Instruments

The Imaging FlowCytobot (IFCB) is an in-situ automated submersible imaging flow cytometer that generates images of particles in-flow taken from the aquatic environment. https://mclanelabs.com/imaging-flowcytobot/

The ASL Environmental Sciences (e.g. IPS4 or IPS5) ice profiler is an upward looking sonar device deployed on a mooring for measuring ice keel drafts. The distance between the instrument and the bottom of the ice is measured by sonar at an operating frequency of 420 kHz with a beam width of 1.8 degrees and sampling rate of up to 2Hz. Water depth is measured by a pressure sensor and ice draft is calculated by the difference.

TriOS ARC Hyperspectral Radiometer Sensor

Hygrometers are used for measuring relative humidity. This term is used when details of the make, model number and measurement principle are not known.

A hydrophone is a microphone designed to be used underwater for recording or listening to underwater sound. Most hydrophones are based on a piezoelectric transducer that generates electricity when subjected to a pressure change.

Hydrolab DataSonde Multiparameter Probes have sensors for temperature, conductivity, salinity, specific conductance, TDS, pH, ORP, dissolved oxygen, turbidity, chlorophyll a, blue-green algae, Rhodamine WT, ammonium, nitrate, chloride, ambient light (PAR), and total dissolved gas.

The Hydroacoustic Technology Inc. (HTI) multi-frequency system is a towed digital split-beam/single-beam hydroacoustic system designed specifically to assess the abundance and distribution of fish and plankton. Digital signal processing hardware is combined with a MS Windows2000/XP -based user interface to produce results in real time. (http://www.htisonar.com/multi_frequency_echo_sounder.htm)

Human Occupied Vehicle (HOV) Alvin is part of the National Deep Submergence Facility (NDSF). Alvin enables in-situ data collection and observation by two scientists to depths reaching 6,500 meters, during dives lasting up to ten hours.

Commissioned in 1964 as one of the world’s first deep-ocean submersibles, Alvin has remained state-of-the-art as a result of numerous overhauls and upgrades made over its lifetime. The most recent upgrades, begun in 2011 and completed in 2021, saw the installation of a new, larger personnel sphere with a more ergonomic interior; improved visibility and overlapping fields of view; longer bottoms times; new lighting and high-definition imaging systems; improved sensors, data acquisition and download speed.  It also doubled the science basket payload, and improved the command-and-control system allowing greater speed, range and maneuverability.

With seven reversible thrusters, it can hover in the water, maneuver over rugged topography, or rest on the sea floor.  It can collect data throughout the water column, produce a variety of maps and perform photographic surveys.  Alvin also has two robotic arms that can manipulate instruments, obtain samples, and its basket can be reconfigured daily based on the needs of the upcoming dive.

Alvin's depth rating of 6,500m gives researchers in-person access to 99% of the ocean floor.  Alvin is a proven and reliable platform capable of diving for up to 30 days in a row before requiring a single scheduled maintenance day.  Recent collaborations with autonomous vehicles such as Sentry have proven extremely beneficial, allowing PIs to visit promising sites to collect samples and data in person within hours of their being discovered, and UNOLs driven technological advances have improved the ability for scientific outreach and collaboration via telepresence

Alvin is named for Allyn Vine, a WHOI engineer and geophysicist who helped pioneer deep submergence research and technology.

(from https://www.whoi.edu/what-we-do/explore/underwater-vehicles/hov-alvin/, accessed 2022-09-09)

A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.

A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase.

High (5-50 MHz) frequency radar transmits electromagnetic waves and records the backscattered signal. Oceanographic usage includes sea surface radar in which the backscattered signals are analyzed to obtain surface current and wave parameters.

The Hensen Net was invented by Christian Andreas Victor Hensen (February 10, 1835 - April 5, 1924) who was a German researcher considered by many to be the 'father' of Biological Oceanography. Hensen is credited with first using the term 'plankton', and the Hensen Net is one of several sampling devices he invented to help with sample collection. The Hensen Net has a 'reducing cone' forward of the net mouth, a simple closure system and a cod end collection device.

References:
Hensen, V., 1887. Uber die Bestimmung des Planktons oder des im Meere treibenden Materials an Pflanzen und Thieren. Berichte der Kommssion wissenschaftlichen Untersuchung der deutschen Meere in Kiel 5, pp. 1-107.

Hensen, V., 1895. Methodik der untersuchungen. Ergebnisse der Plankton-Expedition der Humbolt-Stiftung, Lipsius and Tischer, Kiel.

Membrane desolvation module that reduces solvent derived polyatomic interferences in the ICPMS mass spectrum. Both aqueous and organic solutions can be desolvated.

A Hand-held plankton net is a fine-meshed net designed for sampling microzooplankton, mesozooplankton or nekton.

The HADAL-Lander is a free-falling baited lander composed of two major components; the scientific payload and delivery system.

HADAL-Lander A

HADAL-Lander-B

Portasal Salinometer 8410A

Guildline 8410A Portasal is a truly portable, high precision instrument from the world leader in salinometers. The Portasal will deliver salinity calculations on-board ship with laboratory level accuracy. It measures accurate conductivity ratios and displays calculated salinity directly as well as measured parameters.

http://www.osil.co.uk/Products/Ignore/tabid/56/agentType/View/PropertyID/68/Default.aspx

An artificial colonization substrate (or "settlment plate") made from PVC pipe cut length-wise and engraved with lines to roughen its surface. It is used to determine the extent of colonization and/or the diversity of settled organisms in a marine or artificial environment.

The gravity corer allows researchers to sample sediment layers at the bottom of lakes or oceans. The coring device is deployed from the ship and gravity carries it to the seafloor. (http://www.whoi.edu/instruments/viewInstrument.do?id=1079).

GO-FLO Teflon-lined Trace Metal free sampling bottles are used for collecting water samples for trace metal, nutrient and pigment analysis. The GO-FLO sampling bottle is designed specifically to avoid sample contamination at the surface, internal spring contamination, loss of sample on deck (internal seals), and exchange of water from different depths.

A gas flow multicounter (GM multicounter) is used for counting low-level beta doses. GM multicounters can be used for gas proportional counting of 32Si to 32P. For more information about GM multicounter usage see Krause et. al. 2011.

Gillnetting uses curtains of netting that are suspended by a system of floats and weights; they can be anchored to the sea floor or allowed to float at the surface. A gillnet catches fish by their gills because the twine of the netting is very thin, and either the fish does not see the net or the net is set so that it traps the fish.

A barrel used to collect water samples in oceanography. It holds 250 liters of sea water.

The GeoFish towed sampler is a custom designed near surface (<2m) sampling system for the collection of trace metal clean seawater. It consists of a PVC encapsulated lead weighted torpedo and separate PVC depressor vane supporting the intake utilizing all PFA Teflon tubing connected to a deck mounted, air-driven, PFA Teflon dual-diaphragm pump which provides trace-metal clean seawater at up to 3.7L/min. The GeoFish is towed at up to 13kts off to the side of the vessel outside of the ship's wake to avoid possible contamination from the ship's hull. It was developed by Geoffrey Smith and Ken Bruland (University of California, Santa Cruz).

An automated analyzer designed for a wide range of sequencing and fragment analysis applications with the ability to perform comparative sequencing, linkage analysis, STR analysis, SNP detection, discovery and validation, mutation detection, and many other applications.

Instruments separating gases, volatile substances or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay by a mass spectrometer.

Gas Analyzers - Instruments for determining the qualitative and quantitative composition of gas mixtures.

shore fishing gear

Fukui produces multi-species, multi-purpose collapsible or stackable fish traps, available in different sizes.

Instrument that measures forces such as dynamic and quasistatic tensile and compression forces.  Units commonly as Newtons (N).

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

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.

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)

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)

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)

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.

Used to catch fish.

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.

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.

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]

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

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|

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.

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.

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

 a heated chamber for drying

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.

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

Digital Polymerase Chain Reaction (dPCR)

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.