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EXPERIMENTAL DESIGN AND METHODS:
Zooplankton samples are collected and processed by PIE researchers according to the following:
NOTE: Only data from the greater than 335 micron and greater than 150 micron  sample fractions are contained in this dataset.
Collections for plankton monitoring are done annually in the early Spring and late Summer, seasons of high and low discharge respectively. Collections are typically synchronized to occur during the same weeks as dawn/dusk whole system metabolism studies, sediment benthic flux studies and whole estuary nutrient transect water collections. Planktonic collections generally occurr during mid-low ebb tides.
Plankton are collected at four sites in the estuary representing varying salinities from near fresh water to near seawater.
The four site names were
P2 (MON-PLNKT-EST-PR-21.75), P5 (MON-PLNKT-EST-PR-14), OTL (Old Town Landing, MON-PLNKT-EST-PR-10.5) and IBYC (Ipswich Bay Yacht Club, MON-PLNKT-EST-SO-2.5).
Sample collection
Four  plankton size classes are collected at each site, whole water, 20 micron, 150 micron and 335 micron.
The 20 micron sample is collected from the surface water using a calibrated bucket and pouring known volumes of water through a Sea Gear, 25 cm diameter, 20 micron student plankton net. The cod end sample is transferred into a 500 ml wide mouth Nalgene container.
The 150 micron and 335 micron samples are collected via plankton tow using Sea Gear, 50 cm diameter, 150 or 335 micron plankton nets with General Oceanics Inc. Model 2030R mechanical flowmeters for measuring water volumes. The cod end samples from the 150 and 335 micron nets were transferred into 1000 ml wide mouth Nalgene containers. All samples were stored in a cooler for transport back to the field station for preservation.
Plankton nets were towed for 30 – 300 seconds to ensure enough material for identification without exceeding the maximum amount that could be preserved adequately in 250 ml bottles.
For the small 20 micron student plankton net, buckets of known water volume were poured into the net and recorded.
For the larger plankton net tows, 150 micron and 335 micron with General Oceanics Flowmeter attached across the diameter of the hoop (0.5m), Start and stop counts were recorded prior to and after the plankton tow.
Calculations using Model 2030R standard flowmeter rotor:
10 counts are equal to 1 rotor revolution on the graphic labels on all flowmeters.
The cts/sec. Is “counts per second” and must not be used as revolutions per second for calculations.
Standard Speed Rotor Constant = 26,873
A. DISTANCE in meters = (Difference in COUNTS X Rotor Constant) / 999999
(Example: Where the graph may indicate 100 cts/sec this is also equal to 10 revolutions/sec). Therefore please ensure the correct units are being used when measuring and calculating.
B. SPEED in cm/sec = (Distance in meters X 100) / Time in seconds
C. VOLUME cubic meters =( (3.14 X (Net Diameter)squared ) X Distance) / 4
Sample preservation
Whole water
25 ml was sub sampled, saved in a wide mouth 250 ml polyproplylene bottle and 75 ml of 95 percent EtOH added for final 70 percent EtoH sample solution.
20 micron, 150 micron and 335 micron samples
To decrease the volume, the 20 micron, 150 micron and 335 micron plankton material was filtered through 20 micron mesh Nitex and the filtered material was saved in a labeled wide mouth 250 ml polyproplylene bottle and preserved with EtOH to make a final conc of 70 percent EtOH (ie. 25 ml sample and 75 ml 95 percent EtOH for 1:3 ratio water to EtOH). The samples were rinsed down on the 20 micron Nitex using the corresponding ambient site water from the 20 micron filtrate fraction.
Taxonomy and counts of zooplanton samples from 2001-2011 were performed by Peter Milligan, in the laboratory of Dr. Jefferson Turner at U Massachusetts, Dartmouth, as follows:
Samples were reduced to aliquots of at least 250 animals with a Folsom plankton splitter, and animals are counted under a dissecting microscope and identified to the lowest possible taxon. In most cases, this will be to species; adult copepods will be additionally characterized by sex. Counts of all copepodite stages of a given copepod genus will be combined. Copepod nauplii will not be identified to genus or species because nauplii species cannot be reliably identified to those levels by using a dissecting microscope. Meroplankters cannot be identified to genus or species in most cases, and such organisms will be identified to the lowest reliable taxon, such as barnacle nauplii, fish eggs, or gastropod veligers. Concentrations of total zooplankton and all identified taxa are calculated based on the number of animals counted, multiplied by the aliquot concentration factor, and divided by the volume of filtered by the net.  
For instance, if 400 animals were counted in a 1/256 split, and the volume filtered was 4.2 cubic meters, then the calculation would be 400 x 256 = 102,400, and 102,400 divided by 4.2 = 24,381 animals per cubic meter.