Instruments

The chemiluminescence method for gas analysis of oxides of nitrogen relies on the measurement of light produced by the gas-phase titration of nitric oxide and ozone. A chemiluminescence analyzer can measure the concentration of NO/NO2/NOX.

One example is the Teledyne Model T200: https://www.teledyne-api.com/products/nitrogen-compound-instruments/t200

A CHN Elemental Analyzer is used for the determination of carbon, hydrogen, and nitrogen content in organic and other types of materials, including solids, liquids, volatile, and viscous samples.

A device designed to regulate the temperature of a vessel by bathing it in water held at the desired temperature. [Definition Source: NCI] 

Instruments that measure the proportion of the sky covered by cloud (cloud amount) and/or the height of the cloud above the ground (cloud base). Also called ceilometers.

CO2 Adsorber - an instrument designed to remove CO2 and moisture from compressed air.

A CO2 coulometer semi-automatically controls the sample handling and extraction of CO2 from seawater samples. Samples are acidified and the CO2 gas is bubbled into a titration cell where CO2 is converted to hydroxyethylcarbonic acid which is then automatically titrated with a coulometrically-generated base to a colorimetric endpoint.

Crab pots modified to catch cod. Variously designed: floating v. static; large v. small; two or more large entrances v. one small entrance, rigid v. collapsible.

Natural or artificial materials deployed in a marine or artificial environment for a given period to act as standardised, passive settlement sampling devices (e.g. settlement plates). They are used to determine the extent of colonization and/or the diversity of settled organisms.

Measures the total condensation nucleus concentration of aerosol particles.

A laser scanning confocal microscope is a type of confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction-limited) focal volume within or on the surface of a specimen.

The confocal microscope uses fluorescence optics. 'Confocal' means that the image is obtained from the focal plane only, any noise resulting from sample thickness being removed optically. 'Laser scanning' means the images are acquired point by point under localized laser excitation rather than full sample illumination, as in conventional widefield microscopy.

A sample is injected into a flowing carrier solution passing rapidly through small-bore tubing. 

CBASS, which stands for "Coral Bleaching Automated Stress System", are portable, field-deployable experimental tanks used to apply rapid, acute heat stress challenges. This system is described in:

Voolstra, C. R., Buitrago‐López, C., Perna, G., Cárdenas, A., Hume, B. C. C., Rädecker, N., & Barshis, D. J. (2020). Standardized short‐term acute heat stress assays resolve historical differences in coral thermotolerance across microhabitat reef sites. Global Change Biology, 26(8), 4328-4343. Portico. https://doi.org/10.1111/gcb.15148

An apparatus for counting and sizing particles suspended in electrolytes. It is used for cells, bacteria, prokaryotic cells and virus particles. A typical Coulter counter has one or more microchannels that separate two chambers containing electrolyte solutions.

from https://en.wikipedia.org/wiki/Coulter_counter

A reusable instrument that always simultaneously measures conductivity and temperature (for salinity) and pressure (for depth).

This term applies to CTDs that are fixed and do not measure by profiling through the water column. For profiling CTDs, see https://www.bco-dmo.org/instrument/417.

CTD measurements taken by the Falmouth Scientific Instruments sensor.

The Neil Brown Instrument Systems Mark 5 CTD is used to measure conductivity, temperature, and depth of sea water. The MK5 profiler has a higher sampling rate then the SeaBird SEACAT. (For the GLOBEC Georges Bank project the Mark 5 was instrumented with an expanded suite of sensors and deployed almost exclusively at GLOBEC Standard stations.)

This is an integrated instrument package comprising a Neil Brown Instrument Systems Mark III Conductivity, Temperature, Depth (CTD) profiler unit with a Tracor Acoustic Profiling System (TAPS). (see TAPS entry for a description of that instrument)

Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics, no specific unit identified. This instrument designation is used when specific make and model are not known. See also other SeaBird instruments listed under CTD. More information from Sea-Bird Electronics.

The Sea-Bird SBE 41 CTD module was originally developed in 1997 for integration with sub-surface oceanographic floats. It uses MicroCAT Temperature, Conductivity, and Pressure sensors.

The Sea-Bird SBE 911 is a type of CTD instrument package. The SBE 911 includes the SBE 9 Underwater Unit and the SBE 11 Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). More information from Sea-Bird Electronics.

The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics

The CTD SEACAT recorder is an instrument package manufactured by Sea-Bird Electronics. The first Sea-Bird SEACAT Recorder was the original SBE 16 SEACAT developed in 1987. There are several model numbers including the SBE 16plus (SEACAT C-T Recorder (P optional))and the SBE 19 (SBE 19plus SEACAT Profiler measures conductivity, temperature, and pressure (depth)). More information from Sea-Bird Electronics.

CTD measurements taken during a SeaSoar tow.

A CTD-fluorometer is an instrument package designed to measure hydrographic information (pressure, temperature and conductivity) and chlorophyll fluorescence.

The CytoSense is a portable, benchtop autonomous flow cytometer designed for phytoplankton species classification and analysis of filamentous algae. It can also be used in situ to reveal temporal and spatial phytoplankton variability. It can be remotely controlled, and has been specifically designed to record the optical pulse shapes of suspended particles between <1 and 800 micrometres in diameter and up to 4 millimetres in length (for chain-forming cells recording) in relatively large volumes of water (several centimetres cubed per sample). The instrument combines high sensitivity with an extremely wide particle size range (from sub-micron up to 1.5 millimetres in diameter) and acquires multiple data points per particle, which distinguishes the CytoSense from conventional flow cytometers. The CytoSense has a modular design, with various upgrades and accessories available to suit user requirements. These include additional lasers, optional cameras to take pictures of particles and a widened flow cell. The sample intake speed ranges from 0.07 - 17 microlitres per second, allowing high particle loads (thousands of particles per second) as well as very low concentrations.

Alternate name: CytoBuoy CytoSense flow cytometer

The Daly detector was designed by N.R Daly in the 1960’s. The design uses a conversion dynode to convert incident ions into electrons. It also separates the multiplication electronics away from the ion beam preventing secondary ion production on the multiplication dynodes.

The Deep Autonomous Profiler (DAP) is described in detail in the following publication:
Muir, L., Roman, C., Casagrande, D., and D'Hondt, S. (2021) The Deep Autonomous Profiler (DAP), a Platform for Hadal Profiling and Water Sample Collection. Journal of Atmospheric and Oceanic Technology, vol. 38, no. 10, pp. 1833–1845, 2021. doi:10.1175/JTECH-D-20-0139.1. URL: https://journals.ametsoc.org/view/journals/atot/38/10/JTECH-D-20-0139.1.xml

To summarize:
DAP is a full-ocean-depth profiler rated to 11 kilometers. It was designed to expand the capabilities of a CTD system to the full ocean depth (11 km) by removing the constraints associated with wire-based operations. Removing the tether allows the vehicle to autonomously profile and sample seawater into the hadal region. Because it only requires the ship for deployment and retrieval, the ship can perform other tasks while the DAP is underway. The only source of communication to the DAP while deployed are the acoustic releases.

The DAP is built around a 24-bottle Sea-Bird SBE 32 rosette for 10- or 12-Liter Niskin bottles. The large aluminum bottle-support rings from the standard rosette were modified to reduce weight and are held by the vehicle's custom frame. Syntactic foam provides buoyancy and drop weights are used for descent.

The DAP stands 3.2 meters tall and has a mass of approximately 1400 kilograms (kg) in air empty and 1700 kg when full of water. The titanium electronics bottle, tested to 960 decibars (dBar) in a pressure facility, was designed to house the embedded Raspberry Pi computer and power circuitry. This computer logs data from the SBE 9plus CTD and SBE 43 oxygen sensor, sends commands to the SBE 32 sampler carousel to trigger the sample bottles, and controls the burnwire release. Power for a nominal 24-hour operating time is provided by a 24-volt, 40-amp-hour oil-filled DeepSea Power and Light SeaBattery.

Using drop weights, the profiler descends at a nominal speed of 60 meters per minute through the water column, collecting CTD data. Upon reaching the bottom, a timer is activated and an onboard algorithm processes the descent profile to set the trigger depths for any sample bottles set with an adaptive criteria. Bottom water samples can also be collected according to any preset delays. The bottom time can vary anywhere from 5 minutes to 18 hours. During the ascent, at a nominal speed of 60 meters per minute, the Niskin bottles are triggered at any preset depths specified in the mission file or at adaptively calculated depths based on downcast data. When the DAP surfaces, a radio beacon, Iridium beacon, strobe, radar reflector, and flag are used for recovery by the ship.

The vehicle can currently hold up to 24 Niskin bottles, and up to four pressure-maintaining sample bottles provided by the Scripps Institution of Oceanography.

The Deep-Sea Current Meter and Larval Trap Mooring is a seafloor anchored mooring equipped to collect sediment/invertebrate larva, and record deep-sea ocean current and acoustical data.

Instruments on the mooring have included sediment traps and a Falmouth Scientific Inc. Acoustic Current Meter with vector-averaged current speed and direction.

A Digital Inline Holographic Microscope (DIHM) uses coherent (laser) light and a digital camera to image objects with micrometer scale resolution. A portion of the light scattered by illuminated objects interferes with incident light in a predictable manner. The resulting interference patterns projected onto a two-dimensional plane (i.e. digital camera sensor) are recorded as holograms. These digital holograms are then numerically reconstructed to produce an in-focus image at a given distance from the recording plane. A relatively large illuminated volume (>100 mL) can be reconstructed in this manner to produce a single image with an extended depth of field. 

Discrete analyzers utilize discrete reaction wells to mix and develop the colorimetric reaction, allowing for a wide variety of assays to be performed from one sample. These instruments are ideal for drinking water, wastewater, soil testing, environmental and university or research applications where multiple assays and high throughput are required.

A diving mask (also half mask, dive mask or scuba mask) is an item of diving equipment that allows underwater divers, including, scuba divers, free-divers, and snorkelers to see clearly underwater.

Snorkel: A breathing apparatus for swimmers and surface divers that allows swimming or continuous use of a face mask without lifting the head to breathe, consisting of a tube that curves out of the mouth and extends above the surface of the water.

Digital Polymerase Chain Reaction (dPCR)

An unmanned instrumented platform drifting freely in the water column that periodically makes vertical traverses through the water column (e.g. Argo float).

A core drill is a drill specifically designed to remove a cylinder of material, much like a hole saw. The material left inside the drill bit is referred to as the core.

Core drills are used frequently in mineral exploration where the coring may be several hundred to several thousand feet in length. The core samples are recovered and examined by geologists for mineral percentages and stratigraphic contact points. This gives exploration companies the information necessary to begin or abandon mining operations in a particular area.

 a heated chamber for drying

A single-beam echo sounder is an instrument that measures water depth at a single point below the platform by timing pulses of sound reflected on the seafloor. The echo sounder transmits and receives sound, accurately measuring the time it takes to leave the sounder, reach the bottom and return to the sounder. It then converts this information into digital or graphic representations of the bottom depth and relief.
The average echo sounder consists of a transmission and reception unit that sends sound signals through the water, receives and decodes information and converts that information into either a graphic or visual form. Attached to the receiver is a transducer that acts as a microphone and a speaker under the water. Sound waves travel at approximately 1500 m/s through the water dependent on water temperature". more from LMS Technologies

An electronic jig machine is used to mechanically jig a fish hook or lure with a bait casting reel without using the fishing rod to jig the lure. Normally to jig a fish hook or lure one must move the fishing rod either vertically, horizontally, or jerk the fishing line by hand. The jigging action of this bait cast reel (how rapid and how long in distance the jig will travel) will determine the desired intensity and resonance of the rattle used in the lure to attract or snag the fish. With very simple controls, the equipment functions automatically since it is programmed to suit the actual fishing area, the fishing method and the type of fish.

Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.

The MBARI Environmental Sample Processor—the ESP—provides on-site (in situ) collection and analysis of water samples from the subsurface ocean. The instrument is an electromechanical/fluidic system designed to collect discrete water samples, concentrate microorganisms or particles, and automate application of molecular probes and qPCR which identify microorganisms and their gene products. The ESP also archives samples so that further analyses may be done after the instrument is recovered.

Environmental Sample Processor

See references below for methodology used on the ESP:
Greenfield, D.I., R. Marin III, S. Jensen, E. Massion, B. Roman, J. Feldman, C. Scholin (2006). Application of the Environmental Sample Processor (ESP) methodology for quantifying Pseudo-nitzschia australis using ribosomal RNA-targeted probes in sandwich and fluorescent in situ hybridization.  Limnology and Oceanography: Methods 4: 426-435.

Greenfield, D., R. Marin III, G.J. Doucette, C. Mikulski, S. Jensen, B. Roman, N. Alvarado, and C.A. Scholin (2008).  Field applications of the second-generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006-2007.  Limnology and Oceanography: Methods 6: 667-679.

Marin III, R., and C. Scholin (2010). Sandwich Hybridization.  In: Microscopic and molecular methods for quantitative phytoplankton analysis (Chapter 12), edited by B. Karlson, C. Cusack, and E. Bresnan, E.. IOC Manuals and Guides, no. 55. (IOC/2010/MG/55)  Paris, UNESCO. 110 pp.

Ottesen, E.A., R. Marin III, C.M. Preston, C.R. Young, J.P. Ryan, C.A. Scholin, and E.F. DeLong (2011). Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. The ISME Journal, 5: 1881-1895, doi: 10.1038/ismej.2011.70.

Ottesen, E.A., C.R. Young, J.M. Eppley, J.P. Ryan, F.P. Chavez, C.A. Scholin, and E.F. DeLong (2013). Pattern and synchrony of gene expression among sympatric marine microbial populations. Proceedings of the National Academy of Sciences, 110: E488-E497, doi: 10.1073/pnas.1222099110.

Ottesen, E.A., C.M. Young, S.M. Gifford, J.M. Eppley, R. Marin III, S.C. Schuster, C.A. Scholin, and E.F. DeLong (2014). Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science, 345: 207-212, 10.1126/science.1252476.

Preston, C.M., A. Harris, J.P. Ryan, B. Roman, R. Marin III, S. Jensen, C. Everlove, J. Birch, J.M. Dzenitis, D. Pargett, M. Adachi, K. Turk, J.P. Zehr, and C.A. Scholin (2011). Underwater application of quantitative PCR on an ocean mooring. PLoS ONE, 6:e22522, doi: 10.1371/journal.pone.0022522.

Robidart, J.C., C.M. Preston, R.W. Paerl, K.A. Turk, A.C. Mosier, C.A. Francis, C.A. Scholin, and J.P. Zehr (2011). Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation. The ISME Journal, 6: 513-523, doi: 10.1038/ismej.2011.127.

Robidart, J., M.J. Church, J.P. Ryan, F. Ascani, S.T. Wilson, D. Bombar, R. Marin III, K.J. Richards, D.M. Karl, C.A. Scholin, and J.P Zehr (2014). Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean. The ISME Journal, 8: 1175-1185, 10.1038/ismej.2013.244.

Saito, M.A., V.V. Bulygin, D.M. Moran, C. Taylor, and C. Scholin (2011). Examination of microbial proteome preservation techniques applicable to autonomous environmental sample collection. Frontiers in Aquatic Microbiology, 2: doi: 10.3389/fmicb.2011.00215.

Scholin, C.. (2010).  What are “ecogenomic sensors?” A review and thoughts for the future. Ocean Science 6: 51-60.

Ussler III, W., C.M. Preston, P. Tavormina, D. Pargett, S. Jensen, B. Roman, R. Marin III, S.R. Shah, P.R. Girguis, J.M. Birch, V.J. Orphan, and C. Scholin (2013). Autonomous application of quantitative PCR in the deep sea: In situ surveys of aerobic methanotrophs using the deep-sea Environmental Sample Processor. Environmental Science and Technology, 47: 9339–9346, doi: 10.1021/es4023199.

Varaljay, V.A, J. Robidart, C.M. Preston, S.M. Gifford, B. Durham, A.S. Burns, J.P. Ryan, R. Marin III, R.P. Kiene, J.P Zehr, C.A. Scholin, M. Moran. 2015. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. ISME Journal, doi:10.1038/ismej.2015.23|

The Eppley Precision Infrared Radiometer (PIR) pyrgeometer measures longwave (infrared) radiation. It is housed in a weatherproof titanium canister that has been painted with a very flat black paint that absorbs radiation. A small glass dome at the top of the instrument is covered with an 'interference coating' which allows only infrared radiation to come through. Light levels are detected as temperature changes creating voltages in fine wire coil detectors. more from Eppley Labs

Cassar N, Barnett BA, Bender ML, Kaiser J, Hamme RC, Tilbrook B., Continuous high-frequency dissolved O2/Ar measurements by equilibrator inlet mass spectrometry. Anal Chem. 2009 Mar 1;81(5):1855-64. doi: 10.1021/ac802300u. 

Source: Department of Geosciences, Princeton University, Princeton, New Jersey 08544, USA. ncassar@princeton.edu

Abstract
The oxygen (O(2)) concentration in the surface ocean is influenced by biological and physical processes. With concurrent measurements of argon (Ar), which has similar solubility properties as oxygen, we can remove the physical contribution to O(2) supersaturation and determine the biological oxygen supersaturation. Biological O(2) supersaturation in the surface ocean reflects the net metabolic balance between photosynthesis and respiration, i.e., the net community productivity (NCP). We present a new method for continuous shipboard measurements of O(2)/Ar by equilibrator inlet mass spectrometry (EIMS). From these measurements and an appropriate gas exchange parametrization, NCP can be estimated at high spatial and temporal resolution. In the EIMS configuration, seawater from the ship's continuous intake flows through a cartridge enclosing a gas-permeable microporous membrane contactor. Gases in the headspace of the cartridge equilibrate with dissolved gases in the flowing seawater. A fused-silica capillary continuously samples headspace gases, and the O(2)/Ar ratio is measured by mass spectrometry. The ion current measurements on the mass spectrometer reflect the partial pressures of dissolved gases in the water flowing through the equilibrator. Calibration of the O(2)/Ar ion current ratio (32/40) is performed automatically every 2 h by sampling ambient air through a second capillary. A conceptual model demonstrates that the ratio of gases reaching the mass spectrometer is dependent on several parameters, such as the differences in molecular diffusivities and solubilities of the gases. Laboratory experiments and field observations performed by EIMS are discussed. We also present preliminary evidence that other gas measurements, such as N(2)/Ar and pCO(2) measurements, may potentially be performed with EIMS. Finally, we compare the characteristics of the EIMS with the previously described membrane inlet mass spectrometry (MIMS) approach.

PMID: 19193192 [PubMed - indexed for MEDLINE]

An aXBT is an Expendable Bathythermograph (XBT) designed to be launched from an aircraft (often a P3 type aircraft) as opposed to a ship. The aXBT collects data in a similar fashion to an XBT, and once the probe hit the sea surface, it free falls through the water column.

A Faraday cup is a metal (conductive) cup designed to catch charged particles in a vacuum. The resulting current can be measured and used to determine the number of ions or electrons hitting the cup.

Used to catch fish.

A flame ionization detector (FID) is a scientific instrument that measures the concentration of organic species in a gas stream. It is frequently used as a detector in gas chromatography. Standalone FIDs can also be used in applications such as landfill gas monitoring, fugitive emissions monitoring and internal combustion engine emissions measurement in stationary or portable instruments.

Pound nets are passive, stationary gear used for live entrapment of fish species. The gear is composed of fiber netting. Floating pound nets use floating toggles and buoys at the surface and are held taught below the surface using anchors.


A pound net consists of: (1) a net body or crib where the entrapment takes place, (2) a least one mesh heart that helps funnel fish into the crib, and (3) a straight leader or hedging which leads fish toward the crib. Fish swimming along the shore are turned toward the crib by the hedging, guided into the heart, and into the crib where they are removed.



(Description from Maryland Dept of Natural Resources)

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

An analytical system used to determine concentrations of chemical species in a sample based on the fluorescence from the reaction between lumogallion and the species of interest. The system typically comprises individual components typically including pumps, injection and autosampler valves, preconcentration columns and a fluorometer. The system is normally uniquely assembled for each analysis.
(From SeaDataNet)

Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.