the invention may be better understood by reference to the following detailed description , taken in conjunction with the figures . various embodiments of the invention relate to a system for analyzing aquatic parameters in both freshwater and saltwater . other configurations and variants will be apparent to those skilled in the art from the teachings herein and are considered to be within the scope of the invention . the phorcys system is in various embodiments an expandable and versatile family of instruments containing one or more incubation chambers and a unique combination of sample collection systems and sensors that are used to measure photosynthesis and respiration in aquatic and marine systems under in situ conditions . the phorcys system may be deployed directly into aquatic and marine environments , operate underwater , and incubate fluidic samples in situ . the system , in various embodiments , makes use of the classical approach of tracking dissolved species involved in photosynthesis and respiration ( i . e ., oxygen , nitrate , carbon dioxide , ph , etc .) over an incubation period . various embodiments may share four basic elements : 1 ) an optically clear and / or opaque incubation container / chamber that collects water ; 2 ) a system to open and close the incubation container ( s ), thereby initiating and terminating the incubation period ( s ); 3 ) oxygen , nitrate , carbon dioxide or ph sensors , and / or variants thereof ( including for concentration ); and 4 ) an electronics unit / control module , which may provide power , record data , and / or transmit data . still other embodiments of the phorcys instruments include apparatus to add substances such as solutions and / or particles to determine their impact on respiration or primary production . other embodiments include devices to take water samples during the course of incubation , and automated valves for opening , rinsing and closing the incubation chambers . some embodiments may depend on external rigging to position the phorcys instrument in the appropriate location of the water column and proper orientation to collect and incubate samples under in situ conditions , such as a drifting array , anchored mooring , or lowering it from a pier or ship into the water . other embodiments may be self - ballasting and self - orienting , and may be part of a networked ocean observatory system or incorporated into autonomous underwater vehicles and permanently reside in the ocean . communications systems to transmit data to and / or receive data from a remote location are also contemplated and considered within the scope of the invention . one embodiment of an aquatic sample analysis system 100 may be seen in fig1 . the system 100 includes an incubation chamber 102 a with a substantially optically clear ( i . e ., transparent , translucent ; allows for passage of ambient light ) portion 103 a ( the clear chamber ) and an incubation chamber 102 b with a substantially optically opaque ( i . e ., blocks ambient light ) portion 103 b ( the dark chamber ), each of which contains a sensor , such as an oxygen optode ( as described in greater detail below ). the incubation chambers 102 a , 102 b may be generally cylindrical and are mounted to a common frame 104 with a control module housing 106 that houses a control module in communication with one or more sensors . the control module 106 also operates spring - loaded caps 108 between an open position to allow water to enter the incubation chambers 102 a , 102 b ( and similarly to allow any water already present to leave ) and a closed position to enclose water ( e . g ., obtain a fluidic sample ) in the incubation chambers 102 a , 102 b to initiate incubation . in certain embodiments , the chambers 102 a , 102 b may be sealed with hinged caps or some other closure mechanism or seal ( e . g ., ball valves ). fig1 depicts the chambers 102 a , 102 b having openings at both ends , though it is possible there is only one opening to the chamber 102 a , 102 b ( and the opening does not necessarily have to be at one end thereof ). the system 100 also includes a power source disposed in the control module housing 106 . the components of the system 100 allow a water ( freshwater or saltwater ) sample to be enclosed , incubated in situ , and monitored for changes in oxygen concentration at a depth of interest . in some embodiments , only a single incubation chamber ( e . g ., incubation chamber 102 a ) may be used . in variations having only one open end , only one closure may be necessary to seal a chamber opening . another embodiment of an incubation chamber 202 for use with the system 100 ( either in addition to , or instead of , at least one of the incubation chambers 102 a , 102 b ) is depicted in fig2 . the incubation chamber 202 has at least one ball valve 210 ( there may be more than one , such as dual ball valves ) to seal the incubation chamber 202 . the ball valve 210 may be only on one side of a semi - transparent portion 203 a of the incubation chamber 202 , thereby allowing water in and out on one side of the semi - transparent portion 203 a . sensors 212 , such as those described above , including an oxygen optode , may be located opposite the ball valve 210 on the opposite end of the semi - transparent portion 203 a . a separate control module housing 206 containing a control module to control the ball valve 210 and / or the sensors 212 is also located opposite the ball valve 210 . in certain embodiments , the ball valve ( s ) 210 may be configured to repeatedly open and close the incubation chamber 202 . two or more semi - transparent portions 203 a may be used , particularly when the chamber 202 is intended to be deployed in dark ambient settings where replicate respiration measurements are made . the chamber 202 can be attached to other devices , such as sediment traps , in order to enhance particle concentrations within the chambers . fig3 a depicts an oxygen optode 314 for use with an aquatic sample analysis system , and may be particularly adapted to be disposed in a chamber as described above ( also in a chamber 302 with opaque walls as depicted in fig3 b ). the oxygen optode 314 may contain optical sensors that utilize a fluorescent platinum porphyrin complex embedded in a gas permeable foil that is exposed to the surrounding water . the fluorescence phase of the foil is proportional to the concentration of oxygen in the surrounding water . this sensing foil is attached to a window in a watertight titanium housing that contains the optical instruments . through the window , the foil is excited by modulated blue light and the phase of a returned red fluorescent light is measured using a photodiode . these sensors are designed to work under in situ pressures and temperatures . unlike o 2 electrodes , optodes do not consume oxygen and are thus advantageous for measuring changes in oxygen concentration in confined vessels , such as the incubators . some oxygen optodes , such as the aanderaa oxygen optode ( aanderaa data instruments , inc ., attleboro , massachusetts ) can measure oxygen with high resolution and accuracy and allow the phorcys system to measure respiration rates as low as about 1 μmol o 2 l − 1 d − 1 . in it present embodiments , the sensitivity of the phorcys system is limited only by the stability , accuracy and precision of the sensors , such as the oxygen optode , that are contained with in it . this sensitivity , which is similar to and may exceed the resolution of the winkler titration method ( comparative results using both methods are shown in table 1 ), supports effective determination of respiration rates in most aquatic waters with oxygen optodes . moreover , whereas the winkler method relies on solely a few measurements to establish rate - of - change of o 2 concentration , thousands of respiration rate measurements may be made with optode - based respirometers , providing greatly improved confidence in measured data results . such systems , according to the invention , may be deployed effectively in various applications , such as on wired ocean observing networks or autonomous profilers / gliders . the system 100 instruments collect data over time , such as oxygen concentrations as detected by an optode - type oxygen sensor , as depicted in fig4 , though other data may be collected depending on the sensors used , including nitrate concentration , carbon dioxide concentration , and ph . the dark / opaque incubation chamber 102 b records the decrease in oxygen due to respiration . respiration is also observed in the clear incubation chamber 102 a during the night . upon sunrise ( approximately 6 am in the graph in fig4 ) oxygen concentrations in the clear chamber 102 a reflect the sum of gross respiration and gross primary production ; this sum is also known as net primary production . in the above example , the gross respiration rate is 0 . 91 ± 0 . 02 μmol o 2 hr − 1 and the net primary production rate is 1 . 17 ± 0 . 08 μmol o 2 hr − 1 . thus , the gross primary production rate is 2 . 08 ± 0 . 08 μmol o 2 hr − 1 , as determined by the difference between the gross respiration rate ( negative slope ) and the net primary production rate ( positive slope ). fig5 depicts oxygen concentration results from additional testing , plotting results from the clear chamber 102 a , the dark chamber 102 b , and from shipboard incubations on the same graph . these results were obtained when the system 100 was disposed at a depth of approximately 29 m , at depth in the ocean that was effectively dark . the clear chamber 102 a and the dark chamber 102 b provide continuous results throughout the testing , allowing a user to follow variations in results to identify specific times of interest , in contrast to the periodic observations from shipboard incubations . since the clear chamber 102 a and the opaque chamber 102 b remained in situ throughout the incubation , these results will be recognized by those skilled in the art as being more authentic representations of natural respiration rates than the shipboard incubations . further , as evidenced by the much smaller errors in respiration rates , the continuous measurements in the clear chamber 102 a and the dark chamber 102 b demonstrate greater sensitivity to changes in the fluidic sample than the results from the onboard incubations ; this is particularly true of respiration rates based on the winkler method , which is mostly widely practiced by those skilled in the art . the operational ranges of the system are generally dictated by the sensors . presently , oxygen sensors , such as those from aanderaa mentioned above , are rated to 6 , 000 m depth ( approximately 95 % of all of the ocean is shallower than 6 , 000 m ). the temperature range of this sensor is − 5 to + 40 ° c . however , the use of other sensors with greater pressure handling capabilities and different temperature ranges is contemplated , and considered within the scope of the invention . also , the incubation chambers may typically each have a volume between about 1 and about 10 liters , though the chambers may be as small as about 1 ml or less or as large as about 50 l ( or more ), depending on the application . in principle , the chambers may be configured to be any shape or volume , and may be made of any functionally biologically inert material , such as quartz or polytetrafluoroethylene . in some embodiments , the system 100 is programmed before being deployed , e . g ., by programming the control module . the programmable parameters may include the times at which the chambers 102 a , 102 b close and open to control the incubation period , the frequency of data collection by the sensors , power management , and mechanisms for data storage and / or transmission . these parameters may also be controlled in real time through wired or wireless communications with the control module . in other embodiments , the system &# 39 ; s incubation chambers 102 a , 102 b close automatically , and then remain closed until the incubation period is over . for example , the spring - loaded lids 108 depicted in fig1 may snap shut on the chambers 102 a , 102 b after they are triggered by a burn wire once the system reaches a desired depth . some embodiments of the system 100 can conduct multiple incubations by closing and opening the chambers 102 a , 102 b repeatedly , and acquire , process , and transmit data from multiple incubations . some embodiments include injection systems to introduce other materials , such as particulate matter or dissolved chemicals , into the incubation chambers 102 a , 102 b , so that the impact of these other materials on respiration or primary production can be assessed . various embodiments and features of the present invention have been described in detail with particularity . the utilities thereof can be appreciated by those skilled in the art . it should be emphasized that the above - described embodiments of the present invention merely describe certain examples implementing the invention , including the best mode , in order to set forth a clear understanding of the principles of the invention . numerous changes , variations , and modifications can be made to the embodiments described herein and the underlying concepts , without departing from the spirit and scope of the principles of the invention . all such variations and modifications are intended to be included within the scope of the present invention , as set forth herein . the scope of the present invention is to be defined by the claims , rather than limited by the forgoing description of various embodiments . accordingly , what is desired to be secured by letters patent is the invention as defined and differentiated in the claims , and all equivalents .