20080868 Ver 2_Methodology for Monitored Parameters_20190628

A. Salinity Monitoring Methods
The YSI 600XLM multi -parameter water quality monitors were used for
recording water salinity and depth from January 2007 to August 2008, when they were replaced
with In -Situ Aquatroll 200 water quality monitors. The YSI monitors (sondes) automatically
calculated salinity readings from conductivity and temperature. The salinity sensor range is 0-70
parts per thousand (ppt), with an accuracy of +/- 1.0 percent of the reading or 0.1 ppt, whichever
is greater. The resolution is 0.01 ppt. The depth sensor is a stainless steel strain gauge pressure
sensor with a range of 0-30 feet, an accuracy of +/- 0.7 inch, and a resolution of 0.01 inch.
Unlike the sondes, the conductivity and temperature sensors on the Aquatrolls are located below
the depth sensor, allowing salinity measurements to still be taken at low water levels even when
the depth sensor is out of the water.
The Aquatroll 200 is manufactured by In -Situ, Inc. Like the YSI monitors, the
Aquatrolls generate salinity readings from temperature and conductivity. The salinity sensor
range is 0-42 practical salinity units (psu), with an accuracy of +/- 0.5 percent of the reading.
The resolution is 0.001 psu. Practical salinity units are essentially equivalent to parts per
thousand; however, psu is considered a more appropriate descriptor since it refers to the practical
salinity scale that is used to calculate salinity (Reid 2006). The depth sensor is a titanium/silicon
strain gauge pressure sensor with a range of 0-35 feet, an accuracy of +/- 0.003 inch, and a
resolution of 0.001 inch.
The salinity monitors are programmed to record a salinity and depth reading every
1.5 hours (16 readings per day). Twice a month the salinity monitors are downloaded and
conductivity calibrated as necessary. The probes are also cleaned and batteries checked and
replaced as necessary. Sensors are located near the bottom of the stream to ensure continuous
data collection during most low water conditions. Depth readings are compensated for the
distance from the sensor to the creek bottom. Occasional gaps in the continuous data in some
years exist due to dead batteries, equipment malfunctions, and low water levels not allowing
sensors to be fully submerged.
To aid in the interpretation of factors that may influence salinity fluctuations,
continuous salinity data from each salinity monitor are displayed on graphs along with the
continuous water level data from that monitor, data from the nearest upstream flow station(s),
and data from the Tar River U.S. Geological Survey flow gauge at Greenville, NC
(http://waterdata.usgs.gov/nwis/uv?02084000). The Tar River becomes the Pamlico River at the
US Hwy 17 bridge in Washington. These graphs are used for a qualitative assessment of the
relative effects of wind tides, local drainage basin input, and Tar River input on salinity
fluctuations in the subject creeks.
To compare factors that may influence salinity, a Spearman Rank Order
Correlation is employed. Variables used include monthly averages of Tar River discharge, PCS
Phosphate rainfall, salinities, and Huddles Cut discharge. Significance is set at 0.05.
One-way analysis of variance (ANOVA) is used to test for differences between
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pre -disturbance salinity and post -disturbance salinity using monthly averages due to the large
amount of data within each month. When variances are unequal, Kruskal-Wallis one-way
ANOVA on ranks was used.
B. Wetland Hydrology Monitoring Methods
Each manual well consists of a 54-inch length of 1 1/4-inch diameter PVC well
screen (0.010-inch slots) and an 18-inch long riser made of solid -walled 1 1/4-inch diameter
PVC pipe. The well screen and riser are connected by a PVC coupler. The manual wells are
installed to a depth of 60 inches, with 12 inches of the riser extending above the ground. The top
of the riser is covered by a PVC cap, and a hole in the side of the riser provides air exchange
during water level fluctuations.
Ecotone TM WM80 water level monitors (manufactured by Remote Data Systems)
are used to provide semi -continuous data. The units measure water depth across an 80-inch
range with an accuracy of +/-3mm. The measurement probe is housed inside a 2-inch diameter
PVC well screen (0.010-inch slots). Most units were installed with 60 inches of the
measurement probe below ground and 20 inches above ground. This installation method allows
for the capture of both subsurface and surface water level fluctuations. The units record the
water level every 1.5 hours (16 times per day). To prevent damage by bears, the aboveground
portions of the Ecotones were surrounded by a 4-by-4-foot fence enclosure made of four metal
T-posts connected with two or three strands of barbed wire.
All monitoring wells are checked and downloaded either once or twice a month.
Using rainfall data and well data, wetland hydroperiods are calculated for each monitoring well
during the growing season. A wetland hydroperiod is defined as the greatest number of
consecutive days during the growing season that the water table is within 12 inches of the surface
or the surface is inundated, and is expressed as a percentage of the growing season. For this
project the growing season is defined by the Beaufort County soil survey (Kirby 1995) as 14
March through 24 November (256 days). Growing season dates have recently been adjusted by
the US Army Corps of Engineers 2008 Interim Regional Supplement to the Corps of Engineers
Wetland Delineation Manual: Atlantic and Gulf Coastal Plain Region to match the WETS tables.
However, the previously established soil survey growing season dates will continue to be used
for this report in order to maintain consistency with baseline years in hydroperiod calculations.
Existing wells in Tooley Creek and Huddles Cut and new wells for expanded
monitoring have been and will be installed in general accordance with the US Army Corps'
ERDC TN-WRAP-05-2 Technical Standard for Water -Table Monitoring of Potential Wetland
Sites. Existing wells at Tooley Creek and Huddles Cut are semi -continuous WM80 Ecotone
monitors manufactured by Remote Data Systems. Each of the existing wells in Tooley and
Huddles Cut is paired with an In -Situ Level Troll 500 (Level Troll). Data collected with the
Ecotones were compared to Level Troll data and a choice was made to use the Level Trolls
going forward for monitoring of wetland hydrology.
The casing for the Level Troll unit was modified to allow for depth -to -water
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measurements inside the well casing without removal of the probe (depth -to -water measurements
are not possible inside the Ecotone casing without probe removal). During each download at
each well, the depth to water is measured and this depth relative to ground surface is compared to
the real-time readings of the Level Trolls to verify the accuracy of the instrument. If the Level
Troll is reading >0.5 inch difference from the true reading, the Level Troll is calibrated
according to manufacturer specifications. If a difference of >0.5 inch exists after calibration, the
Level Troll is to be replaced. During each download, the download time, manual water level
measurement, real-time Level Troll measurement, file name, and any other pertinent information
are recorded in the field. This information is transferred to a well download sheet (Figure 5) kept
in a binder at the CZR Wilmington office for reference. Wells are downloaded once or twice a
month to minimize data loss from faulty equipment.
C. Water Quality Monitoring Methods
Twice a month field measurements include water depth, Secchi disk depth,
temperature, salinity, conductivity, turbidity, dissolved oxygen, and pH. Water depth is
measured to the nearest quarter inch in close proximity to the monitoring well where water
samples are collected and all other measurements taken. Temperature, salinity, conductivity, and
dissolved oxygen are measured with a YSI Pro Plus multi -parameter water quality instrument.
These measurements are made in the middle of the water column when possible. Turbidity is
measured with a Hazco DRT-15 Portable Turbidimeter. Turbidity water samples are collected in
the field and turbidity is measured at the time of collection. Care is taken to exclude detrital
particles from the substrate and surface in turbidity samples. A Hanna Instruments pHep 2 pH
meter is used to measure pH.
The creek water samples are collected twice a month in polyethylene bottles and
stored inside an ice -filled cooler for daily shipment to the Central Environmental Laboratory at
East Carolina University. There, subsamples are taken for the various analyses. Precombusted
Whatman 934-AH (glass fiber) filters are used to separate particulate and dissolved fractions.
The filtrate is stored frozen in a polyethylene bottle for later analyses of total dissolved
phosphorus (TDP), dissolved orthophosphate (PO4-P), ammonium nitrogen (NH4-N), nitrate
nitrogen (NO3-N), and dissolved Kjeldahl nitrogen. The filter pads are also stored frozen for
particulate nitrogen (PN), particulate phosphorus (PP), and chlorophyll a determinations. Total
fluoride analyses are carried out using unfiltered water samples. These methods are identical to
those used for the PCS Phosphate Pamlico River estuary water -quality monitoring program (see
Stanley 1997 for example).
With implementation of the new creeks monitoring plan in 2011, the samples
are also analyzed for TOC/DOC/POC. The ECU geology lab provides CZR with
previously ashed glass 50 mL vials covered with aluminum foil and screw caps. Samples
for carbon analysis are taken directly in the vials at the same locations as the other water
quality locations. Wearing sterile gloves, a biologist tilts the 50 mL vial into the water and
slowly allows the vial to fill avoiding disturbance of sediment or collection of any scum or
sediment. The vial is recovered with the aluminum foil and the screw cap, labeled, and put
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into the iced cooler. Samples are not collected if shallow water depth prevents sample
collection without sediment or scum.
The data for each hydrographic and water quality variable are summarized by
means of three standardized graphical formats, with the third format including a separate graph
for each sampling location. The first graph addresses INTRAANNUAL (i.e., seasonal)
variability (the top graph on the two -graph pages). Individual station values are plotted along
with the mean value (from the four stations) for each sample date. Raw data for the each year are
contained in tabular format in an appendix of each annual report.
The second graph format indicates INTERANNUAL variability and provides a
look at pre- versus post -impact sampling years (the bottom graph on the two -graph pages). The
yearly mean, and the range of values are indicated for each year and each sampling site (the top
"error bar" shows the maximum value recorded, and the bottom "error bar" indicates the
minimum value).
The third graphical format shows monthly means and 95 percent confidence
intervals (also called confidence limits) about the mean for the pre -impact and post -impact
periods. A conservative statistical evaluation is to look for the amount of overlap between the 95
percent confidence limits- if the intervals do NOT overlap the two sampling periods (pre- and
post -impact) are hypothesized to be different. Each sampling location is represented on a
different graph. Station abbreviations H and HWQ are the same (e.g., station H1 is the same as
station HWQ 1).
D. Metals Sampling Methods (Water Column and Sediments)
Prior to the collection of sediment samples, the water column sample is
collected. Leaning over the bow of the boat while it is slowly underway, using a 500 mL
container previously cleaned in the CZR lab with deionized water and alconox, a biologist
wearing sterile latex gloves rinses the container twice with creek water. The sample is then
collected in the container and poured into the 250 mL bottle provided by the laboratory
which contains HNO3 preservative. The sample bottle is then sealed, labeled (location,
date, and time), and placed upright in a cooler packed with ice. The same collection
container is used for each creek although it is twice rinsed with the water from the creek to
be sampled prior to collection in each creek and new sterile latex gloves are worn during
each creek collection. As a back-up sample, the biologist also collects a 250 mL lab -
provided bottle using the same process. Samples are shipped or hand delivered at the
laboratory using the chain of custody form provided by the laboratory. The lab also
provides a test bottle for temperature fluctuation. The samples are analyzed for
concentrations of silver (Ag), arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu),
iron (Fe), and selenium (Se) by Method 6020, and zinc (Zn) and molybdenum (Mo) by
Method 6010 (aluminum is not commonly analyzed in water samples).
The ponar device is deployed and retrieved from the boat and the collected
sediment is dumped into a plastic tray from which —0.5 gallon of sediment is scooped from the
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sample into a Ziploc bag using a plastic or stainless steel scoop. As the sediment sample is
scooped, sediment that may have touched the metal of the ponar is avoided. Each bag is labeled
with creek name and date and, to minimize the potential for leaks, each sample is double bagged.
The ponar itself, plastic tray, and scoop/spoon are thoroughly rinsed with deionized water
between each sample to avoid cross -contamination. A second sample is collected from each
station in case there is a problem with the shipment to the laboratory or a problem encountered
by the laboratory during analyses. The backup samples are kept at CZR until results of the
analyses are completed at which time the samples are discarded. The sediment samples are
shipped chilled to Dr. John H. Trefry at the Florida Institute of Technology (FIT) The samples
are analyzed for concentrations of aluminum (Al), silver (Ag), arsenic (As), cadmium (Cd),
chromium (Cr), copper (Cu), iron (Fe), molybdenum (Mo), selenium (Se), and zinc (Zn). The
FIT lab calculates bulk density for each sample.
E. Vegetation Monitoring Methods
Drainage basin modifications are most likely to affect vegetation communities
found along the relatively narrow riparian wetlands upstream of the CAMA jurisdiction markers.
For this reason, vegetation assessments and monitoring sites were concentrated in these areas.
Vegetation sampling focuses on the shrub and herb layers. Compared to trees,
shrubs and herbs respond more quickly to changes in salinity and hydrology and therefore
provide better indicators of changes in the vegetation over time. At each vegetation monitoring
site, 10 permanent sample quadrats were established along a 40-meter transect that proceeds on a
random compass azimuth from the monitoring well. The quadrats are arranged on alternating
sides of the transect axis, such that each quadrat shares a corner with the quadrat behind it and
the quadrat in front of it. However, no quadrat shares a boundary with any other quadrat. Each
sample quadrat consists of a 4-by-4 meter woody shrub vegetation plot with a 1-by-1 meter herb
plot nested in the proximal corner. These will be used throughout the duration of the study to
monitor density, coverage, and species composition of the herb and shrub strata layers.
Shrubs and woody vines, defined as woody plants greater than 3.2 feet in height
but less than 3 inches in diameter at breast height (DBH), are inventoried in each of the ten 4-by-
4 meter plots located in the vicinity of each monitoring well in the riparian wetlands. For each
species, the number of stems present is counted and percent cover estimated. Herbs, defined as
all herbaceous vascular plants regardless of height and woody plants less than 3.2 feet in height,
are inventoried in each of the 1-by-1 meter plots nested within the 4-by-4 meter plots. For each
species, the number of stems present is counted and percent cover estimated. Qualitative
descriptions of the overstory are made in the vicinity of each monitoring well.
An importance value is calculated for each shrub and herb species present in each
transect. Relativized values of average percent cover, average stem count, and frequency of
occurrence in the 10 quadrats are used to calculate importance values. Dominant plants in each
transect are determined by applying the 50/20 rule to the importance values. The 50/20 rule was
described in the 1989 wetland delineation manual (Federal Interagency Committee for Wetland
Delineation 1989) and still is used in delineating wetlands (Williams 1992, USACOE 2008).
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The 50/20 rule uses the quotient obtained from dividing each species' importance value by the
sum of all of the importance values for that transect (shrubs and herbs are treated separately).
This calculation expresses each species' importance value as a percentage of the cumulative
importance value of the entire transect. Beginning with the species having the highest
importance value and continuing in descending order, all species are listed until, cumulatively,
50 percent of the overall importance value has been reached. These species, along with any
additional species that individually comprise at least 20 percent of the overall importance value,
are considered to be dominant.
To further assist in determining whether changes in the plant communities have
occurred, the tolerance of brackish conditions was assessed for each dominant species. The
determination of each species' tolerance was based on habitat descriptions provided in Radford
et al. (1968), Beal (1977), Godfrey and Wooten (1979, 1981), Odum et al. (1984), and Eleuterius
(1990). A species was considered tolerant of brackish conditions if any of the habitats listed
were brackish, even if most of the habitats were fresh. The percentage of dominant species
intolerant of brackish conditions is calculated for each transect. Any significant changes in the
salinity of the creek should be reflected by a shift in this percentage.
A similar analysis is performed using the wetland indicator status (Reed 1988) of
the dominant plants. The percentage of dominant species with a wetland indicator status of
FAC- or drier is calculated for each transect. Any major change toward drier conditions should
be reflected by a change in this percentage.
NOTE: During the latter stages of development of the final PCS Plan of Study to monitor the
creeks, NCDWQ suggested that vegetation be monitored according the Carolina Vegetation
Survey (CVS) methodology. After consideration of this suggestion and discussion with the
Corps and NCDWQ, PCS believes that in order to adequately compare available and future
monitoring data the existing vegetation survey methodology should be maintained in the new
plan. The purpose of the vegetation monitoring required by the PCS permit condition is not to
describe the complete biotic community at each creek, but to be able to document potential shifts
in the herbaceous and shrub community. While thorough and interesting, the CVS approach is
more complex than necessary to meet the purposes of the permit conditions and be congruent
and comparable with the past and future monitoring of the PCS subject creeks.
F. Fish Monitoring Methods
If a monitored stream is too shallow and narrow to sample using a trawl, fyke nets
are used to sample fish. Each fyke net sampling occasion is conducted using two fyke nets (one
net fished upstream and one fished downstream) anchored for a set time of approximately 16
hours (late afternoon until the following morning). Each fyke net is deployed across the entire
width of the sampled stream and consists of 0.25-inch mesh net with four 21-inch hoops, a 6-
inch throat, and a 22-foot wingspan.
For monitored stream large enough to trawl, each fish trawl sample is conducted
using a two -seam otter trawl. The trawl was constructed with a 10.5-foot head rope, 0.25-inch
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bar mesh wings and body, and 0.12-inch bar mesh cod end. The trawl is towed for
approximately one minute, covering approximately 75 yards, from a beginning point marked in
the field with flagging (GPS coordinates also known) near the mouth of each monitored creek.
Tow direction is always toward the creek mouth.
All fish captured by either method are identified and counted. Those that are
easily identified in the field are released; others are preserved for later identification. Total
length is measured to the nearest millimeter for the first 30 specimens of each species.
Representative photographs of sampling stations are taken during the first sampling occasion and
are on file with CZR Incorporated.
To compare fish communities in each creek, CPUE, total abundance, species
richness, and species diversity are examined. Two standard diversity indices are used to measure
species diversity. The first, a modified Simpson's index (ds) (Simpson 1949; Brower and Zar
1984), is defined as:
ds N(N-1)/Eni(ni-1), where
I ...i
n;= number of individuals of the ith species and
N= total number of individuals of all species.
Simpson's index is especially informative if a community is dominated by one or a few species.
The second diversity index used is the Shannon index (H') (Shannon 1948), defined as:
H'=- Epi lnpi, where
I ...i
pi= ni/N and
ni and N are defined as for Simpson's index.
The Shannon index incorporates not only species richness, but also how evenly individuals are
distributed among the total number of species present in the community.
The above indices may be used to compare species diversity, but they tell nothing
about whether similar species are found at each site. To compare biotic communities in this
manner, the Jaccard coefficient and the Morisita-Horne index of community similarity are
employed. The Jaccard index (Q (Brower and Zar 1984) is defined as:
Cj=c/(s1+s2-c), where
c= number of species found at both sites and
sI, s2 are the total number of species in community 1 and 2, respectively.
The Morisita-Horne index (Cmh) (Li and Li 1996), while more complicated, has
the additional advantage of incorporating not just the presence of similar species but also the
relative abundance of species found at both sites. Consequently, it is a more comprehensive
descriptor of community similarity. It is defined as:
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C,,,h= 2 Exyi , where
(Xi+ X2)(" IN2)
xi and yi are the total number of the it' species at site land 2,
Ni and N2 represent the total number of individuals at site I and 2, respectively, and,
Xi= Exi xi-1 and X2 is similarly defined.
Ni(Ni-l)
Both the Jaccard and the Morisita-Horn indices of community similarity range
from zero to one, with zero representing completely dissimilar populations and one representing
identical populations.
A two -sample t statistic (t-test) is used to compare CPUE, abundance, and
diversity between pre- and post -disturbance years. Significance is set at 0.05. When normality
failed and the data do not meet assumptions for a parametric test, a nonparametric test is used
(Mann -Whitney Rank Sum Test).
To compare CPUE, abundance, and diversity between years at each site, a one-
way analysis of variance (ANOVA) is used. Significance is set at 0.05. When normality fails
and the data do not meet assumptions for a parametric test, a nonparametric test is used (Kruskal-
Wallis ANOVA on Ranks). When significant differences (p< 0.05) occur between variables for
each year, a corresponding Tukey's or Dunn`s (post hoc) multiple pairwise comparison test is
used to display the relationship between the individual means.
Water quality data are collected with a YSI Pro Plus multi -parameter instrument
prior to deployment and retrieval of fyke nets and/or before each at each creek. Parameters
measured include temperature, pH, salinity, conductivity, dissolved oxygen (DO), and Secchi
depth. For each parameter the deeper creeks, excluding pH and Secchi depth, a measurement is
taken at both surface and near bottom levels. Estimates of the percentage of the water surface
covered by submerged aquatic vegetation are also made. Water quality data are examined with
regard to how well each site provided habitat appropriate for the preservation of fish
communities. Particular attention is given to dissolved oxygen, as low DO levels are commonly
implicated in fish kills.
G. Benthos Monitoring Methods
a. Timed Sweeps
Timed sweep methodology is used to sample benthic invertebrates along
the shoreline at each upstream and downstream location on subject creeks. The timed sweep
samples consist of 10-minute collections with a D-frame 0.5 mm net in representative shoreline
and near -shore habitats. Within each sampling station, three replicate samples are collected from
the same three locations from year to year. Basic hydrographic data also are collected during the
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sweep sampling. The following data is recorded at each station:
• Depth
• Canopy cover
• Aufwuchs
• Bank erosion
• Substrate (% sand, silt, detritus)
• Water flow
• Water quality + pH
Organisms collected are preserved and returned to the laboratory for
sorting, enumeration, and identification to the lowest practical taxonomic level (usually species).
Each replicate is enumerated and the mean number of individuals per taxa and a 95 percent
confidence interval are calculated for the most abundant taxa (an average of at least 40
individuals per one year) at each station. One replicate sample from a dedicated collection site in
each sampling station is used to calculate an Estuarine Biotic Index (EBI) in each creek
(NCDENR 1997). An EBI is an average of the water quality tolerance values for each taxon in
the sample, weighted by abundance values of the taxa. Only those taxa for which tolerance
values are available can be used to calculate an EBI. An EBI can be used at all salinities to make
comparisons and assess differences in site water quality (NCDENR 1997). All tolerance values
for taxa encountered are verified and assigned by Larry Eaton, Surface Water Protection, North
Carolina Division of Water Quality (NCDWQ) in an effort to standardize and evaluate benthic
data from past study years.
b. Ponar Grab
Five ponar grabs are taken near mid -stream at each upstream and
downstream station on each subject creek. Basic hydrographic data are collected at each
sampling station. Collected sediments are placed in 1 gallon plastic bags, with a full bag
constituting a sample. Samples are sieved in the field through a 0.5 mm mesh screen. All
organisms retained on the screen are preserved and returned to the laboratory for sorting,
enumeration, and identification to the lowest practical taxonomic level (usually species). For
each taxon, the average number of individuals per grab and a 95 percent confidence interval are
calculated. The 95 percent confidence intervals can be used as a rough gauge of the statistical
significance of differences between years. However, such comparisons must be made with care
since very abundant taxa are not fully enumerated, which may cause the width of the confidence
intervals to be underestimated for those taxa. An EBI is calculated for each sampling station
based on total individuals of each taxon collected from all five replicate grabs.
The Shannon -Wiener diversity index (H') (Shannon 1948), is used to
detect differences in species diversity in ponar samples. Ponar replicates are pooled for EBI and
H' calculations. The index is defined as:
H'=- Epi logpi, where
I ...i
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n;= number of individuals of the ith species,
N= total number of individuals of all species, and
pi= ni/N.
A two -sample t statistic (t-test) is used to compare Shannon -Wiener
diversity indices scores and total abundance between pre- and post -disturbance years.
Significance is set at 0.05. When normality fails and the data do not meet assumptions for a
parametric test, a nonparametric test is used (Mann -Whitney Rank Sum Test).
To compare Shannon -Wiener diversity indices scores and total abundance
between years at each site, a one-way analysis of variance (ANOVA) is used. Significance is set
at 0.05. When normality fails and the data do not meet assumptions for a parametric test, a
nonparametric test is used (Kruskal-Wallis ANOVA on Ranks). When significant differences
occur (p<0.05) between variables for each year, a Tukey's (post hoc) multiple pairwise
comparison test is used to display the relationship between the individual means.
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