Examining Spatial and Temporal Changes within

the Raritan Bay Estuary

Fall 2023

Simon J. Bitan, Julia Cancro, Brianna Estevez, Mohrail M. Girgis, Colin Sabol, Eamon J. Taylor

Department of Marine and Coastal Sciences, Rutgers University

OMDA Biological & Chemical (11:628:363:01)

Dr. Lee Kerkhof and Dr. Robert Sherrell

Dates of Cruises: 09/12/2023 and 10/10/2023

Abstract

By observing various features of the Raritan Bay, differences in temporal and spatial patterns of
the water column can be observed. Through trial and error over the course of two cruises, several
conclusive changes can be observed over the course of a month through temperature, salinity,
and density. Many tests were conducted after the cruises that allowed for the observance of these
differences such as the concentration of phosphate, dissolved oxygen, and primary productivity.
However, due to some errors there are some tests that could not be relied on for accurate
information such as chlorophyll concentration. One of the most significant measures of change
collected over the semester was DNA sequencing. By obtaining the species concentrations that
are present in saltwater or freshwater, spatial differences can be determined. To get a more
accurate picture of the changes that happen over time, more cruises would need to be conducted.

Introduction

The Raritan Bay is part of the much larger Hudson-Raritan Estuary

system. Estuaries can be defined as where the mouth of rivers meet
the ocean. This includes both the body of water itself that is formed
by this interaction as well as the surrounding wetlands (NOAA,
2019). Due to the dynamic nature of the input of both fresh and
saltwater into this system there is a significant amount of both
chemical and biological diversity found here. To further add to this,
the Hudson-Raritan Estuary is surrounded by some of the most
urbanized regions in our country (NOAA, 2019).
This changes the water quality and further adds to
the dynamic nature of this environment and its
respective ecosystems. Another reason for such
differences in biology and chemistry is the physical
structure estuaries tend to take on, that being the
interface between the fresh and saltwater tend to cause what’s called a salt wedge. Since seawater
is more dense than the freshwater that is entering the estuary from rivers the freshwater rests
above the saltwater which is then being pushed towards the shore and under the freshwater due
to tidal activity. This means that there is going to usually be significantly more stratification in
these environments due to the stronger changes in salinity as seen in Figure 1 (Webb, 2023).

The physical structure can be heavily influenced by both extreme weather events as well as
seasonal changes along with already being an ever changing system. As such, to begin to
completely understand these systems the physical properties need to be studied. The structure of
the water column in the estuary determines what biology is able to live where. Along with the
physical structure the chemicals present in the estuary also have an impact on the types of
organisms that are going to be present. The chemistry of an estuary is determined by its
geographic location as well as where its water is coming from. As previously stated the
Hudson-Raritan Estuary system is located in a very developed area runoff from which enters the
rivers and bay altering the nutrient levels that are found in the water column. Additionally, both
the Hudson and Raritan river feed into the bay. These river systems are both fairly large and pass
by heavily developed areas. As thus nutrients and other chemicals are coming into the system
from a large number of sources furthering the dynamic nature of the system since pollutants from
these areas vary throughout the year. Naturally all of these factors have an effect on the biology
found in this system.

The biology of estuaries in general is important to study as more than 68% of all commercially
valued fish require estuary systems at some point in their life cycle (NOAA, 2022). The Raritan
Bay specifically is used as a spawning area, nursery, or residence for a variety of commercially
valued fish, (MacKenzie Jr., 1990). These fish include but are not limited to Atlantic menhaden,
bluefish, summer flounder, weakfish, and winter flounder,(MacKenzie Jr., 1990). As such, it is
important to study the ecosystems and biological systems found here so that we can ensure that
these fisheries remain viable both economically and environmentally. Since the biology in this
system is heavily influenced by both the physics and the chemistry of the system it is vital to take
a multidisciplinary approach to study the Hudson-Raritan Estuary system and estuaries overall to
make sure these important environments are preserved (Day Jr. et al., 2012).

These cruises were not the first of their kind and in fact there have been a number of projects that
sampled the Raritan Bay. The primary purpose of past cruises was to study the levels of
pollutants entering the estuary system from the surrounding urban areas from which runoff enters
the system. In the mid 1900’s, around 1950-1962, there was a significant amount of pollutants
entering the estuary system to the point that many fisheries that pursued various shellfish and
finfish were suffering because their catch was so heavily polluted that they couldn’t be put on the
market, (Pierce, 1979). While conditions in the bay have improved dramatically since then there
is still a lot of nutrients entering the system via runoff as will be seen in the results.

Methods and Materials

Study Design

Data was collected over the course of two cruises of Raritan Bay, in New Jersey. Upon loading
our sampling instruments onto R/V Rutgers, we departed from Morgan Marina at the beginning
of each cruise. The first cruise took place on September 12, 2023, and the second on October 10,
2023. Three stations were visited on each cruise, with the station farthest from the river mouth
being the first, and the station closest to the mouth of the river being the third (Figure 2).
Figure 2: Map of Stations 1-5 in Raritan Bay, NJ. MapCustomizer Software used to create map.

Once we arrived at each station, we noted the following: the coordinates, depth of the water
column, and weather conditions. Then, we began our data collection, using a conductivity,
temperature, depth rosette (CTD). From samples collected with this CTD rosette, we were able
to gather samples from various depths at each station (Table 2). Once back in the lab, we set out
to measure chlorophyll a concentrations, dissolved oxygen (DO), primary production, and
phosphate concentrations. We were also able to gather data regarding which prokaryotes and
eukaryotes were present in the water column. It is important to note that while we do have five
stations listed in Table 1, extensive data was collected only for Stations 1-3: the only data
obtained from Stations 4 and 5 was in regards to prokaryote community assemblages. Upon
analyzing this data altogether, combined with that from the CTD, we were able to achieve a
bigger picture of the dynamic environment of the Raritan Bay.

​Table 1: Coordinates for Stations 1-5 in Raritan Bay, NJ. Microsoft Word used to create table.
Station 1 Station 2 Station 3 Station 4 Station 5
40° 29' 17"N, 40° 29' 12.11"N, 40° 28' 13.04"N, 40° 29' 15.04"N, 40° 29' 25.92"N,
-74° 2' 5"W -74° 7' 17.48"W -74° 12' 15.48"W -74° 25' 22.95"W -74° 26' 6.14"W

CTD

A CTD is an essential tool for any sampling of the water column’s properties. CTD stands for
conductivity, temperature, and depth which are the properties that it measures in the water
column. Understanding these characteristics of the water column are vital for oceanographic
research whether it be related to physics, chemistry, or biology. CTD’s are often attached to a
larger rosette of Niskin bottles for water sampling or simply protected by a steel frame to prevent
damage to its more sensitive components. For our sampling we primarily utilized a CTD with a
Niskin rosette surrounding it. This way we were able to measure the temperature and salinity,
conductivity, with depth at our sampling stations within the Raritan Bay while also collecting
water samples at the top, middle, and bottom of the water column at each station.
Secchi Depth

Secchi Depth is a measure of the turbidity or transparency of the water and gives us insight on
the particles in the water and how that affects light attenuation. We calculated Secchi depth at
each station using a Secchi disk which was connected to a rope that had markings every meter.
The disk was lowered into the water and we took note of when the disk was no longer visible and
how many degrees (if any) off vertical the disk ended up. The true depth was calculated using
trigonometry (below) where “l” signifies length of rope in meters, and “𝜃” is degrees off vertical.
𝑠𝑒𝑐𝑐ℎ𝑖 𝑑𝑒𝑝𝑡ℎ = 𝑙𝑠𝑖𝑛θ

Chlorophyll a

The samples were collected by pouring 100mL of water from the Niskin bottles onto our vacuum
filtration apparatus that was loaded with glass microfiber filters. Once the filters were noticeably
green/brown, the filters were put in centrifuge tubes and placed in ice until brought to the lab
where it was put in a freezer until sample analysis. During analysis, it is crucial to keep the
samples from excessive exposure to light, which degrades the chlorophyll pigment. The samples
were prepared using acetone, crushing the filters by a pestle, and centrifuging to ensure all of the
chlorophyll collected is in the acetone solution. Once ready to use the fluorometer, a blank is
prepared by placing 1mL acetone in a cuvette tube and recording the reading from the
fluorometer (Fo blank); we added 2 drops of 1.2M hydrochloric acid to our blank and recorded
the fluorometer reading (Fa blank). Our samples were also placed in the cuvette tubes with a
900µL of acetone for dilution of our 100µL sample and mixed by inverting the tube. This gave
us the Fo readings of our samples and 2 drops of HCl was added and mixed to give us Fa
readings. Chl-a was calculated from the fluorometer specific calibration coefficients Fm and K,
the Fo and Fa data of each sample, extraction and filtered volume ratio, and the dilution ratio.
Phaeophytin, the degradation product of chl-a, was also calculated using the same variables in a
separate calculation (“SOP 5”, 2023).

Dissolved Oxygen (DO)

Using water samples collected from the Niskin bottles on the cruise while ensuring that no air
bubbles are present in the sample bottles, the water samples were preserved for a later date to be
analyzed using the Winkler titration methods. This method entails using several reagents:
Manganese (II) chloride, sodium iodide, sulfuric acid, starch indicator, sodium thiosulfate, and
potassium iodate. Sodium thiosulfate is as the titrant indicating the end of the titration by
reacting with iodine, sulfuric acid is used to dissolve the precipitate in the sample, the starch
indicator is then used to react with the rest of the iodine (“SOP 8”, 2023). Before starting the
titration, the thiosulfate needed to be standardized to get the precise concentration of thiosulfate
(“SOP 8”, 2023). After this is determined, a blank is run to determine if there are any impurities
in the reagents. This is when the titration of the seawater samples began. The Winkler titration
facilitates the oxidation-reduction reaction in the sample and the DO concentration can be
determined from this reaction.
Primary Production

The samples for primary productivity were collected two different ways over the course of both
cruises. For the first cruise, seawater was collected in a plastic carboy and stored until we
analyzed it. The second cruise samples were collected on board from the Niskin bottles. To
conduct the analysis, the sample was split into 5 different bottles exposed to varying amounts of
light: 0%, 25%, 50%, 75%, and 100%. Before allowing the samples to incubate, a measure of
DO, using a calibrated DO sensor, was taken from each sample. By allowing these samples to
incubate at different lights for five hours, this allows for the calculation of primary productivity
using the rate of respiration that occurred from when the first measure was taken (“SOP 6”,
2023).

Phosphate

In order to measure the soluble reactive phosphate in our samples, we first made dilutions of the
stock standard to develop our standard curve. The concentrations of our standard curve were as
follows: 0.00 µM, 1.00 µm, 2.00 µM, 4.00 µM, and 8.00 µM. Following the development of
these standards, we then created a solution composed of four reagents: ammonium molybdate,
sulfuric acid, ascorbic acid, and potassium antimonyl-tartrate (“SOP 10”, 2023). The interaction
of this mixed solution with our seawater samples then produced a tint of blue, the absorption of
which was measured with a spectrophotometer (“SOP 10”, 2023). A darker color indicated the
presence of a higher concentration of phosphate. Measurements were then plotted in Microsoft
Excel, and a visual representation of phosphate with depth across all three stations was created.

Zooplankton

Zooplankton are a varied group of heterotrophic organisms that feed on phytoplankton.

Zooplankton can vary in size, shape, and characteristics to an extraordinary degree. They are
grouped as microzooplankton (20-200 μm; unicellular flagellates as an example),
mesozooplankton (200 μm – 2 mm; copepods as an example) and macrozooplankton (>2 mm;
small jellyfish as an example; “SOP 7”, 2023).

All groups of zooplankton play a pivotal role in food webs of most bodies of water, including
those of estuaries. Zooplankton are a direct control on phytoplankton count, contribute to
nutrient regeneration via metabolic processes, and facilitate the transfer of energy produced by
photosynthetic phytoplankton to higher trophic levels (the fish and other organisms that humans
cultivate). In studying zooplankton, we can gain a better understanding of how to optimally run
fisheries for resource exploitation.

In order to collect zooplankton, we used a plankton net which we attached to the tow line of our
boat. Our plankton net had a device called a flow meter attached to it which allowed us to
measure approximately the distance covered during the tow. The tow itself was performed at
each station for 1 minute at a speed of ~2 knots. Upon retrieving the tow, we used an ocean water
hose to wash the net (from the outside in to avoid altering our sample). This was done to ensure
any zooplankton stuck to the net would make its way into our sample bottles (attached to the
bottom of the net). We stored these samples in a 1:1 ethanol to water mixture, and later analyzed
them in the lab by splitting the samples into calculable sizes, and then manually counting the
individuals found. Later, we used our findings to calculate an approximate abundance of
zooplankton found at each station.

Prokaryotes & Eukaryotes

Prokaryotes and eukaryotes are the two main Kingdoms under which all living organisms fall.
Prokaryotes consist of bacteria and archaea, while eukaryotes include plants, animals, fungi, and
protists. We collected samples of microscopic prokaryotes and eukaryotes; Cruise 1 at all stations
for prokaryotes, and Cruise 1 at Station 1 for eukaryotes. We also observed a number of marine
bird species as well as dolphins on each of our two cruises.

Microscopic prokaryotes and eukaryotes make up a key part of an estuary system. Each species
often has unique characteristics and can serve a different (or multiple) purpose(s) in their
respective environment. These impacts generally include but are not limited to nutrient cycling,
primary production, serving as a base for the food web, detoxification, and sediment
stabilization. Thus, in analyzing data of microscopic organisms, we can gain a better
understanding of the health of the estuary, and why it functions as it does.

Sample collection was taken with 5L Niskin bottles that we deployed to top, middle, and bottom
depths for each station. We later both filtered and then froze these samples for analysis. In the
lab, we used these samples to perform PCR amplification and sequencing of the DNA. We
extracted the DNA by taking the samples through a lysing procedure. After this, we binded the
DNA to magnetic beads in order to separate it from the solution. Once we concentrated the DNA
from the samples using this method, we processed it using agarose gel electrophoresis, and used
the finished product for PCR amplification (Kerkhof et al., 2017). The result was then taken and
analyzed by the MinION sequencer, which gave us raw data in excel format. We took this raw
data and made pivot tables from it to gain a better understanding of species counts.

Results

CTD

The results noted below were obtained through a variety of sampling methods noted above.
Upon dropping down the CTD/rosette, we collected data regarding temperature, salinity and
density for each station and across two cruises (Figure 3). The depths at which the CTD
collected data from at each Station are noted (Table 2). To be able to effectively compare
temperature, salinity and density between cruises, profiles for each water quality parameter were
created for each station (Figures 4-6).

Table 2: Table of sampling depths at Stations 1-3 in Raritan Bay between Cruises 1 and 2. Microsoft Word used to
create table.
Cruise 1
Station 1 Station 2 Station 3
Top 1m 1m 1m
Middle 7m 5m 3m
 Bottom 14m 9m 6m
Cruise 2
Station 1 Station 2 Station 3
Top 1m 1m 1m
Middle 8m 8m 3m
Bottom 14m 14m 6m

In regards to temperature, the temperature of the water column across all three stations was
roughly 9 oC higher on Cruise 1 than on Cruise 2 (Figure 4). Additionally, the temperature did
not vary as widely with increasing depth during Cruise 2, as opposed to Cruise 1, where there
was a slight thermocline present (Figure 4). Temperature decreased slightly from Station 3 to
Station 1 (Figure 4). Looking at the profiles for salinity and density, they both tend to increase
with increasing depth (Figures 5 & 6). At Stations 2 and 3, we notice what appears to be a sharp
decrease in salinity and density on Cruise 1 (Figures 5 & 6). This is likely a result of the
CTD/rosette dragging along the bottom substrate, which could have caused some interference
with the readings for these parameters.

The density of the water column was higher throughout Cruise 2 than Cruise 1 (Figure 6). Both
density and salinity were highest at Station 2, which has a less direct influence from the Raritan
and Hudson Rivers as do Stations 3 and 1, respectively (Figures 5 & 6). Salinity varied more
widely than the other two parameters: at Stations 1 and 2, salinity was higher at the top of the
water column for Cruise 1 (Figure 5). Alternatively, salinity was higher at the bottom of the
water column for Cruise 2 (Figure 5).

Figure 3: Left: Temperature v. Depth profile; Middle: Salinity v. Depth profile; Right: Density v. Depth profile.
Data from a CTD downcast has been plotted across all three stations within Raritan Bay. Microsoft Excel used to
create graphs.
Figure 4: Temperature v. Depth profiles for a CTD downcast at Stations 1-3 within Raritan Bay from each cruise.
Microsoft Excel used to create graphs.

Figure 5: Salinity v. Depth profiles for a CTD downcast at Stations 1-3 within Raritan Bay from each cruise.
Microsoft Excel used to create graphs.

Figure 6: Density v. Depth profiles for a CTD downcast at Stations 1-3 within Raritan Bay from each cruise.
Microsoft Excel used to create graphs.

Secchi Depth
Regarding a trend that we observed towards the mouth of the bay, the Secchi depth decreases in
Cruises 1 and 2. In Cruise 1, the highest Secchi depth was about 3m and the lowest was 1.6m
(Table 3). In Cruise 2, the highest depth was 1.1m and the lowest was 0.9m (Table 3). Cruise 1
had the highest recorded Secchi depths of the two cruises, which was about three times greater
than Cruise 2 at Stations 1 and 2, and two times greater than Cruise 2 at Station 3.

Table 3: Secchi depth across all stations and during both cruises of Raritan Bay. Microsoft Excel used to create
table.
Station 1 Station 2 Station 3
Cruise 1 3.0m 2.9m 1.6m
Cruise 2 1.1m 1.0m 0.9m

Chlorophyll a

The chl-a concentrations were calculated from Cruise 2 and two replicates were taken at each
station. It is important to note that the incorrect fluorometer module was used when calculating
Rep A, therefore these values may not reflect the true phytoplankton biomass.

For Station 1, we see that the chl-a concentration in Rep A is lowest at the middle of the water
column at 8m, and increases with depth where it is highest at 14m ; the phaeophytin
concentration mirrors the chlorophyll trend where it is highest at the 8m mark and lowest at 14m
which is a negative number (Figure 7). Station 2 Rep A also follows this trend; 8m has the
lowest chl-a concentration which is a negative number and the highest phaeophytin
concentration whereas the highest chl-a concentration and lowest phaeophytin concentration is
located at 14m (Figure 7). Station 3 Rep A shows the highest chl-a concentration at the surface
and the lowest is at the bottom depth, 6m, which shows a negative concentration. The
phaeophytin concentration mirrors the chl-a trend where it is lowest at the surface and higher at
the bottom.

Station 1 Rep B the chl-a concentration is highest at the surface and decreases with depth; the
phaeophytin concentration is lowest at the middle depth, 8m, and highest at the bottom depth.
Station 2 Rep B shows that the chl-a concentration is lowest at the middle depth and highest at
the surface and bottom (~0.32µg/L). The phaeophytin concentration at this station shows that the
highest is at the bottom depth (6m) and lowest at the middle 3m depth. Station 3 Rep B has the
highest concentration of chl-a at the surface and the lowest at the bottom, which is a negative
number. The phaeophytin concentration is lowest at the middle depth and highest at the bottom
(Figure 7).
Figure 7: Chlorophyll a and phaeopigment concentrations for duplicates at Stations 1, 2, and 3 in Raritan Bay, NJ.
Microsoft Excel used to create graphs.

Dissolved Oxygen (DO)

After calculating the DO in micromoles per kilogram, a relationship can be established with
depth. Figure 8 shows this relationship for all three stations of Cruise 2. For all three stations,
DO concentration is highest at the top with a drop in concentration at the middle of the water
column. This observation was particularly prominent in Station 3, with a very exaggerated dip in
the middle of the sample and increasing at depth (Figure 8). Atmospheric dissolved oxygen at 25
degrees celsius (left) and 18 degrees celsius (right) are indicated by the black arrows.
Figure 8: Dissolved oxygen (DO) concentration v. depth profile for a CTD downcast at Stations 1-3 in Raritan Bay
from Cruise 2. Microsoft Excel used to create graphs.

Primary Production

Primary production was calculated using the DO content before beginning the incubation process
and the DO in the sample after. Gross primary productivity was calculated using the difference
between DO concentrations. This gross productivity is a key factor in the respiration rate of the
cell as well as the total amount of oxygen being produced (“SOP 6”, 2023).

Table 4 depicts these measurements taken from each station for both Cruises 1 and 2.
Measurements were taken using a sample of water from Station 3 of Cruise 1, and Station 1 of
Cruise 2. The table depicts gross productivity in units of milligrams of carbon per liter per hour
to obtain the rate of formation of new material. For Cruise 1, there is an increase in gross primary
productivity at the deeper depth (Table 4). Cruise 2 has a similar pattern between the top sample
and middle sample with a minimum increase of 0.01 mgC/L/h (Table 4). However, this trend
does not continue to the deepest sample because the gross productivity decreases at the deepest
depth. This could have been the same case with cruise one but there were limitations in the
measurements. These limitations in accuracy occurred due to human error leaving the samples in
warm temperatures, and oxygen loss in the second cruise samples.
Table 4: Primary Production data from 3 locations within the water column: G1 (top), G2 (middle), G3 (bottom).
Samples incubated at 18 oC. Cruise 1 (top) Cruise 2 (bottom). Microsoft Word used to create table.

Phosphate

Upon creating our standard concentrations for phosphate analysis, we created a standard curve,
which had an R2 value of 1.00 (Figure 9). On Cruise 2, phosphate decreases with depth across all
stations (Figure 10). On Cruise 1, the patterns are a bit different: phosphate concentrations
increase with increasing depth at Station 2, and increase slightly with depth for Station 1 (Figure
10). At Stations 1 and 2 on Cruise 1, phosphate concentrations were noticeably lower at the
surface of the water column than they were on Cruise 2: for Station 1, this difference was of
about 1.00 µmol/kg, and for Station 2, of about 1.70 µmol/kg (Figure 11). The opposite,
however, was true of Station 3, where the top phosphate concentration during Cruise 1 was about
4.30 µmol/kg as compared to 3.30 µmol/kg during Cruise 2 (Figure 11).
Figure 9: Standard curve for 5 standards of the following concentrations: 0.00 µM, 1.00 µM, 2.00 µM 4.00 µM, and
8.00 µM. R2 value of 1.00.
Figure 10: PO4 concentration v. depth profiles for a CTD downcast at Stations 1-3 in Raritan Bay for each cruise.

Figure 11: Phosphate (PO4) concentration v. depth profiles for a CTD downcast at each station between both cruises
of Raritan Bay.

Prokaryotes & Eukaryotes

Results from samples indicate that the prokaryote families shown in Table 5 and Figure 12
were the most abundant in the Raritan for the period of Cruise 1. Both saltwater and freshwater
stations had abundant counts of different species. While most prokaryote families as a whole did
show a preference for either more saline or more freshwater environments, there were a number
of families, such as Microbacteriaceae, which had several genera and species that were dominant
in the opposite kind of environment as the rest of the same family.
Table 5 is a pivot table of all prokaryote count data that we were able to collect at each station,
and is sorted by count of species from highest to lowest. Freshwater oriented stations included
Boathouse 1 and 2 (BH_1 and BH_2 respectively), as well as Donaldson Park 1, 2, and 3 (DP_1,
DP_2, DP_3). The “W” added to certain stations indicates a different group who sampled on a
Wednesday, as opposed to Tuesday of the same week. Saltwater oriented stations included
Midbay (MB) and Sandy Hook (SH). The saltwater stations contained samples from the bottom,
middle, and top layers of those stations (labeled as bot, mid, and top respectively).

Table 5: Pivot table of most abundant prokaryotes across all stations in Raritan Bay. Excel used to create chart.

The data represented in Table 5 is the same as is represented in Figure 12, taken as relative
abundance. Station 1 is Sandy Hook, Station 2 is Midbay, Station 4a is Donaldson Park 1, 4b is
Donaldson Park 2, and Station 5a is Boathouse 1, 5b is Boathouse 2.
Figure 12: Relative abundance bubble chart of most abundant prokaryotes across Stations 1-2 (saltwater) and
Stations 4-5 (freshwater) in Raritan Bay. RStudio used to create chart.

There were a few instances in our prokaryote data wherein a prominent genus or species was
marked as “unclassified”, “candidatus”, or otherwise. Below in Table 6 is one such example of
an unclassified genus of the Rhodobacteracea family making up the majority count of the entire
family.

Table 6: Pivot table of the most abundant genus of the rhodobacteraceae prokaryote family across all stations in
Raritan Bay. Notice the top species count being “unclassified_Rhodobacteriacea”. Excel used to create chart.
Eukaryote data was taken for Station 1 (Sandy Hook) only. The most abundant genus found was
Skeletonema, followed by Cyclotella. Skeletonema represented a significant portion of the total
species count, and thus we created a distinct pivot table and bubble plot for it to analyze specific
species (Table 7 and Figure 13).
Table 7: Pivot table of genus Skeletonema. Microsoft Excel used to create table.

Below in Figure 13, on the left is a plot of dominant diatoms within the water, of the Genus,
Skeletonema, specifically – we can see the two dominant taxa, and it is apparent that individuals
of this Genus are more abundant at the bottom of the water column (roughly 33% more abundant
– consistent with fresh to saltwater ratio). On the right is a plot of all other Diatom taxa found
within the blast analysis – we can see that Cyclotella and Thalassiosira are most abundant
relative to all other taxa, though they are distributed more evenly throughout the water column
(Figure 13).

Figure 13: Most abundant species of the Genus Skeletonema (Left). Other abundant eukaryotes of different taxa at
Station 1 in Raritan Bay (Right). *The same relative abundance was used to calculate the presence of each strain
within each location in the water column: top, middle, and bottom. RStudio used to create chart.
Below in Figures 14-16, we created pie charts to represent the relative abundance of different
strains within different Genera: Skeletonema, Cyclotella, and Thalassiosira species. This was
done to gain a better understanding of which species dominate the water column at Sandy Hook.
Other observed data included a variety of different seabirds which we did not classify. We also
encountered dolphins on each of our two cruises, some of which at least we believe were
Common dolphins due to their noted appearance in the Raritan over the course of 2023 (Kratovil,
2023).

Figure 14: Skeletonema sp. at the bottom (left) and top (right) of the water column at Station 1 in Raritan Bay.
Microsoft Excel used to create charts.

Figure 15: Skeletonema sp. at the bottom (left) and top (right) of the water column at Station 1 in Raritan Bay.
Microsoft Excel used to create charts.
Figure 16: Thalassiosira sp. at the top (left) and bottom (right) of the water column at Station 1 in Raritan Bay.
Microsoft Excel used to create charts.

Zooplankton

Data collected on zooplankton ended up being sparser than intended; we forgot to bring the
zooplankton tow for Cruise 1, so we were only able to get data for Cruise 2 (Tables 8-10).
Further, Eukaryote Pivot data for Cruise 1 Station 1 did not provide much data on zooplankton
either: roughly 10-15 total entries out of thousands.

Table 8: Zooplankton tow data for Cruise 2, Station 1.

Table 9: Zooplankton tow data for Cruise 2, Station 2.

Table 10: Zooplankton tow data for Cruise 2, Station 3.

Discussion

CTD

With regards to the CTD data that we compiled over the course of our surveys, we were able to
assemble several vertical profiles that highlighted the trends we observed for each parameter
versus depth. Beginning with temperature, at a broad glance we could point out the major
difference between the two cruises was the temperature average by a margin of eight degrees
Celsius for all three stations. Furthermore, there was a marked difference in the visibility of the
thermocline for each station.This temperature difference is most simply explained by the time
range that we took these measurements in. Sampled a month apart from each other in September
and October respectively, the decrease in global light exposure that occurs as a result of the
Earth’s axis shifting with the changing seasons could be interpreted as a cause of this
temperature change. Another explanation could have been the lateral shifting of water at depth.
In the case of the Cruise Two readings for Station One, the thermocline took on an appearance
that closest resembles the thermoclines of Cruise One. Extending to around two meters before
decreasing with depth. We reasoned that this was almost certainly due to Station One being the
farthest from shore and as such would have not only the deeper sampling depth maximum, but
also it would be the least affected by factors such as turbidity, and sediment runoff. Moreover,
Station One’s proximity to the greater Atlantic Ocean exposes it to mixing with the more
offshore waters. For Stations Two and Three, the thermocline took on a more vertically linear
appearance rather than a sloped angle which is more typical of a thermocline. We reasoned that
this was either due to an error in the CTD recordings itself or an uncharacteristic albeit accurate
display of the thermocline for these two stations at this particular point in time. The shorter
depths to which we deployed the CTD were the most likely overall factor that contributed to this
graph discrepancy as the water columns of these two stations were markedly more turbid and
vertically well-mixed than Station One. Furthermore, the closer proximity of Stations Two and
Three to the shore would have made them more susceptible to being affected by the factor of
sediment runoff. All of which could have contributed to these resultant readings.

Moving into salinity, the surface salinity readings for each cruise closely resembled each other
and increased gradually with depth. At the surface, salinity differed only by a margin of two ppt
in the case of Station One, while the other two stations had virtually the same recorded surface
salinity. This twp ppt was either the result of sampling error from the CTD itself or possibly due
to the shifting if the salt wedge that we know is present in the estuary. As well as the strong input
of fresh water stemming from the adjacent rivers. An absence of this wedge during the Cruise
Two sampling would almost certainly have resulted in the lower salinity reading that we find at
Station One. The Station Two readings for both cruises were the most “baseline” in that they
were characterized by a surface reading of twenty-three ppt and their sloping increasing with
depth closely mirrored each other. Lastly the Station Three reading for both cruises was marked
by having the lowest surface salinity reading. We reasoned that this would have been due to the
Station’s proximity to the freshwater source points of the Hudson and Raritan Rivers, which is
how the Hudson-Raritan Estuary is formed. It is within reason to assume that with these specific
compositions, Station Three is indicative of a well-mixed water column while Station One is
more saline and stratified, with Station Two occupying the middle ground.

Lastly we sampled for density, which is a function of both temperature and salinity. At the
surface we detected a range of 1014 to 1016 kg/m3 with Station Three having the lowest
recorded surface density. We reasoned that this was again due to Station Three’s proximity to
freshwater source-points which decrease the water salinity and by extension the density. For
both cruises, Stations One and Two had the highest recorded surface water densities, again due in
part to their proximity to the more saline Atlantic Ocean. Across the board, the density at each
station for each cruise increased gradually with depth, as the water profile would have turned
colder and more saline. Readings for Station Two and Three were also marked by a sudden
“tail-end” around ten meters with regards to the density line. We assumed this was the result of
the CTD coming into contact with the seafloor and dragging or scraping along the bottom. This
was further evidenced by the total absence of such a line at Station One where the water column
was much deeper and as such we never came into contact with the bottom. As a whole, the
density readings were in line with what had been expected and had no real unexplainable
aberrations. Taken together, these three parameters of the water column that we sampled provide
us with a composite look of the Hudson-Raritan Estuary as a whole and further allowed us to
make inferences based on the data that we gained later through our several lab experiments.

Secchi Depth

Between the two cruises, there was a storm before the first cruise that mixed the water column
which could explain why there was less turbidity and the Secchi depth was deeper for the Cruise
1 data (Table 3). The particles were most likely dispersed throughout the water column, so there
was not an accumulation of particles in the surface water. These particles could be inorganic
particles coming from the land/rivers or organic particles from biological activity in the water
column.. Not only were there temporal differences between the two dates, the spatial difference
in turbidity between the three stations is evident in Cruise 1. There were differences between
each station in Cruise 2, which was ~0.1m difference in depth between each station.

Station 3 is closest to the Raritan River at the mouth of the bay and is where we see the highest
turbidity, shown by the low Secchi depth (Table 3). Since this station is closest to the shore, it is
influenced by land runoff and the Raritan River, causing station 3 to have the highest amount of
inorganic particles. These particles act like an umbrella, decreasing the clarity of water and the
amount of sunlight that can enter the water column. The high turbidity may also have been
caused by wave attenuation stemming from wind and boats in the area which resuspends the
bottom mud particles affecting the clarity of the water, especially since this station has the lowest
recorded depth of all three stations we sampled from. Another reason could be that the particles
This decrease in clarity affects the biological biomass of phytoplankton, since they require
sunlight for growth, so we should expect to see less phytoplankton at this station depicted by the
low chl-a concentrations.

Stations 1 and 2 are the farthest from the mouth of the bay and have similar Secchi depths across
both Cruises (~0.1m difference) (Table 3). We can say that these two stations have little to no
influence from the Hudson and Raritan Rivers due to their deep Secchi depths, meaning that
there are little to no particles in the surface waters at these two stations. Also, the particles may
have settled with the water mass moving deeper water; the sampling depth of these two stations
were much deeper than Station 3 (9-14m). Therefore, resuspension of bottom mud particles may
not have a great influence on surface clarity like we thought for Station 3. Consequently, the
water is less turbid at Stations 1 and 2 which could have been influenced by phytoplankton
growth intaking the organic particles. This would be supported by the higher chl-a
concentrations and low phosphorus at these stations, which could make the waters less turbid and
result in a deeper Secchi depth.

Chlorophyll a

It is important to note that the negative numbers of chl-a and phaeophytin concentrations means
that too much acid was added to our samples which impacted our data and may not have given us
a true value of what we see in our sampled water column. Also, the operator error with the use of
the incorrect fluorometer module affects the conclusion we reach with our data. The replication
duplicates for stations 2 and 3 are not similar, meaning the replicates for these stations do not
agree with one another.

Looking at Rep A for stations 1 and 2, we see a similar trend that chl-a decreases until we reach
the middle depth, then increases as we go deeper into the water column. This is the opposite of
what we would have expected since deeper into the water column, less light penetrates the
system, meaning that it creates an inadequate environment for phytoplankton growth. Looking at
Rep B for Station 1, we see that chl-a concentration does decrease with depth until the middle
depth, 8m, then it slightly increases until 14m; the phaeopigment shows a slight decrease until
the middle depth, then increasing until the bottom (Figure 7). This also goes against our
expectations since we should not see the chlorophyll increasing where there is less light for
phytoplankton growth; in reality what we could be seeing is that phytoplankton increase their
antennae size as the light decreases which could explain this trend we see. Rep B for Station 2
shows both chl-a and phaeopigment decreasing until the middle depth, then increasing as we go
deeper into the water column. The phaeophytin and chl-a should not show similar trends like this
since phaeopigment is the degradation product of chl-a; we expect these two lines to be opposite
of each other.

For Station 3, Reps A and B show chl-a highest at the surface and decrease with depth. The
phaeophytin concentration shows an opposite trend in that it is lowest at the surface and
decreases with depth. Station 3 demonstrates what we expected in terms of the trend, but our data
shows negative numbers for chl-a concentrations meaning there was error in how we handled the
sample in the lab, which we believe was the result of adding too much acid. Still, chl-a should
decrease with depth since both phytoplankton and light attenuation decrease as you go deeper
into the water column. As we get closer to shore, we expected less chl-a in the surface compared
to Station 3, since there is less light in the surface water which limits phytoplankton growth. It is
unclear from our data whether this trend is shown since the negative numbers for chl-a hinders
our true understanding of the data.

Dissolved Oxygen (DO)

Dissolved oxygen and nutrients are responsible for the amount of aerobic activity that can take
place in a system. In low levels of oxygen, not much activity can take place. With high levels of
oxygen, it is no longer a limiting factor and allows for an increase in biological activity. Because
of this, it is an important factor to measure in order to estimate how well the system is doing.

Dissolved oxygen measurements using the winkler titration method were only obtained for
Cruise 2, however these results can be tentatively compared to the initial DO read in Table 4
which shows an increase between the top and middle samples. The deepest sample was not
measured in Table 4 so it can not be used to compare if the DO will increase at the deepest
depth. Since dissolved oxygen is dependent on pressure and temperature atmospheric
concentrations will vary between 235 μM at 18 degrees celsius and 210 μM at 25 degrees celsius
(Sherrell, 2023). All three stations from cruise two have surface water temperatures around 18
degrees celsius (Figure 4). This means that at stations one and two are in excess of atmospheric
concentrations and thus are a source of oxygen. However, station three is not which could be due
to it being the closest station to the river. Air sea interactions will keep the DO concentration in
equilibrium meaning if the surface waters had exceeded the atmospheric concentrations the
ocean would be a source of oxygen (Mader et al., 2017). The dip in the middle of the water
column in Figure 8 can be explained due to it being the location in the water column that is right
below light penetration. Being below the greatest depth of where light penetrates, phytoplankton
sinks into this zone are being respired and consumed.This depth is where the most amount of DO
is being consumed or respired because of biological activity, these patterns can be seen in Figure
8 and Table 4 where DO is the highest at the top and is being respired or consumed in the
middle, however this can vary over periods of time. With less biological activity, the middle
depth would not have such a drastic decrease in DO. Across all three stations there is an increase
in DO at the lowest depth this could be because this depth is below the compensation depth,
where respiration is no longer equal to photosynthesis. There could be less respiration happening
at this depth as well as less photosynthesis, so the increase could be attributed to sinking or
circulation.The limitations in what can be observed in a temporal pattern happened as a result of
not being able to obtain the DO concentration from Cruise 1. The expected pattern was that, as a
result of more biological activity, the first cruise would have shown this in decreased levels of
DO in the photic zone where the primary productivity would occur.

Primary Production

Primary Production as a function of DO can be used to observe the health of the system and the
biological interactions happening. Whether there is more growth or respiration will influence
what the gross primary production is. Table 4 depicts this relationship with the depths showing a
similar trend to DO. The difference between the two is that there is an increase in production at
the middle station in both cruise one and two. This could explain the decrease at the middle
depth from Figure 8 because there is an observed decrease in DO at this depth most likely due to
biological activity.

Primary productivity calculations from cruise two show a pattern similar to what is expected of
ocean systems. Having the highest productivity in the middle of the water column where most of
the production and respiration happens, since gross primary productivity takes into account the
amount of respiration, it would not be highest at the top because mostly photosynthesis happens
in this area and not as much respiration. The bottom depth is where mostly respiration occurs and
not as much photosynthesis.

Over the course of measuring the primary productivity, the samples need time to incubate to find
the rate of respiration. However, for the first cruise, while conducting this experiment, the
samples were stored in an area that caused the sample to overheat. Overheating the sample would
cause the rate of respiration to be skewed because in increased temperature respiration increases
(Li et al., 2021). Thus, having the samples incubate and get hotter would have caused the
samples to have lower rates of DO which is what is observed. However, it might have been
higher if the temperature remained constant. Overheating might have also caused expulsion of
the gases causing the dissolved oxygen measurements to be too low. The second cruise samples
could have also failed due to loose caps, allowing oxygen loss or contamination. For future
experiments, these issues could be avoided by not letting the bottles overheat and using winkler
bottles with glass stoppers.
Phosphate

Looking at the phosphate (PO4) data, we notice a trend, across both stations, and between both
cruises (Figure 7). Station 3 has the overall highest PO4 concentrations, relative to Stations 1 and
2, which is the case for both cruises. Considering that this station is positioned where the Raritan
River flows into the Raritan Bay estuary, this peak in PO4 makes sense, as the majority of
phosphorus in aquatic systems originated on land. While there is some atmospheric deposition of
phosphorus, weathering events tend to carry things such as waterfowl waste, urban and
agricultural runoff, fertilizer, sewage, and pet waste off the land, and into aquatic ecosystems
(NHDES, 2019). The presence of high PO4 concentrations at this station is consistent with the
high turbidity and low chlorophyll concentrations found here (Table 3 and Figure 7,
respectively). Essentially, with high turbidity, light cannot penetrate as far into the water column.
As such, we would expect to see a lower abundance of phytoplankton, lower chlorophyll
concentrations, and high PO4 concentrations (due to its influx from the Raritan River and the fact
that there is less biology taking it up in comparison to the less turbid Stations 2 and 3).

Aside from the differences present between stations, we also notice some differences between
cruises. Looking at Stations 1 and 2, the PO4 levels were considerably lower at the surface of the
water column on Cruise 1 than they were on Cruise 2—roughly 1 µmol/kg lower at Station 1,
and 1.7 µmol/kg lower at Station 2 (Figure 11). One likely explanation for these patterns has to
do with the higher light levels and temperatures present during Cruise 1, in comparison to Cruise
2. If we recall, the dates of the cruises were 09/12/2023 and 10/10/2023, a time period during
which it is likely that temperature decreased, along with light levels, which would stump
phytoplankton growth. Looking between Cruises 1 and 2 for Station 3, we notice that the
opposite pattern is true—PO4 levels were higher during Cruise 1 than Cruise 2 (Figure 11). It is
likely that the same patterns in phytoplankton growth were observed between Cruises 1 and 2 at
Station 3, though a major rain event prior to Cruise 1 is a likely reason for the observed spike in
PO4 from Cruise 1. This increased rainfall may have carried down excess phosphorus into the
estuary, thus leading to the very high signal we observe (Figure 11).

Relating this back to our DO reads from Cruise 2, we see opposite patterns for this parameter and
PO4. While there are higher DO concentrations at the surface at Station 1 (relative to Station 3)
there are low PO4 concentrations here (relative to Station 3). Once again, primary production
could be a cause for its inverse relationship between DO concentrations and PO4 concentrations.
Peaks in DO at the surface are likely a result of phytoplankton growth producing DO as a
byproduct, and depleting the PO4 here (Figure 11).

Prokaryotes:

Of the families of prokaryotes sampled during these cruises Comamonadaceae were one of the
most abundant families in the freshwater samples. Having high abundance at Station 3 near the
mouth of the river. They are a large and diverse family of betaproteobacteria. They are
traditionally aerobic, gram negative, rod shaped, and oxidase positive. When looking at the
sampling done at Station 3, 4, and 5 it’s clear that the most common genus in this family that
appears are the Limnohabitans. These stations were dominated by an unknown species of
Limnohabitans followed far behind by Limnohabitans curvus which was still found in numbers
almost double that of the prokaryotes behind it in abundance for this family. Interestingly, when
looking at Station 1, which had the highest recorded salinity of all our sampling stations, the
Limnohabitans once again beat out the other prokaryotes of the Comamonadaceae family. Once
again the unknown Limnohabitans species is dominating when compared to the other
prokaryotes here albeit their absolute abundance has decreased by about 600 individuals when
compared to the freshwater systems. This time Limnohabitans parvus are second to this
unknown species, like L. curvus the margin between L. parvus and this unknown species is
substantial but it still beats the other prokaryotes measured here in this family by a large margin.
This genus is only expected in freshwater which is why it's unusual that they are prevalent in a
high salinity environment that they shouldn’t be able to tolerate. The background information on
Limnohabitans is that all known species are heterotrophic and they are good at cohabitation due
to specialized niches which allow them to utilize diverse organic compounds. While they also
aren’t tolerant of higher salinities their primary limiting condition is pH as they tend not to grow
in acidic conditions, (Šimek et al., 2011). While it has yet to be directly studied it is believed that
both L. parvus and L. planktonicus, another species in the genera, may be tolerant of brackish
water. This proposes a potential explanation for how they were able to make it so far off shore
and seems to be supported by the sampling at Station 1. In which case I propose that the
unknown Limnohabitans species is either L. planktonicus or a novel species that shares its
potential tolerance for brackish waters (Zhang et al., 2013). Knowing this, some potential
reasons for the high abundance here is that the surface water is bordering on their habitable
salinity which is why there is a substantial presence in both the surface and bottom samples as
this is where they are beginning to die and sink. Other potential explanations for their presence
here include increased flagellate grazing further away from the pollution of urbanized runoff and
these organisms may already be dead at this point and the physics of the water column are simply
pushing the material out to sea.

The Microcolaceae family were very prevalent in our saltwater samples. Microcoleaceae are a
family of cyanobacteria that can be either filamentous or unicellular. Since they are
cyanobacteria this means that they are photosynthetic as opposed to heterotrophic. This family is
very interesting because despite having the third highest number of individuals out of all the
prokaryotes sampled, it effectively only had one genus present. This genus being Symploca.
While it was only identified by the genus level it can be speculated that it's likely that this was
the species Symploca atlantica because from my research it is the only species present in this
region capable of tolerating fresh and saltwater environments, (Encyclopedia of Life, 2023).
Although it’s worth noting that most of the research done on this genus is on species in the
Pacific that have potential anti-cancer applications and as thus members of this genus in the
Atlantic may be underrepresented. This species traditionally dominates when phosphate
concentrations are high so it was a little unusual that the numbers were so low in the river. We
can speculate that this is likely because they are being outcompeted by another organism or being
heavily grazed upon by heterotrophs in the river. While it’s also possible that this effect is from
pollutants cyanobacteria are traditionally fairly good at detoxifying the pollutants found in the
Raritan such as lead.

The Microbacteriaceae family, while mostly dominant in freshwater environments, had a number
of species which actually showed saltwater dominance. In our pivot table for Microbacteriaceae,
a cluster of Rhodoluna and Aquiluna proved to be the dominant genera of the Microbacteriaceae
family with a preference for freshwater environments, mostly towards the Boathouse stations.
The second most dominant genus, Aurantimicrobium, was also freshwater dominant, albeit
towards the Donaldson Park stations. However, the three next most dominant genera
(Microbacterium, Pontimonas, and Curtobacterium) were all more dominant in saltwater
environments, and their distribution was largely in line with the salinity gradients found in
Figure 5. As shown, salinity was highest at Sandy Hook / Station 1 bottom, which is where,
generally speaking, these genera were most dominant (with the exception of Pontimonas, which
leaned more towards Midbay in population counts, likely due to nutrient distributions shown in
Figures 10 and 11. The bubble plot at Figure 12 also demonstrates the more intermediate
distribution of Microbacteriaceae between saltwater and freshwater environments, compared to
some of the other abundant prokaryote families.

Another prokaryote family we studied, Rhodobacteraceae, was unique in that the most abundant
genus within this family was marked as “unclassified” (Table 6). We were unable to identify this
species using the accession number as there is no data of its complete genome in the NCBI
public database. Still, it is evident from the figure that this is a genus dominating in saltwater
environments and following the halocline recorded by the CTD (Figure 5). The point being is
that, even if unclassified, the species dominant within the rhodobacteraceae family is affected by
spatial trends found in the Raritan Bay.

Methylophilaceae is a family of bacteria that makes up three percent of the total abundance. As a
family, they can be found in freshwater sediment and serve a role in the carbon cycle by using
single carbon compounds for energy (Salcher et al 2015). Of this family, the main species
making this up includes: Candidatus Methylopumilus rimovensis, Candidatus Methylopumilus
turcinensis, Candidatus Methylopumilus universalis. While these species have not been accepted
officially, there are things that can be concluded about the water column due to their presence.
The primary source of methanol that feeds Methylophilaceae comes from pectin and lignin
which are associated with plant growth and decay (Salcher et al 2015). Since Methylophilaceae
use these two sources of methane for energy, it would make sense that they are most abundant in
the freshwater of the Raritan river and quickly dissipate as soon as saltwater from the ocean is
introduced. Being found in the samples means that there is a source of methane in the river that
these species can survive off but not in the more marine environment of the bay. This source of
methanol could be from the fermentation of saltmarsh grasses near the raritan bay.

A prokaryote in low abundance that we observed that of the freshwater Candidatus

Nanopelagicae, that we observed across the board at each freshwater station. Candidatus
Nanopelagicae is a provisional name for prokaryotes that have well observed characteristics but
are so far uncultured. They are a relatively new order in the phylum Actinobacteria and
reportedly thrive in freshwater systems. They have been described as possessing “streamlined
genomes and small cell size” (Gao et al., 2022) which has helped them adapt to nutrient-poor
environments. Furthermore they are characterized by having habitat preference variability among
their different species, with some observed as abundant in freshwater systems but absent in
marine, and low in brackish water.
Among the many Prokaryotes detected during our trawls, we observed in relatively low
abundance the presence of one or more unclassified Nitrosomondales species. Unsurprising, as
the Nitrosomonas bacteria is extremely common in marine systems and plays a pivotal role in the
nitrogen cycle of the ocean. At a glance, Nitrosomonas bacteria are characterized as a
gram-negative bacteria, typically rod or bacillus-shaped with three basic morphological types of
varying length. Composed of several different species, the Nitrosomonas bacteria is found in
both marine and fresh water with species habitat variability exhibiting preferences for each body
of water.

The most notable feature of Nitrosomonas is that it is an Ammonia-oxidizing bacteria. Within

this process, ammonia is first converted to the compound hydroxylamine by the enzyme
ammonia monooxygenase before being catalyzed by the enzyme hydroxylamine oxidoreductase.
While we were unable to identify which specific species of Nitrosomonas were detected, it is
within reason to assume that Nitrisomonas europaea would have been one of those detected.
Largely due to its tendency to thrive in areas high in ammonia. While this was not something we
deliberately measured for, given the proximity of the stations to New York City and the Hudson
River it is well within reason to expect its presence in the Raritan. Additional, potential
candidates would have been Nitrosomonas eutropha and Nitrosomonas aesturii that thrive in
similar conditions.

Eukaryotes

When looking at the bubble plot for diatoms of the Genus Skeletonema, we notice a similar
pattern to that of salinity. In particular, Skeletonema species appear to be roughly 33% more
abundant at the bottom than at the top of the water column (Figure 13). Similarly, the bottom of
the water column has roughly 30% more saltwater than it does freshwater (Figure 5). This may
indicate that Skeletonema, as a Genus, tends to prefer saltwater. As discussed by Balzano et al.
(2011), the growth responses of Skeletonema strains at low salinities varies significantly;
however, from salinities of 10-35 ppt, all strains showed signs of growth.

We also created another bubble plot that shows some other major taxa found at Station 1 on
Cruise 2 of Raritan Bay (Figure 13). Considering that we used the same total counts to calculate
relative abundance, it appears that Cyclotella cryptica is found in nearly the same abundance as
are S. dohrnii and S. menzelli (Figure 13). In comparison to strains of the Genus Skeletonema,
those of the Genus Cyclotella appear to be more tolerant of freshwater, as their abundance does
not appear to decrease with decreasing depth, or salinity, as is the case with Skeletonema strains
(Figure 13). Balzano et al. (2011) discuss that species of both aforementioned
Genera—Cyclotella and Skeletonema—are known to proliferate in estuarine environments with
strong gradients of salinity, thus their presence is expected within a system such as the Raritan
Bay estuary. Considering the peak in DO concentration at Station 1, and our understanding of
eukaryote assemblages here, we can confidently conclude that both Cyclotella and Skeletonema
are responsible for DO production (Figure 8). Though the top of Station 1 does not have a DO
concentration in equilibrium in the atmosphere (which would be around 282 µmol/kg), it does
have a significantly higher concentration than the subsurface. This tells us that there is some
influence of the aforementioned Genera producing oxygen via photosynthesis.
Looking a little more into strains of the Genus Skeletonema, we notice what appears to be some
preferences for different salinities, consistent with what Balzano et al. (2011) found in their
study. Particularly, S. dohrnii is in greater abundance at the bottom of the water column (saltier
water), as opposed to the top of the water column (fresher water); the opposite, however, is true
for S. menzelii (Figure 14). While both are capable of tolerating different salinities, as are
present within the water column, the former appears to survive better in a more marine
environment, and the latter in a more freshwater environment. As S. dohrnii gets mixed into the
upper part of the water column, it appears to shut down, with its relative abundance decreasing
from 47% to 24%, relative to all other strains of this Genus (Figure 14). As S. menzelii get
mixed into the upper part of the water column, they grow, with their relative abundance
increasing from 40% to 68% (Figure 14). While we did not analyze the eukaryote data from
Stations 1 and 2, and considering our results at Station 1, it is likely that S. menzelii might be
responsible for the DO peaks that we see at the surface at these stations (Figure 8).

In our analyses, we notice that what should be a widespread species in this system, according to
Khan et al. (1998), is actually found in low relative abundances—2% and 3% at the top and
bottom of the water column, respectively. S. costatum is commonly found in estuarine
environments, though we found it in this low relative abundance in our samples. While this
species grows well at a wide range of nitrate, it tends to be sensitive to high phosphate
concentrations. Their low abundance, thus, might suggest that phosphate concentrations within
Raritan Bay are too low for them to tolerate. This, combined with the low species evenness
within the Genus Skeletonema provides support that nutrient concentrations within the Raritan
Bay estuary may be so high that only few tolerant species can grow here.

High nutrient concentrations may not be the only cause for a low abundance of S. costatum. In
fact, a species of Cyclotella, C. cryptica, actually secretes an exudate, or a mass of cells and
fluid, that can suppress the growth of other phytoplankton species (“NOAA Great Lakes”, 2023.
In particular, it is known to have a negative effect on S. costatum (“NOAA Great Lakes”, 2023.
This effect is also more noticeable in environments with high concentrations of vitamin B12,
which is likely the case within the Raritan Bay estuary (“NOAA Great Lakes”, 2023). In order
for phytoplankton to obtain this B-12, like plants, they form symbiotic relationships with bacteria
(Watanabe and Bito, 2023). This B-12-containing bacteria typically originate from excess fecal
matter, which may suggest that Raritan Bay is laced with these toxics, potentially originating
from combined sewage overflow events (CSOs), or other sources of untreated sewage.

As with strains of the Genus Skeletonema, we expected to see a similar difference in the relative
abundance of different Cyclotella species. However, we saw roughly the same relative
abundance of two dominant species: C. cryptica and C. meneghiniana (Figure 15). Interestingly,
however, the absolute abundance of both species decreased as they reached the top of the water
column, in roughly the same ratio. There are a few plausible explanations for this observation.
The first of which could be that we have a heterotroph at the top of the water column that is
consuming both species at the same rate. Another reason could be that these two strains happen
to have the same relative tolerance to different salinities (those present at the bottom versus top
of the water column).
Thalassiosira is a centric diatom that is one of the most abundant genera in the water column at
Station 1 (Figure 13). The abundance of Thalassiosira is similar in both top and bottom samples
that we have collected (Figure 16). Previous studies have shown that Thalassiosira pseudonana
are able to grow in a large temperature range (5-32 ºC) and under high/low light, that their
growth is only limited by nutrients (Laws et al., 2020). Based on our CTD data, the top and
bottom temperatures are relatively similar to one another (Figure 4) and considering the Secchi
depth analysis, the top 3.0m (Table 3) had enough light to support phytoplankton growth.
Thalassiosira pseudonana that we got from our samples support what the studies show, we see a
similar abundance regardless of light entering the water column, phosphate levels decrease at the
bottom (Figure 11), and we see a decrease in Thalassiosira pseudonana.

Zooplankton

It is difficult to come to any real conclusions regarding zooplankton data in the Raritan Bay due
to the limited amount of zooplankton data we were able to collect. Any zooplankton data
collected in the Eukaryote Pivot is essentially inconclusive considering the fractional counts of
zooplankton analyzed. As for the zooplankton tow, the data (Tables 8-10) could be used to make
some inferences regarding the main species, Acartia tonsa, and its living patterns.

Abundance levels of Acartia tonsa were remarkably higher at Stations 1 and 2 than at Station 3
(0.36, 0.25, and 0.03 per m3, respectively). This likely indicates that the environment Acartia
tonsa prefers to live in is likely more saltwater based. Additionally, it is likely that their preferred
food source is also saltwater dominant. These could include Skeletonema and Cyclotella genera
among other genera of diatoms (Table 7 and Figure 13). However, zooplankton abundance was
still insignificant compared to the counts of these other species, and so it’s possible that Acartia
tonsa was feeding on a different phytoplanktonic species of much lower counts.

It is also possible that the data we collected was not representative of Acartia tonsa or other
zooplankton species as a whole. We were unable to accurately get a count of bottom, middle, and
top zooplankton considering the tow was done on only the top level of the water column.
Zooplankton are mobile species capable of traveling vertically as well as horizontally within the
water column, so it is not unreasonable to consider that our tow simply missed them as they were
feeding in another location. The assumption that zooplankton data was insignificant to make
conclusions is thus also reasonable to assume, especially considering zooplankton abundance
was so low compared to other eukaryotic and even prokaryotic (Table 5) abundance.
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