey Bay Research Aquarium Institute (MBARI) that operates below the oceans surface, sampling raw seawater and executing a variety of sample manipulation and analytical protocols, in situ. It uses DNA and antibody probes to identify marine planktonic organisms and substances they produce. Initial prototypes of the ESP were hosted on an Intel i486 CPU running a commercial real-time operating system (OS). The application, coded in C++, included a custom ‘macro’ language interpreter to direct biochemical analyses. To achieve greater flexibility and minimize the development effort for the 2nd generation of the ESP (2G ESP), MBARI replaced its ‘macro’ language with a general purpose, open-source scripting language, selecting Ruby for its unique combination of a succinct, English-like syntax with a seamless underlying object-oriented paradigm. The 2G ESP application, aside from custom servo control firmware, is coded entirely in Ruby, hosted on a low-power ARM9 CPU running Linux. Servo control was distributed onto a network of dedicated microcontrollers to cope with the nondeterministic delays inherent in the Linux operating system and Ruby interpreter.

Linking phytoplankton community composition with juvenile-phase growth in the Northern QuahogMercenaria mercenaria (L.)

This study examined whetherMercenaria mercenaria (L.) (quahog) growth is influenced by variability in phytoplantkon community composition in the waters of Long Island, New York. Field studies conducted during 1999 and 2000 compared juvenile quahog growth and phytoplankton assemblages between West Sayville (WS), an embayment in Great South Bay along Long Island’s south shore where quahog landings have recently declined, and Oyster Bay (OB), an embayment on Long Island’s north shore where quahog landings are still high. Quahogs grew better at OB than WS during both study years. Centric diatoms were typically the dominant phytoplankton species at OB, and pennate diatoms and dinoflagellates characterized WS. At WS, the phytoplankton community consisted of heterotrophic dinoflagellates during a brown tide in 2000 and pennate diatoms afterward. Nanoflagellates were abundant (105–106 cells ml−1) at WS throughout the summer of 2000. Multiple regression analysis revealed a significant effect of site and temperature on individual clam biomass during both years, but brown tide was only significant during 2000. Biomass comparisons of dominant phytoplantkon taxa with laboratory physiology studies showed that 0B, with its abundance of centric diatoms, likely represented a more nutritional diet for quahogs than pennate diatoms, which were abundant at WS. Small flagellates, which were common at WS, may also have been important for sustaining growth during some months. Variability in plankton assemblages between OB and WS likely represented two distinct, diets that were critical influences on clam growth.

Long-term fish community dynamics from a blackwater stream receiving kraft mill effluent between 1973 and 1988

Archived data from a long-term (1973–1988) monitoring study were used to assess the impacts of kraft mill effluents (KME) on fish community dynamics in Elevenmile Creek, a small blackwater stream located in Cantonment, Florida, compared to a neighboring stream, Black Creek, that did not receive KME. The fish community in Elevenmile Creek was generally lower in species richness and diversity than the reference stream. The exception was the mill outfall site, which had similar species richness and diversity to the reference stream. Neither species richness nor diversity changed substantially during the survey period in either stream. Throughout the survey, Elevenmile Creek was numerically dominated by bluegill, Lepomis macrochirus, and eastern mosquitofish, Gambusia affinis. Black Creek had greater abundances of minnows, suckers, and darters. Time series analysis of L. macrochirus for Elevenmile Creek showed that this species was more abundant during winter than summer, but no overall long-term trend was found. Although data used in this study may not be representative of the fish community in Elevenmile Creek as it exists today, results suggest that Elevenmile Creek was highly disturbed during the survey and that species diversity did not increase following mill treatment upgrades.

A spatial assessment of baseline nutrient and water quality values in the Ashepoo-Combahee-Edisto (ACE) Basin, South Carolina, USA.

The Ashepoo-Combahee-Edisto (ACE) Basin (South Carolina, USA) National Estuarine Research Reserve System (NERRS) encompasses some of the least developed USA coastline. Yet, periodic sampling showed that certain regions have higher nutrient, fecal coliform, and chlorophyll a levels, often with lower dissolved oxygen, than other South Carolina estuaries. To evaluate the spatial extent of these issues, a summer (2008) baseline study was conducted. Physical water quality, total nitrogen and phosphorus, chlorophyll a, dissolved organic carbon, and suspended solids were measured from surface waters of 67 stations (30 tidal creek, 37 open water). Nutrient and chlorophyll a levels were significantly (p<0.01) and negatively correlated with the extent of open water (% land cover), and chlorophyll a and nitrogen levels were, at times, elevated relative to concentrations typical of other estuaries in the state, reinforcing previous findings. This survey also identified several creeks not previously monitored that exhibited elevated nutrients.