A fish sampling protocol for the Musquash Estuary Marine Protected Area

A fish sampling protocol for the Musquash Estuary Marine Protected Area
A fish sampling protocol for the Musquash Estuary Marine
Protected Area
E. Ipsen
Prepared for:
Oceans and Coastal Management Division
Ecosystem Management Branch
Fisheries and Oceans Canada
Maritimes Region
Bedford Institute of Oceanography
PO Box 1006
Dartmouth, NS
B2Y 4A2
2016
Canadian Technical Report of
Fisheries and Aquatic Sciences 3160
Canadian Technical Report of Fisheries and Aquatic Sciences
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Canadian Technical Report of
Fisheries and Aquatic Sciences 3160
2016
A fish sampling protocol for the Musquash Estuary Marine Protected Area
E. Ipsen
Prepared for:
Oceans and Coastal Management Division
Ecosystem Management Branch
Fisheries and Oceans Canada
Maritimes Region
Bedford Institute of Oceanography
PO Box 1006
Dartmouth, NS
B2Y 4A2
iii
© Her Majesty the Queen in Right of Canada, 2016
Cat. No. FS97-6/3160E-PDF ISBN 978-0-660-04733-1 ISSN 1488-5379
Correct citation for this publication:
Ipsen, E. 2016. A fish sampling protocol for the Musquash Estuary Marine Protected Area.
Canadian Technical Report of Fisheries and Aquatic Sciences. 3160: vi + 34 p.
iv
TABLE OF CONTENTS
LIST OF TABLES / LIST OF FIGURES………………………………………………………..vi
ABSTRACT / RÉSUMÉ .............................................................................................................. vii
1.0 OVERVIEW OF FISH SAMPLING PROTOCOLS ................................................................ 1
1.1 Long-term Monitoring .......................................................................................................... 1
1.2 Estuarine Monitoring ............................................................................................................ 1
1.3 Use of Fish as Monitoring Tools .......................................................................................... 2
2.0 MUSQUASH ESTUARY MONITORING PLAN .................................................................. 3
2.1 Monitoring Musquash Estuary.............................................................................................. 3
2.2 Overview of Protocol ............................................................................................................ 6
3.0 PERSONNEL AND TRAINING ............................................................................................. 6
4.0 SAMPLING GEARS ................................................................................................................ 7
4.1 Beach Seine Sampling Methods ........................................................................................... 7
4.2 Fyke Net Sampling Methods ................................................................................................ 8
4.2.1 Tidal Considerations ...................................................................................................... 9
5.0 FREQUENCY OF SAMPLING ............................................................................................... 9
6.0 SAMPLING LOCATIONS .................................................................................................... 10
6.1 Sampling within Musquash Estuary MPA .......................................................................... 11
6.1.1 Nearshore Beach Seining and Fyke Net Locations...................................................... 12
6.1.2 Salt Marsh Fyke Netting Locations ............................................................................. 15
6.1.3 MPA Sampling Considerations.................................................................................... 16
6.2 Reference Sampling Locations Outside the MPA .............................................................. 17
7.0 NEKTON COMMUNITY SAMPLING................................................................................. 19
7.1 Community Assessments .................................................................................................... 19
7.1.2 Large Abundances of Nekton ...................................................................................... 21
7.2 Contaminantion Indicator through Sentinel Species Collections ....................................... 21
8.0 SUMMARY ............................................................................................................................ 22
6.0 REFERENCES ....................................................................................................................... 24
Appendix A: Equipment checklist for field .................................................................................. 28
Appendix B: Sample tidal sampling ............................................................................................. 29
Appendix C: Summary table of sampling sites and times ............................................................ 32
Appendix D: Species list............................................................................................................... 33
Appendix E: Nekton Sampling Sheet Template ........................................................................... 34
v
LIST OF TABLES
Table 1: Example of raw data collected within Musquash Estuary at sites Black Beach and Five
Fathom Hole during either the first two week period of the month or the last two week period. 20
Table 2: Tide table. ....................................................................................................................... 30
Table 3: Summary table of sites, habitats and gears with estimates of sampling time, including
the commute from the city of Saint John, and number of personnel needed. ............................... 32
Table 4: Species list of fish caught within and around Musquash MPA. ..................................... 33
LIST OF FIGURES
Figure 1: Musquash Estuary Marine Protected Area and Administered Intertidal Area.. .............. 4
Figure 2: Beach seine sampling gear .............................................................................................. 8
Figure 3: Fyke net sampling gear and poles.. ................................................................................. 9
Figure 4: Google Earth image showing estuaries to be sampled for proposed long-term
monitoring ..................................................................................................................................... 11
Figure 5: Musquash Estuary proposed sampling sites. ................................................................. 12
Figure 6: Black Beach sampling site. ........................................................................................... 13
Figure 7: Five Fathom Hole beach seining site and fyke net location in the channel .................. 13
Figure 8: Hepburn’s Basin seining site and fyke net locations ..................................................... 14
Figure 9: Gooseberry Cove seining site and potential fyke net location. ..................................... 15
Figure 10: Potential salt marsh sampling locations for fyke net. .................................................. 16
Figure 11: Saints Rest Marsh seining site and fyke net locations................................................. 18
Figure 12: Chance Harbour potential seining site and fyke net locations. ................................... 18
Figure 13: Dipper Harbour seining site and fyke net locations .................................................... 19
Figure 14: Atlantic silverside, Menidia menidia........................................................................... 22
Figure 15: Example of high and low tidal cycles showing both spring and neap tides for
Lorneville, New Brunswick. ......................................................................................................... 31
vi
ABSTRACT
In 2006, the Musquash Estuary was designated as a Marine Protected Area (MPA). To support
the monitoring of the MPA, a fish sampling protocol is proposed in this document. The main
objectives of this protocol are to: 1) Understand the nekton community within nearshore habitats
of Musquash MPA by characterizing baseline spatial and temporal variability and environmental
drivers; 2) Assess the health of the estuary across multiple habitats for long-term evaluation of
potential human sources of contamination; and 3) Compare Musquash fish community to
reference locations outside of the MPA. Two sampling gears (beach seine and fyke net) are
proposed for the collection of nekton data at four Musquash Estuary nearshore habitat sites
(Black Beach, Five Fathom Hole, Hepburn’s Basin and Gooseberry Cove) and three reference
sites (Saints Rest Marsh, Dipper Harbour and Chance Harbour). The protocol also recommends
potential locations for salt marsh habitat sampling by fyke net. Sampling considerations such as
timing of sampling and specific site accessibility are discussed. Data to be collected on fish
communities includes: species richness, abundance, and lengths. Atlantic silversides are also
proposed for collection for use as a sentinel species to assess potential impacts of contamination.
Data to be collected on free-swimming invertebrates includes species richness and abundance,
which will provide complementary data on the community utilizing nearshore habitats. This
information will provide insight into the annual variability associated with the Musquash Estuary
MPA fish community.
RÉSUMÉ
En 2006, l'estuaire de la Musquash a été désigné zone de protection marine (ZPM). Un protocole
d'échantillonnage pour le poisson a été mis en place dans le cadre du suivi de la ZPM et est décrit
dans le présent document. Le protocole a trois principaux objectifs : 1) comprendre l'activité du
necton au sein des habitats littoraux de la ZPM de l'estuaire de la Musquash en caractérisant la
variabilité temporelle et spatiale normale ainsi que les facteurs environnementaux; 2) mesurer la
santé de l'estuaire dans de multiples habitats pour évaluer à long terme les sources de
contamination humaines; et 3) comparer l'activité des poissons de la Musquash et des sites de
référence à l'extérieur de la ZPM. On propose de réaliser la collecte des données sur le necton
avec deux des engins d'échantillonnage (senne de plage et verveux), dans quatre endroits
d'habitats littoraux de l'estuaire de la Musquash (la plage Black Beach, le trou Five Fathom Hole,
l'anse Hepburn Basin et l'anse Gooseberry Cove), ainsi que dans trois sites de référence (le
marais Saints Rest Marsh, le havre Dipper Harbour et le havre Chance Harbour). Le protocole
recommande aussi des emplacements d'habitat de marais salé pour l'échantillonnage par verveux.
Sont également discutés certains éléments à prendre en compte tels que le moment de
l'échantillonnage et l'accessibilité des sites. Voici certaines données à recueillir sur les
communautés de poissons : richesse, abondance et longueur des espèces. On propose également
de faire des échantillonnages pour de la capucette, laquelle constituerait une espèce sentinelle
pour évaluer les incidences potentielles de la contamination. Des données doivent être recueillies
sur les invertébrés nageant librement, entre autres la richesse et l'abondance des espèces. Elles
fourniront des données complémentaires sur la faune vivant dans les habitats littoraux. Ces
renseignements donneront un aperçu de la variabilité annuelle associée à la communauté de
poissons dans la ZPM de l'estuaire de la Musquash.
vii
1.0 OVERVIEW OF FISH SAMPLING PROTOCOLS
1.1 Long-term Monitoring
Monitoring programs vary in intensity based on objectives. Biological data collection can range
from low intensity collection such as public observations or landings from commercial vessels to
more intense forms including rigorous systematic sampling designs involving multiple sampling
techniques with members of the scientific community and/or trained community groups (Singh et
al. 2000, Honey et al. 2004, Thériault et al. 2006, Weldon et al. 2007, Higdon and Paulic 2013).
Data collected from sampling protocols also vary in terms of answering questions at the
histological, individual, population or community level (Doyle et al. 2011).
Long-term sampling protocols are usually established in areas that are in need of conservation,
considered to be ecologically sensitive areas at high risk of being altered, or in need of
restoration (Raposa et al. 2003, De Mutsert and Cowan 2012). Monitoring can coincide with
restoration efforts or occur in areas that will experience a major alteration (addition of a dam,
dredging, or impact of point and non-point pollution sources; De Mutsert and Cowan 2012).
Long-term studies of fish assemblages in ecologically and commercially important areas are
essential in order to establish natural variability. Without understanding the natural shifts in fish
communities both spatially and temporally, it becomes difficult to distinguish between
natural/annual shifts based on physical cues (e.g., temperature, salinity, and lunar cycles) from
overexploitation or other anthropogenic disturbances (Macdonald et al. 1984, Ayvazian et al.
1992, Lazzarri et al. 1999). For example, data collected from a five-year study (inshore and
offshore sampling) in the Passamaquoddy Bay area (Macdonald et al. 1984) revealed that fish
assemblages migrated inshore during summer months (June – October) and then offshore during
winter months with returns beginning in the early spring. These changes in assemblages were
largely influenced by small fluctuations in temperature. The study from Macdonald et al. (1984)
emphasized the need for monitoring fish in inshore habitats, particularly estuaries, as being
important for commercially important species. Understanding fish movements at a local scale
allowed for more accurate estimations of fish abundances. The authors from this article suggest
that important inshore recruiting cohorts were highly correlated with successful offshore fishing
the following year.
1.2 Estuarine Monitoring
Estuarine systems are sensitive areas in need of conservation and preservation (Able and Fahay
1998, Elliot and Hemingway 2002). They are considered the most productive environments
alongside tropical rainforests (Blaber et al. 2000). Because of this, they are ecologically
important areas for fish and crustaceans, acting as nursery areas-supporting large numbers of
juveniles, providing feeding grounds, migration routes for anadromous species, as well as
overwintering sites (Macdonald et al. 1984, Able and Fahay 1998, Elliot and Hemingway 2002).
It has been found that a continued decline in estuarine habitats is highly correlated with declines
in abundance of early life stages of fishes (Able and Fahay 1998). However, estuaries are part of
coastal areas, which suffer the most from anthropogenic disturbances (e.g., filling,
channelization, industrial outputs; Able and Fahay 1998, Elliot and Hemingway 2002).
Therefore, monitoring these locations is important for the assessment of ecosystem health and
the maintenance of their productive capacity (Ayvazian et al. 1992).
1
1.3 Use of Fish as Monitoring Tools
Fish species that are considered permanent residents in estuaries are rare (Able and Fahay 1998).
Estuarine waters have been found to carry only 10% of the species found in adjacent waters
(Able and Fahay 1998). Fishes must be highly tolerant of abrupt changes in temperature, salinity,
oxygen, turbidity and strong seasonal changes for them to be able to cope with environmental
changes associated with estuaries (Able and Fahay 1998). Adult stages of most marine species
are typically absent from estuaries while larval and juvenile stages of these species are more
tolerant of the environmental variability. Productivity in estuaries is high, as large biomasses of a
small number of species tend to dominate the ichthyofauna. Thus, collecting fish within estuarine
environments typically focuses on smaller bodied species or larvae/juveniles, as these fish
typically are the most tolerant. Sampling methods typically used in estuarine systems depend on
the study objectives, but largely focus on the nearshore area (<5m depth) and include: seines,
trap nets, and trawls, which usually target fish <200mm in length (Methven and Schneider 1998).
Estimates on productivity and habitat use can be made by monitoring the nearshore community,
thus providing insight into the health of the estuary.
The collection of fish within estuaries is important to assess across multiple habitats of varying
salinity, substrate type and vegetation differences. Fish characterization of an area often involves
both the biological and environmental collection of parameters. Biological parameters that are
widely used include:



Richness, for identifying invasive, indicator, commercially important species or species
at risk (Macdonald et al. 1984, Methven and Schneider 1998, Raposa et al. 2003)
Abundance, for estimates of Catch Per Unit Effort (CPUE) and biomass (Gibson et al.
1996)
Individual lengths, for age estimations (Able and Fahay 1998, Methven and Schneider
1998).
Monitoring programs have been found to be more successful when they combine physical,
chemical and biological data (Carlisle et al. 2002). Monitoring factor interactions allows for the
potential to detect disturbances that may be causing habitat degradation or changes in species
compositions (i.e., reduction of indicator, rare, commercially important species or increasing
numbers of invasive species; Raposa et al. 2003). Environmental characteristics taken along with
fish samples often included: temperature, salinity, dissolved oxygen, turbidity, and sediment
samples. Other characteristics such as fish weight or sex are sometimes assessed but are difficult
to establish in the field, requiring fish to be euthanized and brought back to the laboratory
(Macdonald et al. 1984, Gibson et al. 1996, Honey et al. 2004). An alternative to this issue is
through the collection of a sentinel species, which can be used to characterize sex ratios, weights,
somatic indices and condition factors (Doyle et al. 2011).
Incorporating both fish and crustaceans into long-term estuarine monitoring programs is
common. Thériault et al. (2006) used nekton collected under the Community Aquatic Monitoring
Program (CAMP) to assess the impacts of a seafood processing plant on overall estuarine health.
A Before-After-Control-impact (BACI) study by the Louisiana Department of Fisheries and
Wildlife used nekton community characteristics collected from 1986 to 2007 in a similar way as
the CAMP protocol. Data collected was found to be successful in monitoring the effects of
freshwater discharge into the estuary on commercially important species (De Mutsert and Cowan
2012). These programs established a once to twice monthly sampling regime and found that
2
sampling nekton alongside other physical characteristics provided data that could be used as an
indicator for monitoring estuarine health. Additional measures, such as collaboration with other
established monitoring programs, as well as the use of sentinel species have been found to
complement these protocols to give a more holistic picture of estuarine health.
Biological sampling in estuaries have been shown to include a unique set of challenges.
Successful monitoring programs and studies of these habitats have demonstrated strong links
between fish (or nekton) characteristics and physical factors influencing the environment.
Piecing together the dynamics of the fish community as it pertains to local climate, tidal
dynamics, habitats within the estuary, and potential anthropogenic threats requires a multi-level
approach of monitoring. Collecting information on richness, abundance and size alongside
abiotic factors such as time of year, temperature, salinity, dissolved oxygen, turbidity and habitat
type (salinity gradient, substrate type), provides information on the community and how it may
be utilizing its environment. Combining this information with additional sampling gears
(differing mesh size, active vs passive gear types) as well as with the use of sentinel species
enables researchers to obtain a holistic representation of how fish (or nekton) are utilizing the
estuary. Previous monitoring techniques have also been shown to be successful when they
involve members of the community since they offer a sense of stewardship over these
ecologically sensitive areas.
2.0 MUSQUASH ESTUARY MONITORING PLAN
2.1 Monitoring Musquash Estuary
It has been estimated that approximately 85% of the salt marsh habitats within the Bay of Fundy
have been either significantly altered or destroyed (Harvey et al. 1998, Singh et al. 2000).
Musquash Estuary remains a valuable system as it’s considered to be the last of the remaining
ecologically intact estuaries in the Bay of Fundy (Singh et al. 2000). As a result of its designation
as a Marine Protected Area (MPA) in 2006, Musquash has been protected from a wide variety of
activities. The establishment of management zones allows for restrictive human use of different
habitats based on sensitivity (Singh et al. 2000, Cooper et al. 2014, Greenlaw et al. 2014; Figure
1). Because of its size and importance to wildlife, the protection and monitoring of Musquash
Estuary is a priority for conserving its valuable habitats, high biodiversity, productivity and
influence on the surrounding environment (Blaber et al. 2000, Singh et al. 2000).
The biological monitoring framework of the Musquash MPA requires that protocols allow for
the ability to identify changes in ecological characteristics, and monitor current activities and
perceived threats (Singh et al. 2000, DFO 2011). Conservation objectives, as stated in the CSAS
monitoring framework (DFO 2013), aim to achieve an ecosystem-level monitoring framework to
“ensure that there is no unacceptable reduction or human-caused modification in productivity,
biodiversity or habitat”. Twelve indicators are listed to monitor the conservation objectives
associated with monitoring the MPA. The conservation objectives and associated indicators
(bold letters associated with indicators established in the Musquash Monitoring Framework;
DFO 2013) include: Productivity, Biodiversity and Habitat.
3
Figure 1: Musquash Estuary Marine Protected Area (MPA) and Administered Intertidal Area
(AIA).
Productivity
This protocol will provide data regarding the total biomass and spatial distribution of nekton
species (both fishes and free-swimming invertebrates) representing different trophic levels (P1).
Fish abundance (biomass) and length data (to estimate life stage) will be collected using beach
seine and fyke net samples from zone 2 (Figure 1), and fyke net samples from zone 1.
Standardized sampling with these two gears at specific locations will provide information on
CPUE measures that can be compared annually and spatially. This monitoring protocol
recommends an intensive baseline-sampling period of 3-5 years, which will include sampling at
least once monthly from May to October. After a baseline is established, sampling may only
focus on key indicator species or sampling periods as established in the baseline. Sites
recommended in the monitoring protocol within these two zones consider habitats (established in
Greenlaw et al. 2014), the naturally occurring salinity gradient within the estuary as well as
differing substrate types which may provide specific habitat use for fish species (for example,
important nursery sites).
Biodiversity
Indicators of biodiversity addressed in this monitoring protocol will include data collected on
nekton species richness. Frequency of sampling (at least once monthly) will enable the
characterization of species utilizing different habitats within the estuary, including rare (B1) or
species at risk (B2). The monitoring plan identifies external standardized sampling sites adjacent
to Musquash Estuary that can be used as a reference to the species found within the MPA. From
data collected during baseline sampling, as recommended in this monitoring protocol, species
richness can be assessed spatially and annually for natural fluctuations in nekton diversity
followed by long-term assessments to monitor change.
4
Habitat
During standardized sampling as recommended in this monitoring protocol, measurements
associated with habitat will be collected alongside biological data. These contribute to the
characterization of different habitats within the estuary (H5) through salinity, temperature,
dissolved oxygen and turbidity metrics. Indicators of contaminant concentrations through the use
of a sentinel species (Atlantic silverside, Menidia menidia, as mentioned in section 7.2) will also
aid in monitoring chronic impacts of potential contamination (H7) on nearshore fish within the
estuary.
The long-term monitoring of proposed future sampling in this document focuses on fish
communities with additional invertebrate sampling, as indicators of conservation objectives
identified in the monitoring framework. This monitoring protocol aims to further establish a fish
community baseline and provide guidance for long-term monitoring. The objectives of this
protocol are to:
i) Understand the fish community within multiple habitats of Musquash MPA by
characterizing baseline spatial and temporal variability and environmental drivers by
collecting information on:
a. Abundances and lengths of individuals (productivity),
b. Species richness (biodiversity)
c. Environmental characteristics (habitat): Salinity, temperature, dissolved oxygen
ii) Assess the health of the estuary across multiple habitats for long-term assessments of
potential human sources of contamination through:
a. Use of Atlantic silverside as a sentinel species
b. Weight, sex, age, Liver Somatic Index (LSI), Gonadosomatic Index (GSI) and
condition factor (K) of individuals
iii) Compare Musquash fish community to reference locations outside of the MPA.
a. Objectives i and ii are applicable to reference locations outside of the MPA.
A baseline for characterization of Musquash Estuary nearshore fish community has already
begun with sampling events conducted by Arens (2007) and Ipsen (2013). These data allowed
insight into the natural variability and habitat of the Musquash fish community. Arens (2007)
identified sampling methodology issues such as tidal and diel restrictions, as well as the
variability associated with spatial and temporal factors within a small geographic scale. The
author also conducted a spatial comparison across multiple sites, including two of which were
also sampled by Ipsen (2013). Strong temporal shifts due to seasonal changes (temperature) were
apparent. Spatial differences associated with salinity and habitat characteristics were also
observed with regards to fish utilizing areas as nursery sites.
Objectives in Ipsen (2013) were to begin the characterization of nearshore fish communities as
part of a baseline within zone 2 of the MPA (Figure 1). In addition, sampling was to incorporate
two reference sites, Dipper Harbour and Saints Rest Marsh, to serve as comparative sites outside
of the MPA. Species richness, abundances, seasonal and temporal trends were consistent with
other studies in similar areas. This study was comparable to Arens (2007) and attempted to
characterize fish parameters within different nearshore habitats within the MPA along the natural
salinity gradient and included: an intertidal sand and gravel beach, intertidal flat and
brackish/cobble substrate (Black Beach, Hepburn’s Basin, Five Fathom Hole, respectively). This
5
study found that temporal shifts in the community were more dominant than spatial differences,
while each site displayed unique aspects of the community.
Information gathered from both Arens (2007) and Ipsen (2013) can be used as a starting point for
a sampling baseline. This baseline can thus be developed alongside a long-term sampling regime.
A long-term monitoring program within Musquash will allow a further understanding of fish
habitat utilization together with physical, chemical, and biological factors that may be
influencing temporal and spatial changes. The current protocol uses techniques from previous
sampling methods (Arens 2007 and Ipsen 2013) in order for future sampling to be comparable.
In addition, recommendations are given associated with: increasing community data by sampling
both fish and other free swimming invertebrates (nekton); additional environmental parameters
such as dissolved oxygen and turbidity; the use of a sentinel fish species; as well as additional
reference sites to allow comparisons of the Musquash community.
As with the majority of estuarine systems, these environments are associated with extremely high
environmental variability, exhibiting large daily changes in chemical and biological structure due
to high fluctuations in salinity, water levels from tidal and other hydrodynamic processes
(Macdonald et al. 1984, Ayvazian et al. 1992). Therefore, a long-term approach to establishing a
baseline is important to assess the natural variability occurring within the area. This is necessary
in order to identify existing or potential problems associated with human activities and enable
mitigation measures.
2.2 Overview of Protocol
In order to begin sampling within Musquash Estuary MPA, proper permits need to be obtained
from the Department of Fisheries and Oceans Canada (DFO). Proponents of sampling need to
submit 1) an Application Form for Activity within the Musquash Estuary Marine Protected Area
(MPA) and Administered Intertidal Area (AIA), at least 60 days prior to sampling, and 2) an
Application for Licence Issued Pursuant to Section 52 of the Fishery (General) Regulations, at
least 30 working days prior to the proposed date of activity.
Three main techniques are recommended for sampling the nekton community (free swimming
invertebrates and fish) within Musquash Estuary: 1) nearshore sampling, conducted with a beach
seine and fyke net (section 4.1, 4.2 and 7.1); 2) salt marsh sampling completed with a fyke net
(section 4.2 and 7.1); and 3) the collection of Atlantic silversides (Menidia menidia) using the
beach seine, for use as a sentinel species (section 7.2).
3.0 PERSONNEL AND TRAINING
It is recommended that a minimum of two people sample for security reasons during each
sampling event. However, if resources permit, having three or four people is more favourable,
particularly during fyke net setup (establishing pole locations) or during peak season when
abundances of fish are high. At least one person of the group should have a biology background
(minimum Bachelor’s degree) and be trained (by personnel experienced with local species) to be
able to efficiently identify species of both fish and invertebrates. Considerations for a workshop
provided by DFO may be useful, such as for the CAMP program (Weldon et al. 2007). This
person should also have experience with the sampling methods and be able to make decisions in
the field regarding sampling gear placement. Other members of the group do not need extensive
training (community group members or interns) but it would be beneficial if they were familiar
6
with, or able to learn, sampling methods (beach seining), species identification techniques, and
fish measurements.
4.0 SAMPLING GEARS
Sampling gears used for estuarine fish collection, for the most part, use seines (Ayvazian et al.
1992), fyke nets (Honey et al. 2004) as well as throw traps (Raposa et al. 2003) for sampling the
nearshore area (water depths <2m). Honey et al. (2004) evaluated the use of a seine in nearshore
environments for long-term monitoring in which fry, juveniles, yearlings and year 2+ fish of
different species were caught. The seines ability to be used relatively quickly in habitats ranging
from beaches to vegetated areas was emphasized as an important attribute. However it has been
noted that seines have low collection efficiency (38%; De Mutsert and Cowan 2012). Therefore,
the seine should be used in conjunction with other sampling gears, as long as both gears are
found to be complementary. In Honey et al. (2004), the seine was often used with other gears
such as trawls and fyke nets to characterize fish assemblages. Specific to the nearshore area, fyke
nets are typically used to capture fish during spawning migrations and tagging studies. Dual
gears (fyke net and beach seine) were also utilized in Musquash (Ipsen 2013). At Five Fathom
Hole anadromous species such as smelt and American eel were often caught in the channel with
the fyke net, while smaller bodied fish and juveniles were captured in the beach seine. This
method also enabled data collection pertaining to the succession of cohorts within the estuary.
For example, Pollachius virens (pollock) were detected in the spring and early summer in the
beach seine followed by catches solely in the fyke net in later summer months.
It is therefore recommended that only two gear types be used for the collection of fish within
Musquash Estuary and reference sites; beach seine and fyke net. Both of these gears are easy to
manage, perform minimal harm to the sampled fish, and are non-destructive to the habitat in
which they are sampling. Both gear types are relatively lightweight (when dry) and can be easily
carried for shore access or placed in a small boat (canoe) to be transported to sites (Gibson et al.
1996). However, sampling gears will get significantly heavier to carry following a sampling
event, and might require two people to transport back to the truck. For a list of other equipment
recommended for sampling see Appendix A.
4.1 Beach Seine Sampling Methods
A beach seine (Figure 2) is an active sampling gear that is commonly used in sampling shallow
water (<1.5 m). A beach seine of 9 x 1.5 m (9 mm stretch mesh) with a central collection bag, is
recommended for use to be comparable with previous studies (Arens 2007, Ipsen 2013).
It is recommended that sampling with a beach seine should take place at, or within a maximum
of 2 hours after a low, slack tide. Sampling within an hour of low tide has been found to yield the
greatest numbers of individuals and highest species richness compared to other tidal stages
(Gibson et al. 1996, Arens 2007). Sampling conducted two hours after low tide may render
access (or departure) from site difficult. Beach seining requires two people to operate. Sampling
involves the seine to be towed so the net is perpendicular to the shore at a depth comfortable for
the outermost person (~1 – 1.5m) and about knee to waist height for the person closest to the
shore.
Seining should be performed for 3 minutes at a slow walking pace. At three minutes the person
closest to the shore will slow their pace, while the person furthest from the shore will begin to
7
curve toward the shore until both people are towing so the net is parallel to the shore. The net is
hauled to the shore, making sure the bag remains centered and the lead line remains on the
bottom. Once the bag end of the seine is out of the water the contents can be emptied into a 20 L
bucket with an aerator. This is considered a single tow. It is important that the lead line remains
against the substrate for the duration of the tow. It is helpful to hold the poles at a slight angle so
that the bottoms of the pole are angled in towards the net. Sampling with the seine should be
conducted during the day.
Figure 2: Beach seine sampling gear. From: https://en.wikipedia.org/wiki/Beach_seine#
4.2 Fyke Net Sampling Methods
A fyke net (Figure 3) is a passive sampling gear. Recommended fyke nets should be 3.7 m long
and consist of four hoops (mesh size 38.1 mm stretch mesh in the wings and body, and 22.2 mm
stretch mesh in cod end) and have two 3 m long wings attached to the opening of the net. Wings
taper from 100 cm deep (where they are secured by metal rods driven into the sediment) to 70
cm at the opening of the net (Ipsen 2013).
The fyke net will take 2-3 people to initially set up, establishing secure pole locations, and two
people to hook up the net and retrieve the following day. This will involve carrying poles (3
rebar poles: at least 8 ft long) and a post driver to each location. It is recommended that the poles
be installed at the sampling location either permanently or for the duration of the sampling
season. Important: Poles and fyke nets should be labeled according to requirements under the
Fishery General Regulations, SOR-93-53. These include:




The name of one person responsible for the gear securely affixed to a tag, float or buoy
The name be legible and readily visible at all times without having to manipulate (raising
the gear or removing ice and snow)
The name be in solid, black capital letters in Roman characters with no ornamentation; at
least 75 mm in height; and in a contrasting colour compared to the background
The tag, float or buoy should be affixed to each end of the gear
Additionally the tag, float or buoy should include the MPA approval number and Section 52
license number.
Fyke nets situated in a channel should be placed so that the opening of the net will face
upstream, catching fish on the ebb tide. Similarly, fyke nets located on a beach will face the
shore, catching fish on the ebb tide. Poles for fyke nets located on beach sampling locations
should be placed in a location either deep enough, or off to the side, as to not interfere with
beach seining tows. The fyke net will be secured onto the poles at low tide, and retrieved 24
hours later, sampling fish through two tidal cycles.
8
Figure 3: Fyke net sampling gear and poles. From FAO 2001.
4.2.1 Tidal Considerations
Bay of Fundy tides provide challenges for sampling with passive gears. Tidal height should be a
consideration while establishing fyke net locations. The following points should be kept in mind
while establishing fyke net locations.






It is important to monitor the fyke net at low tide, when first established at a new
sampling location.
If nets are set at low tide during a spring tide, they may be difficult, or impossible, to
access during neap tidal cycles.
Oppositely, if net locations are established at low tide, during neap tidal events, then fyke
net sampling during different tidal stages may result in the net becoming completely
exposed at low tide. This will result in high mortalities of fish during low tide.
It is recommended that nets be installed at low tide during the transition period between
spring and neap tides. This will allow for greater flexibility in sampling schedule, so as
not to be restricted to extreme tidal events.
Take note of the low water level at the time of sampling (often provided on tidal websites
of the area; Appendix B). This will provide insight into the location’s ideal time to
sample, as well as providing consistency.
When the net is retrieved, 24 hours after setup, specimens will be placed in a bucket with
an aerator for further processing to occur (see section 7 for details and Appendix A, for
equipment).
5.0 FREQUENCY OF SAMPLING
Sampling frequency in estuarine systems varies throughout the literature, and is heavily
depended on resource availability and study objectives. In most cases where the characterization
of fish communities were performed for the establishment of a baseline, sampling frequency
included daily (Honey et al. 2004), twice-monthly (Honey et al. 2004, Arens 2007, De Mutsert
and Cowan 2012, Ipsen 2013), and monthly (Thériault et al. 2006, Weldon et al. 2007, De
Mutsert and Cowan 2012) sampling regimes in order to capture temporal variability.
Increasing sampling frequency is favourable when establishing a baseline as it reduces the
variability between samples (Raposa et al. 2003) and reduces the occurrence of type II statistical
errors. This reduction in variability was noticed in Ipsen (2013) where sampling at Black Beach,
twice a month, allowed for the quantification of 20% more species and 40% more individuals
when compared to once monthly sampling events. High variability in fish communities in
9
temperate estuaries is a common issue. Not only do fish communities differ spatially and
temporally due to factors such as dynamic seasonal temperatures or site characteristics (e.g.,
turbidity, substrate heterogeneity; Able and Fahay 1998, Arens 2007, Ipsen 2013) but also have
been known to change following tidal, diel, and lunar cycles (Gibson et al. 1996, Arens 2007).
Efforts to reduce this variability include utilizing a standardized group of differing sampling
gears to correct for sampling bias (Honey et al. 2004), maintaining consistency in tidal height
and time of day (Gibson et al. 1996, Thériault et al. 2006, Weldon et al. 2007, Arens 2007),
achieving consistent sampling frequency and duration over multiple years (Thériault et al. 2006
and Weldon et al. 2007), as well as having accurate identification of specimens (Thériault et al.
2006).
In order to establish a thorough baseline for Musquash Estuary nearshore fish community, it is
recommended that an intensive sampling period be completed. This will enable an understanding
of the natural variability occurring within the estuary. Baseline sampling should be pursued for at
least a three to five year period, followed by ongoing monitoring periods that are established by
what intensive baseline data reveals. Data collected during baseline collection can also be
compared to Arens (2007) and Ipsen (2013). Previous studies characterizing fish or nekton
communities within estuaries have at least two years (Ayvazian et al. 1992, Able et al. 2002,
Clark et al. 2009, Courrat et al. 2009, Dolbeth et al. 2010); five years (Lazarri et al. 1999,
Selleslagh and Amara 2008); or to up to over a decade of continuous intensive monitoring (De
Mutsert and Cowan 2012).
Sampling should take place at intervals of at least once monthly from May to the end of October,
and be repeated annually, at all locations. Sampling more frequently (twice a month instead of
once monthly) would be beneficial if resources permit. However, due to sampling limitations
enforced by the tides, sampling once monthly is currently recommended for this sampling
protocol. By sampling twice a month, an estimate of spatial and temporal patterns of dominant
species, and rare or transient species, can be more easily identified. Sampling only once a month
may miss rare and transient species, as seen in Ipsen (2013). By sampling once a month,
temporal and spatial trends of dominant species may be characterized. Where resources are
limited, uniquely sampling during summer months (July, August, and September) will provide
an estimate of the spatial distribution of dominant species utilizing nearshore habitats during
peak season. If sampling only during one season is all that is feasible for a sampling, it is first
recommended to sample all three months, twice monthly. Quantitative data on species richness
and abundance can be pooled and compared among sites (n=3, averaged two sampling periods
per month), reducing sample variability when compared to a single monthly sampling design
(n=3).
6.0 SAMPLING LOCATIONS
The following map (Figure 4) shows the location of Musquash Estuary relative to three other
estuaries proposed for sampling as control sites including Saints Rest Marsh (to the east) as well
as Chance Harbour and Dipper Harbour (to the west).
10
Figure 4: Google Earth image showing estuaries to be sampled for proposed long-term
monitoring (DigitalGlobe 2015a)
6.1 Sampling within Musquash Estuary MPA
Musquash Estuary fish sampling can be divided into two separate main habitats of focus; 1) the
nearshore habitat and 2) the salt marsh habitat consisting of salt marsh channels. Sampling these
two main habitats will most likely co-occur during sampling events. It is recommended that the
nearshore sampling use both a beach seine and fyke net, whereas salt marsh channels use a fyke
net. Further considerations regarding the two main habitats (nearshore and salt marsh) can be
seen in section 6.1.3.
Habitats not included in this protocol
Habitats not included in this protocol are those that may be considered for future sampling but
are not recommended as part of a long-term protocol at this time. These habitats include the
subtidal main channel or bay and salt marsh pannes. In the case of the subtidal main channel or
bay, sampling restrictions associated with the use of gears that may alter the habitat, such as
trawls (DFO 2011) make sampling the subtidal portions of Musquash not applicable at this time.
However, sampling this habitat may provide insight into larger species of fish utilizing the MPA
and should be included in future considerations depending on gear type and study design.
The fish community within salt marsh pannes has not been previously documented. Access to
these locations is time consuming. Previous sampling attempts within salt marsh pannes at
Hepburn’s Basin, with minnow traps showed both low catch numbers and low species richness
(Ipsen, personal observation). Future considerations for this habitat are encouraged but are
difficult to justify within a long-term monitoring plan due to the effort (man hours vs outcome)
associated with these locations. Therefore, this sampling protocol focuses on salt marsh channels
as sampled in Gratto (1986) and Ipsen (2013).
11
6.1.1 Nearshore Beach Seining and Fyke Net Locations
The nearshore habitat consists of four sampling sites in zone 2 of the MPA (Figure 5). These
include: Five Fathom Hole, Black Beach, Hepburn’s Basin and Gooseberry Cove. These
recommended sites are chosen based on previous sampling events using similar gears that can be
incorporated into baseline information (Arens 2007, Ipsen 2013) or have been known to be
accessible (Matt Abbott, Conservation Council of New Brunswick; pers. comm.).
Although, these sites are classified as “nearshore”, each of them uniquely represents their own
habitat type. These four locations represent the natural salinity gradient from Five Fathom Hole,
the most brackish site, to Gooseberry Cove, the outermost region of the MPA (Figure 5).
Similarly, substrate types differ among nearshore sampling sites, encompassing rocky cobble
substrates (Five Fathom Hole/ Gooseberry Cove), an intertidal sand and gravel beach (Black
Beach) and an intertidal flat (Hepburn’s Basin) (Greenlaw et al. 2014). These characteristics,
both salinity gradient and substrate type, have been shown to represent differing fish community
characteristics, affecting the occurrence of demersal and pelagic species or presence of juveniles,
within Musquash (Ipsen 2013) and within estuaries in general (Gibson et al. 1996, Albaret et al.
2004). It is recommended that all four of these sites be assessed annually for the establishment of
a nearshore baseline and continue to be sampled for long-term monitoring.
Figure 5: Musquash Estuary proposed sampling sites (DigitalGlobe 2015b). Four sites are
recommended for beach seine and fyke net sampling in zone 2 of the MPA.
Black Beach
With a main road leading to the beach (Figure 6), this site is the easiest site to access and sample.
It is also the most public location of the sampling locations. To prepare sampling equipment and
drive from Saint John to Black Beach sampling can be completed within 2-3 hours depending on
fish abundances.
12
Figure 6: Black Beach sampling site (DigitalGlobe 2015c). Straight line indicates path of
multiple tows at approximate low tide mark and the x marks where nearshore fyke net sampling
could take place.
Five Fathom Hole
Five Fathom Hole is accessed from the Five Fathom Hole wharf (Figure 7). It is necessary to
carry gear to the sampling location (~550m: 10-15 minutes). To access the beach seine location,
Ferguson Creek will need to be crossed. At low tide, this creek is very shallow with gravel
patches, which makes crossing easy. It is important that the sampling team have proper fitting
wader boots at this site, as the terrain in some spots is deep mud where someone can easily get
stuck. Life jackets are also recommended as the beach where seining takes place drops off
quickly. Sampling Five Fathom Hole takes about 2-4 hours. Time saving tip: At Five Fathom
Hole, the fyke net was stored in the woods, hidden in the trees so it did not need to be carried
each time.
Figure 7: Five Fathom Hole beach seining site (marked with a straight line) and fyke net location
in the channel (marked with an x) (DigitalGlobe 2015d)
13
Hepburn’s Basin
Hepburn’s Basin is the most time-consuming site to access (Figure 8). To get to the area to seine
and where the fyke net is placed, is approximately 1.5 km of walking with sampling gear (~1520 minutes). Leaving from Saint John, it takes approximately 4-6 hours to sample at this location
with the beach seine and 4-5 hours to collect the fyke. It is important that researchers wear
proper fitting waders/boots for sampling this location, as it is necessary to cross the intertidal flat
to seine and set up the fyke net. Time saving tip: Similar to Five Fathom Hole, the fyke net was
stored hidden in the woods, so it did not need to be carried to the site for each sampling event.
Figure 8: Hepburn’s Basin seining site (marked with a straight line) and fyke net locations
(nearshore and in the channel; marked with an x) (DigitalGlobe 2015e). For channel sampling
see salt marsh sampling (Section 6.1.2).
Gooseberry Cove
Gooseberry Cove beach (Figure 9) is accessible by vehicle. Accessing this site will take a longer
commute. Estimated time for commute from Saint John and sampling at this location is 3-4 hours
with beach seine, 2-3 hours to collect fyke net.
14
Figure 9: Gooseberry Cove seining site (marked with a straight line) and potential fyke net
location (marked with an x) (DigitalGlobe 2015f).
6.1.2 Salt Marsh Fyke Netting Locations
The salt marsh system in Musquash Estuary is considered very valuable for productivity
parameters in the Bay of Fundy (Singh et al. 2000). The salt marsh system is located along the
channel in zone 1 as well as an area by Hebpurn’s Basin in zone 2 (Singh et al. 2000) (Figure 1,
8 and 10). Accessing salt marsh habitats within Musquash Estuary is challenging. There have
been very few studies characterizing fauna in this system. Gratto (1986) identified species within
a salt marsh channel at Hepburn’s Basin, and Ipsen (2013) identified species utilizing a salt
marsh channel, at Five Fathom Hole within Ferguson Creek. Based on the value placed on the
productivity of the salt marsh system in Musquash Estuary, characterizing the fish community
within this habitat as part of the long-term monitoring program, will provide important
information of species utilizing this habitat type.
Musquash Estuary salt marsh habitats provide unique challenges. Gears used for sampling salt
marsh habitats vary depending on accessibility and resources. Methods used to collect fish in
these habitats include: throw traps, lift nets, minnow traps, breder traps, fyke nets, towed
nets/seines and trawls (Carlisle et al. 2002, Raposa et al. 2003, Ipsen 2013). It is recommended to
use a passive gear such as a fyke net to sample tidal creeks and channels. Small traps, such as
minnow traps, may become easily buried in mud or swept away due to the dynamic force of the
tide. The salt marsh habitat of Musquash consists of narrow channels and is usually surrounded
by steep banks and mud, making access and the use of active sampling gears such as beach
seining difficult. Fyke net sampling in this habitat should be carried out in a similar fashion as
nearshore habitats in that the net should be placed facing upstream to catch fish on the ebb tide
(Section 3.2).
Suggested salt marsh sampling sites within the MPA are located both in the main channel (zone
1; Figure 10) as well as in the salt marsh channel located at Hepburn’s Basin (zone 2; Figure 8
and 10). Approximately 7 channels could be recommended for sampling (Figure 10). However,
most of these, except two (accessible by road, or by foot at Hepburn’s Basin), would only be
accessible by canoe. These sampling locations were chosen based on the width of the channel
15
compared to Ferguson Creek at Five Fathom Hole. Alternative locations may need to be
considered based on site accessibility and resources at the time of choosing sites and sampling.
Figure 10: Potential salt marsh sampling locations for fyke net (marked with an x) (DigitalGlobe
2015g). Sampling location in orange signifies a known road access site. All other locations may
need to be accessed by canoe (zone 1) or by foot (zone 2). Alternative sampling locations to
those portrayed here may be considered depending on ease of access to the channel or other
habitat limitations.
6.1.3 MPA Sampling Considerations
Timing of sampling events
Depending on the site and season (differing abundances of fish), varying times may be required
to successfully sample a location. It is difficult to access multiple sites during the same day
without being rushed, particularly for seining, unless fish abundances are low and quickly
processed. For example, it may be possible to seine Black Beach, at low slack tide, set up the
fyke net, and make it over to Five Fathom Hole within an hour of low slack tide, seine, and set
up the fyke net before water becomes too high. Similarly, it may be possible to retrieve multiple
fyke nets on the same day for nearshore and salt marsh sampling events, but this will depend on
the ability of the group leader to identify species, as well as monitor tidal restrictions. For the
purposes of this proposal, it is recommended that sites be sampled on as few consecutive days as
possible, due to diurnal differences that may affect species compositions (Gibson et al. 1996).
However, differing days may be more realistic for first time sampling at a site. The possibility of
sampling multiple sites will be at the discretion, and comfort level of the lead member of the
group. For an example of a sampling period and tidal restrictions, see Appendix B and Appendix
C.
16
Site accessibility
Musquash Estuary is a challenging environment to access. Sampling locations range from fairly
easy to access to more time consuming. For example Black Beach is the fastest site to sample
because it is a relatively short commute from Saint John, provides the ability to drive right to the
sampling location, and allows for sampling with few obstacles (in contrast, sand and gravel
beach compared to intertidal flats or rocky cobble). Sampling Hepburn’s Basin consists of a
longer commute (45 minutes – 1 hour), and a hike down a trail and across an intertidal flat (1015 minutes).
Although all sites are recommended for sampling annually, limitations arise which may prevent
access to one or more sites. Black Beach is an ideal site to continue monitoring as it has two
previous sampling events (Arens 2007 and Ipsen 2013) and is a very quick site to sample.
However, Black Beach was found to have reduced species richness, with decreased numbers of
rare species and juveniles, compared to other sites within the estuary (Ipsen 2013). This site is
also more public which may provide problems with gear tampering (fyke net) or disturbances
(people swimming). Choosing which sites will be sampled over others will be at the discretion of
the group leader, the resources available (time and people) and the time of year.
Other considerations for sampling sites within Musquash may be the use of a small vessel to
access sites instead of by road. This may be a possibility for reducing time between sampling
events. Accessing salt marsh channels in zone 1 will require a non-motorized vessel as per the
Musquash Estuary Marine Protected Area Regulations (SOR/2006-354). A small-motorized boat
may work between some sites in zone 2 (Five Fathom Hole and Black Beach) but difficulties
may arise while attempting to access other sites, particularly Hepburn’s Basin, from the water.
Hepburn’s Basin is an intertidal flat and has a low gradient of shallow water, making access with
a boat possibly problematic around low tide.
6.2 Reference Sampling Locations Outside the MPA
In areas where fish are highly migratory, Higdon et al. (2013) suggest that sampling in a larger
geographic area (outside the MPA) was an effective way of characterizing the fish community
that may be utilizing a protected area. Fish community comparisons for long-term monitoring
could include Saints Rest Marsh (Doyle et al. 2011, Arens 2007, Ipsen 2013), Chance Harbour
(Arens 2007), and Dipper Harbour (Arens 2007, Ipsen 2013). These sites have already been
established as locations that are accessible and have been previously sampled for nearshore fish
communities. They are also estuaries that bracket Musquash (Figure 4), enabling assessment of
spatial trends associated with potential salinity gradients or anthropogenic disturbances
stemming from point source pollution sites within close proximity (Singh et al. 2000, Doyle et al.
2011). Salt marsh habitats located at Saints Rest Marsh and Dipper Harbour have also been
known to be accessible through extensive studies involving salt marsh vegetation (Dipper
Harbour) and field trips by the University of New Brunswick ecology class (Saints Rest Marsh).
Saints Rest Marsh
Also known as Irving Nature Park or Manawagonish Creek (Figure 11), this site has been
previously sampled for the nearshore fish community by Ipsen (2013), and has been accessed by
the University of New Brunswick ecology field class for sampling of the salt marsh. It is in close
proximity to Musquash Estuary, is not protected and is in close proximity to Saint John Harbour.
It has also been studied for potential contamination impacts in Doyle et al. (2011). At lower tidal
17
heights the beach turns more into an intertidal flat, similar to Hepburn’s Basin, and can be
difficult to walk on, particularly to place the fyke net.
Figure 11: Saints Rest Marsh seining site (marked with a straight line) and fyke net locations
(nearshore and in the channel; marked with an x) (DigitalGlobe 2015h).
Chance Harbour
Chance Harbour (Figure 12), was previously studied in a spatial comparison of fish community
by Arens (2007). This site has easy beach access and a salt marsh that appears to be accessible
by the road.
Figure 12: Chance Harbour potential seining site (marked with a straight line) and fyke net
locations (nearshore and in the channel; marked with an x) (DigitalGlobe 2015i).
18
Dipper Harbour
Located the furthest from Musquash (Figure 13), Dipper Harbour was sampled as part of Ipsen
(2013) for the nearshore fish community. Dipper Harbour’s beach is easily accessible by a road.
However, permission from landowners is needed. Substrate at Dipper was similar to Black
Beach. Dipper Harbour’s salt marsh is easily accessible and salt marsh monitoring from
vegetation studies has been previously conducted by Chmura et al. (1997).
Figure 13: Dipper Harbour seining site (marked with a straight line) and fyke net locations
(nearshore and in the channel; marked with an x) (DigitalGlobe 2015j).
7.0 NEKTON COMMUNITY SAMPLING
7.1 Community Assessments
Both invertebrates and fish species will be counted and identified to species. Fish lengths will be
measured (Fork length (FL)) to estimate age. In instances where high abundances of a single
species of fish are caught, only 30 individuals are measured to decrease likelihood of mortality.
A list of potential fish species either previously collected within Musquash Estuary or in
surrounding habitats can be seen in Appendix D.
Data
Data will be obtained for fyke net and beach seine collections separately. Due to differing mesh
sizes this information should also be analyzed separately. The data collected from the fish
sampling protocol should include: number of fish caught, species identification, and individual
lengths to estimate the life stage of the fish. For a template of metrics sampled see Appendix E.
These data were simple to transfer into an excel file to perform filtering, pivot tables and
analyses. An example of these data can be seen in Table 1.
19
Table 1: Example of raw data collected within Musquash Estuary at sites Black Beach (BB) and
Five Fathom Hole (FFH) during either the first two week period of the month (E- Early) or the
last two week period (L- Late).
Day Month Year Location Gear Tow
L
10
2009
BB
Seine
2
L
10
2009
BB
Seine
2
L
10
2009
BB
Seine
2
L
10
2009
FFH
Seine
1
L
10
2009
FFH
Seine
1
L
10
2009
FFH
Seine
1
L
10
2009
FFH
Seine
1
L
10
2009
FFH
Seine
1
E
11
2009
BB
Seine
1
E
11
2009
BB
Seine
1
E
11
2009
BB
Seine
1
E
11
2009
BB
Seine
1
E
11
2009
BB
Seine
1
E
11
2009
BB
Seine
1
E
11
2009
BB
Seine
1
Species
Winter
Flounder
Winter
Flounder
Winter
Flounder
Atlantic
silverside
Atlantic
silverside
Atlantic
silverside
Atlantic
silverside
Atlantic
silverside
Atlantic
silverside
Atlantic
silverside
Atlantic
silverside
Atlantic
silverside
Atlantic
silverside
Atlantic
silverside
Atlantic
silverside
Length
53
48
37
43
65
43
43
61
64
60
85
66
43
62
66
These data can be analyzed using univariate analyses (ANOVAs for factors site and season, as
well as their interactions), non-parametric analysis on fish sizes, and multivariate analysis
(PERMANOVA's, nMDS plots and SIMPER comparisons for community data in PRIMER; see
Ipsen 2013).
20
7.1.2 Large Abundances of Nekton
During warmer seasons there may be large numbers of fish and invertebrates (counts easily
determined as greater than 300). In such cases, deciding to estimate the total number of
individuals of these species is best, to avoid mortality from overcrowding in the bucket. This
instance is likely to take place for sticklebacks (in the spring) as well as Atlantic silversides and
sand shrimp. Methods used by Weldon et al. (2007) suggest that between 2 to 5 subsamples
(depending on time and number of persons sampling) of individuals is taken using square, 20cm, aquarium dip nets. Individuals in the subsample are enumerated, and the remainder of the
individuals are emptied out of the bucket into the dip net and released, taking note of the counts
of dip nets that are filled. It is important to ensure that only the high abundant species is present
in dip net and all other, less common, species are accounted for and processed in the proper way.
It is also important to do this quickly, particularly for oxygen sensitive species such as Atlantic
silversides.
7.2 Contaminantion Indicator through Sentinel Species Collections
Nearshore environments are subjected to various sources of contamination. Although established
as an MPA, Musquash Estuary, located within 20 km of Saint John Harbour, has the potential to
be impacted by contamination affecting the harbour. Although the evaluation of sediment
contamination sources in Musquash is underway, there is currently no biological monitoring for
chronic effects of potential contamination on fish. The most popular sentinel species used for
characterization of anthropogenic disturbances in marsh ecosystems are the mummichog, rock
gunnel and tomcod. Although present, these fish were not ubiquitously found in large
abundances within Musquash Estuary. In the case of Atlantic tomcod, high catches were limited
to fyke nets (Ipsen, 2013). Based on data of fish abundances within Musquash Estuary (Arens
2007, Ipsen 2013), the only other species that would match the criteria for a sentinel species
would be the Atlantic silverside. Doyle et al. (2011) used the Atlantic silverside as a sentinel
species to characterize contamination gradients in Saint John Harbour. It is therefore
recommended that a baseline for fish health for Atlantic silversides become established as a way
to assess potential impacts of contamination occurring within the estuary.
Menidia menidia or Atlantic silverside (Figure 14) is a common species resident to coastal
habitats, marshes, and intertidal creeks from southern Gulf of Saint Lawrence to northern Florida
(Scott and Scott 1988, Colette and Klein-MacPhee 2002, Able and Fahay 1998). Atlantic
silversides can be found in these nearshore habitats throughout the year (Able and Fahay 1998).
Silversides start spawning at sizes as small as 42 mm total length (Able and Fahay 1998). The
spawning season varies depending on latitude but typically starts in spring (May-June) and
continues to late summer (July-August) (Able and Fahay 1998). Because they are smaller
bodied, these fish are successfully caught in the nearshore environment with a beach seine. In
Ipsen (2013), data collections of Atlantic silversides showed that CPUE was the highest in later
summer months (August – November). Abundances decreased (1-30 individuals) between
December and May. Hepburn’s Basin nearshore sampling showed a spike in abundance in June,
followed by the other nearshore sampling sites. However, silverside catches have the potential to
be highly variable: absent or in small numbers (<50) during one sampling event followed by
numerous individuals (>500) the following event (Ipsen 2013). Silverside collections within
Musquash Estuary align with other observations in the area. Future collections and sampling of
Atlantic silverside for use as a sentinel species are recommended based on Doyle et al. (2011).
21
Figure 14: Atlantic silverside, Menidia menidia. From: http://www.glf.dfompo.gc.ca/Gulf/FAM/IMFP/2000-2004-Silversides-PEI
Atlantic silversides meet many criteria for the use as a sentinel species. Doyle et al. (2011) found
that while inshore, Atlantic silversides are locally resident. However, they tend to leave inshore
areas during late spring to spawn, and again in late autumn for winter. Considerations for sample
size and lab techniques are suggested. However these methods are recommended based on
information collected by a single study using Atlantic silversides collected from Saint John
Harbour (Doyle et al. 2011). As more information is collected on Atlantic silversides found
within Musquash Estuary these recommendations may change. As per the Environmental Effects
Monitoring Program guidelines in Canada, it is recommended to sample spawning fish just prior
to spawning when gonads are developed and at similar growth stages. For Atlantic silverside,
sampling should occur in late May or June, prior to the full moon. However, it is also
recommended that silversides be taken upon their return in late summer as well, when
abundances are higher, to estimate growth (Thériault et al. 2006, Doyle et al. 2011).
During these two sampling periods, it is recommended that at least 60 - 100 adult silversides (to
try to capture at least 20 of each sex) of lengths approximately >45mm FL are kept while
completing nearshore fish community sampling (Section 6.1). Fish brought back to the lab will
be placed in a cooler full of ice and anesthetized with tricaine methanesulfonate (Western
Chemical Inc., Ferndale, Wash., U.S.A.; 160 mg/L for approximately 2 to 5 minutes). Fish will
be weighed and measured to determine the total FL (± 0.1 cm) and the total body weight (± 0.01
g).
After the severance of the spinal cord, the fish will be dissected to determine the gonad and liver
weights to the nearest 0.001 g and the removal of scales or otoliths for the determination of age.
This information will be used to calculate Gonadosomatic Indices (GSI), Liver Somatic Indices
(LSI), and condition factor (K). Comparisons of these factors can then be made between
Musquash Estuary sites and reference sites outside of the MPA. Additionally, a section of the
liver should be taken after weight, and immediately placed in a cryovial to be stored at -80°C for
the analysis biomarkers indicating contaminant exposure (Thériault et al. 2006, Doyle et al.
2011).
8.0 SUMMARY
Sampling Musquash Estuary and its reference sites consists of using two sampling gears (beach
seine and fyke net) for the collection of nekton data. Data collected on fish communities
includes: species richness, abundance, lengths as well as Atlantic silversides for use as a sentinel
species. Data collected on invertebrates includes species richness and abundance, which will
provide complimentary data on the community that is utilizing nearshore habitats. In order to
establish a baseline at recommended sites it is necessary to conduct an intensive sampling period
over the course of 3-5 years depending on resources. Sampling frequency is recommended to
occur at least once monthly between May and October. This information will provide insight into
22
the annual variability associated with the fish community. Based on data collected during the
intensive baseline, further decisions can be made as to the most effective way to sample
Musquash Estuary and its reference sites.
Musquash Estuary is a dynamic system and considerations will need to be made as to the best
sampling regime for each site. It is important to maintain a level of consistency (tidal height,
time of day, sampling methods) as fish communities are highly influenced by physical factors in
these environments. Care must be taken with passive gears as to provide sufficient depth at low
tide to reduce fish mortalities. An estimated timing for sampling for each site can be seen in the
Appendix C as a starting point for establishing a sampling regime.
This protocol does not cover all habitats found in Musquash Estuary. The main channel/bay as
well as salt marsh pannes may be considered for future sampling. These systems may provide
insight into other fish communities utilizing the Estuary.
23
6.0 REFERENCES
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Atlantic Bight. Rutgers University Press, New Jersey. 342 pp.
Able, K.W., Fahay, M.P., Heck K.L., Roman, C.T., Lazzari, M.A., and Kaiser, S.C. 2002.
Seasonal distribution and abundance of fishes and decapod crustaceans in a Cape Cod estuary.
Northeastern Naturalist 9(3): 285-302.
Albaret, J-J., Simier, M., Darboe, F.S., Ecoutin, J-M., Raffray, J., and de Morais, L.T. 2004. Fish
diversity and distribution in the Gambia Estuary, West Africa in relation to environmental
variables. Aquatic Living Resources 17, 13-46.
Arens, C. 2007. Nearshore Fish Community Structure in the Southwest Bay of Fundy and
Northwest Atlantic: Comparing Assemblages Across Multiple Spatial and Temporal Scales.
Master of Science Thesis, Department of Biology, University of New Brunswick, Saint John:
145p.
Ayvazian, S.G., Deegan, L.A., and Finn, J.T. 1992. Comparison of habitat use by estuarine fish
assemblages in the Acadian and Virginian provinces. Estuaries 15(3): 368-383.
Blaber, S.J.M., Cyrus, D.P., Albaret, J.-J, Chong Ving Ching, Day, J.W., Elliott, M., Fonseca,
M.S., Hoss, D.E., Orensanz, J., Potter, I.C., and Silvert, W. 2000. Effects of fishing on the
structure and functioning of estuarine and nearshore ecosystems. Journal of Marine Science 57:
590-602.
Carlisle, B.K., Donovan, A.M., Hicks, A.L., Kooken, V.S., Smith, J.P., and Wilbur, A.R. 2002.
A Volunteer’s Handbook for Monitoring New England Salt Marshes. Massachusetts Office of
Coastal Zone Management, Boston, MA. http://www.mass.gov/eea/docs/czm/habitat/vols-guidesalt-marsh-2002.pdf
Clark, B.M., Hutchings, K., and Lamberth, S.J. 2009. Long-term variations in composition and
abundance of fish in the Berg Estuary, South Africa. Transactions of the Royal Society of South
Africa 64(2): 238-258
Chmura, G.L., Chase, P., and Bercovitch, J. 1997. Climatic controls of the middle marsh zone in
the Bay of Fundy. Estuaries 20(4): 689-699.
Collette, B.B., and Klein-MacPhee, G. (Editors). 2002. Bigelow and Schroeder’s fishes of the
Gulf of Maine 3rd Edition. Smithsonian Institution (Washington D.C.). xxxiv + 748 p.
Cooper, A., Abbott, M., Allard, K., Chang, B., Courtenay, S., Doherty, P., Greenlaw, M., Ipsen,
E., Koropatnick, T., Law, B., Losier, R., Martin, J., Methven, D., and Page, F. 2014. Musquash
Estuary Marine Protected Area (MPA): Data Assessment. DFO Can. Sci. Advis. Sec. Res. Doc.
2014/001. v + 57 p.
Courrat, A., Lobry, J., Nicolas, D., Laffargue, P., Amara, R., Lepage, M., Girardin, M., and Le
Pape, O. 2009. Anthropogenic disturbance on nursery function of estuarine areas for marine
species. Estuarine, Coastal and Shelf Science 81: 179-190.
De Mutsert, K., and Cowan, J.H. Jr. 2012. A before-after-control-impact analysis of the effects
of a Mississippi River freshwater diversion on estuarine nekton in Louisiana, USA. Estuaries and
Coasts 35:1237–1248.
24
DFO. 2011. Musquash Estuary: A Proposed Monitoring Framework for the Marine Protected
Area and Intertidal Area Administered by Fisheries and Oceans Canada. DFO Can. Sci. Advis.
Sec. Sci. Advis. Rep. 2011/040. http://www.dfo-mpo.gc.ca/Library/344331.pdf
DFO. 2013. Review and Assessment of the Baseline Data for the Musquash Estuary Marine
Protected Area Monitoring Indicators. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2013/073.
DigitalGlobe. 2015a. Bay of Fundy coastline, New Brunswick, Canada. 45° 09’ 46.08”N, 66°
14’ 31.06”W, Eye alt 23.02 mi. Google earth V 7.1.2.2041 (October 7, 2013).
http://www.earth.google.com [Accessed February 12, 2015].
DigitalGlobe. 2015b. Musquash Estuary, New Brunswick. 45° 09’ 51.25”N, 66° 14’ 39.30”W,
Eye alt 44,580 ft. Google earth V 7.1.2.2041 (October 7, 2013).
http://www.earth.google.com [Accessed February 12, 2015].
DigitalGlobe. 2015c. Black Beach, Musquash Estuary, New Brunswick. 45° 09’ 14.74”N, 66°
13’ 43.26”W, Eye alt 2829 ft. Google earth V 7.1.2.2041 (October 7, 2013).
http://www.earth.google.com [Accessed February 12, 2015].
DigitalGlobe. 2015d. Five Fathom Hole, Musquash Estuary, New Brunswick. 45° 11’ 26.60”N,
66° 15’ 06.54”W, Eye alt 3802 ft. Google earth V 7.1.2.2041 (October 7, 2013).
http://www.earth.google.com [Accessed February 12, 2015].
DigitalGlobe. 2015e. Hepburn’s Basin, Musquash Estuary, New Brunswick. 45° 09’ 49.77”N,
66° 16’ 07.30”W, Eye alt 8673 ft. Google earth V 7.1.2.2041 (October 7, 2013).
http://www.earth.google.com [Accessed February 12, 2015].
DigitalGlobe. 2015f. Gooseberry Cove, Musquash Estuary, New Brunswick. 45° 08’ 24.83”N,
66° 14’ 18.21”W, Eye alt 10,604 ft. Google earth V 7.1.2.2041 (October 7, 2013).
http://www.earth.google.com [Accessed February 12, 2015].
DigitalGlobe. 2015g. Musquash Estuary, New Brunswick. 45° 10’ 14.26”N, 66° 18’ 06.57”W,
Eye alt 29,485 ft. Google earth V 7.1.2.2041 (October 7, 2013). http://www.earth.google.com
[Accessed February 12, 2015].
DigitalGlobe. 2015h. Saints Rest Marsh, New Brunswick. 45° 12’ 28.31”N, 66° 08’ 24.26”W,
Eye alt 33,471 ft. Google earth V 7.1.2.2041 (October 7, 2013). http://www.earth.google.com
[Accessed February 12, 2015].
DigitalGlobe. 2015i. Chance Harbour, New Brunswick. 45° 07’ 04.44”N, 66° 22’ 25.28”W, Eye
alt 14,350 ft. Google earth V 7.1.2.2041 (October 7, 2013). http://www.earth.google.com
[Accessed February 12, 2015].
DigitalGlobe. 2015j. Dipper Harbour, New Brunswick. 45° 05’ 49.22”N, 66° 24’ 40.29”W, Eye
alt 14,350 ft. Google earth V 7.1.2.2041 (October 7, 2013). http://www.earth.google.com
[Accessed February 12, 2015].
Dolbeth, M., Martinho, F., Freitas, V., Costa-Dias, S., Campos, J., and Pardal, M.A. 2010. Multiyear comparisons of fish recruitment, growth and production in two drought-affected Iberian
estuaries. Marine and Freshwater Research 61: 1399-1415.
Doyle, M.A., Bosker, T., and Munkittrick, K.R.. 2011. The potential use of Atlantic silverside
(Menidia menidia) for monitoring estuarine pollution. J. Environ. Monit. 13: 3168-3177.
25
FAO. 2001. Fishing gear types. Fyke nets. Technology fact sheets. In: FAO Fisheries and
Aquaculture Department [online]. Rome. Updated 13 September 2001. [Cited 25 February
2016]. http://www.fao.org/fishery/geartype/226/en
Elliott, M., and Hemingway, K.L. 2002. Fishes in Estuaries. Blackwell Science, Oxford, 636 pp.
Gibson, R.N., Robb, L., Burrows, M. T., and Ansell, A.D. 1996. Tidal, diel and longer term
changes in the distribution of fishes on a Scottish sandy beach. Marine Ecological Progress
Series 130: 1-17
Greenlaw, M.E., Schumacher, M.N., and McCurdy, Q.M. 2014. A Habitat map and updated
mean high water boundary of the Musquash Estuary. Can. Tech. Rep. Fish. Aquat. Sci. 3093: iv
+ 26p.
Gratto, G.W. 1986. Interactions between vertebrate predators and their benthic prey on an
intertidal mudflat. PhD. Thesis, University of New Brunswick, Fredericton, NB.
Harvey, J., Coon, D., and Aboucher, J. 1998. Habitat Lost: Taking the Pulse of Estuaries in the
Canadian Gulf of Maine. Conservation Council of New Brunswick.
Higdon, J.W., and Paulic, J.E. 2013. Information in support of monitoring protocols and
strategies for selected indicators in the Tarium Niryutait Marine Protected Area (TNMPA). DFO
Can. Sci. Advis. Sec. Res. Doc. 2012/113. iv + 30 p.
Honey, K., Baxter, R., Hymanson, Z., Sommer, T., Gingras, M., and Cadrett, P. 2004. IEP LongTerm Fish Monitoring Program Element Review. Interagency Ecological Program for the San
Francisco Bay/Delta Estuary. State of California The Resources Agency Department of Water
Resources Interagency Ecological Program: 302p.
Ipsen, E. 2013. Nearshore fish diversity in Musquash Estuary: A Marine Protected Area in the
Bay of Fundy. Thesis (MSc), University of New Brunswick, Saint John, New Brunswick. 128
pages.
Lazzari, M.A., Sherman, S., Brown, C.S., King, J., Joule, B.J., Chenoweth, S.B., and Langton,
R.W. 1999. Seasonal and annual variations in abundance and species composition of two
nearshore fish communities in Maine. Estuaries 22 (3A): 636-647
Macdonald, S.J., Dadswell, M.J., Appy, R.J., Melvin, G.D., and Methven, D.A. 1984. Fishes,
fish assemblages, and their seasonal movements in the lower Bay of Fundy and Passamaquoddy
Bay, Canada. Fishery Bulletin 82(1):121-139.
Methven, D.A., and Schneider, D.C. 1998. Gear- independent patterns of variation in catch of
juvenile Atlantic cod (Gadus morhua) in coastal habitats. Can. J. Fish. Aquat. Sci. 55: 1430–144.
Raposa, K.B., Roman, C.T. and Heltshe, J.F. 2003. Monitoring nekton as a bioindicator in
shallow estuarine habitats. Environmental Monitoring and Assessment 81: 239–255.
Scott, W.B., and Scott, M.G. 1988. Atlantic fishes of Canada. Canadian Bulletin of Fisheries and
Aquatic Sciences 219: 731.
Selleslagh, J., and Amara, R. 2008. Environmental factors structuring fish composition and
assemblages in a small macrotidal estuary (eastern English Channel). Estuarine and Coastal
Shelf Science 79: 507-517.
26
Singh, R., Buzeta, M.I., Dowd, M., Martin, J.L., and LeGresley, M. 2000. Ecological overview
of Musquash Estuary: a proposed marine protected area. Can. Manusc. Rep. Fish. Aquat. Sci.
2538: 39 p.
Stevens, J.-A. 1997. UNBSJ Marine Biology Field Course intertidal species list and salt marsh
zonation. Unpublished.
Thériault, M.-H., Courtenay, S.C., Godin, C., and Ritchie, W.B. 2006. Evaluation of the
Community Aquatic Monitoring Program (CAMP) to assess the health of four coastal areas
within the southern Gulf of St. Lawrence with special reference to the impacts of effluent from
seafood processing plants. Can. Tech. Rep. Fish. Aquat. Sci. 2649: vii + 60 p.
Weldon, J., Courtenay, S., and Garbary, D. 2007. The Community Aquatic Monitoring Program
(CAMP) for measuring Marine Environmental Health in Coastal Waters of the southern Gulf of
St. Lawrence: 2005 Overview. Can. Tech. Rep. Fish. Aquat. Sci. 2708: viii + 47 p.
27
Appendix A: Equipment checklist for field



Beach seine
3-6 Fyke net (s)
Other field equipment
o A truck
o Well fitting chest waders
o GPS
o Post pounder (first trip only to set poles for fyke net)
o Weatherproof (Rite in Rain) notepad
o Pencil
o YSI with probes for
 Temperature
 Salinity
 Dissolved oxygen
o Secchi disk
o Buckets
 Three for beach seining events
 Two for fyke net sampling
o Dip nets
o Portable, battery powered oxygen stone and bubbler
o Fish measuring board
o Containers for unknown species
o Containers or bags, cooler and ice for sentinels

General equipment
o Camera
o Lifejackets
o First aid kits for field location and or vehicle
o Cell phone
o Rain gear, polarized glasses
o Sunscreen, hat, bug spray
o Extra batteries for sonde
28
Appendix B: Sample tidal sampling
Consistency was maintained in Ipsen (2013) by sampling in the morning and within tidal ranges
around 1 to 1.8 m (when possible). In Table 2, an example of sampling periods is shown. This
example runs from April 5th to April 12th. Sampling in later months will allow more flexibility
due to the increased daylight period. An example of how sampling may occur would include
going to sites to set up the fyke net prior to low tide events (but not necessarily in the dark). The
sites that are reached at low tide would be seined along with the fyke net being set up (within a
maximum of 2 hours of low tide). As the morning progresses, it would be possible to continue to
set up fyke nets at other sites as the tide rises (as long as the low water mark is known). This is
important so fish don’t become exposed during the next low tide period, and ensures that the net
can be adequately retrieved 24 hours later while not jeopardizing the safety of the sampling crew.
29
Table 2: Tide table corresponding with Figure 15 (below). Table shows example time frame of
when sampling could occur (shaded low tide rows). Sampling times over several days, and
seasons, may change with changing low tide time and light availability (sunrise).
Date
Time
Tidal
height (m)
Phase
0:57
7.44
High tide
0:15
Sunrise
3:36
Low tide
6:50
6:58
7:12
Sunday 5 April
0.9
7:32
Moonset
High tide
10:03
19:33
1.11
Low tide
16:04
19:57
Sunset
20:02
21:16
Moonrise
22:19
High tide
1:10
Sunrise
4:25
Low tide
6:49
7:52
7.48
0.93
8:03
13:56
Moonset
7.41
19:58
20:12
1.22
22:16
2:12
7.48
6:54
8:32
1.01
8:38
14:36
20:52
7.37
1.37
23:16
2:53
7.45
6:52
9:15
1.12
9:18
15:18
7.3
1.54
10:48
High tide
10:55
Sunset
16:55
Low tide
20:03
Moonrise
23:11
High tide
2:02
Sunrise
5:18
Low tide
6:47
Saturday 11 April
11:43
High tide
11:53
Sunset
17:50
Low tide
20:04
Moonrise
0:09
High tide
0:45
Sunrise
2:49
Low tide
6:16
Moonset
20:01
21:34
Friday 10 April
Moonset
19:59
Wednesday 8
April
9:59
7.41
6:56
Tuesday 7 April
Thursday 9 April
Time
13:17
1:34
Monday 6 April
Date
Sunday 12 April
12:42
Sunset
12:56
Low tide
18:50
20:06
Phase
Moonrise
7.41
High tide
Sunrise
1.24
Low tide
Moonset
7.23
High tide
Sunset
1.68
Low tide
Moonrise
7.36
High tide
Sunrise
1.33
Low tide
Moonset
7.16
High tide
Sunset
1.78
Low tide
Moonrise
7.34
High tide
Sunrise
1.36
Low tide
Moonset
7.13
High tide
Sunset
1.76
Low tide
Last
quarter
Moonrise
7.37
6:45
High tide
30
Tidal
height (m)
High tide
Sunrise
1.29
Low tide
Moonset
7.18
High tide
Sunset
Figure 15: Example of high and low tidal cycles showing both spring and neap tides for
Lorneville, New Brunswick. Shaded area represents an ideal sampling cycle (tidal height, time of
day). Example sampling period shown in Table 2 (above). Tide information taken from:
http://www.tide-forecast.com/locations/Lorneville-New-Brunswick/tides/latest
31
Appendix C: Summary table of sampling sites and times
Table 3: Summary table of sites, habitats and gears with estimates of sampling time, including
the commute from the city of Saint John, and number of personnel needed. Fyke net time for
sampling on Day 1, estimated at 10 minutes, is under the assumption that fyke net setup is done
alongside beach seining at that site. Time for sampling estimates marked with a * are based on
fyke net sampling setup in the salt marsh channel within close proximity to nearshore habitats
and could be combined within the same trip. Shaded areas represent sampling within salt marsh
channel.
Area
Zone
Habitat
Site
Map
Gear
Minimum
number of
personnel
Time for
sampling
(hours)
set up sampling Day 1
Zone 2
Nearshore
Five
Fathom
Hole
Black
Beach
7
Seine
Fyke net
6
Seine
MPA
Fyke net
Hepburn's
Basin
8
Outside MPA
Zone 1
9
2
Seine
Fyke net
Gooseberry
Cove
3
3
Seine
2-4
2
10min
2
2-3
2
10min
2
4-6
2
10min
2
3-5
10min
Fyke net
2
2
Day 2
Nekton/sentinel
2-3
Nekton
Nekton/sentinel
2-3
Nekton
Nekton/sentinel
4-5
Nekton
Nekton/sentinel
4-5
Nekton
Salt marsh
Hepburn's
Basin
8
Fyke net
3
2
1*
1-2*
Nekton
Salt marsh
Channel
10
Fyke net
Seine
3
2
2
2-3
3-5
2-4
Nekton
Nekton/sentinel
13
Fyke net
2
13
Fyke net
1-2*
Nekton
Dipper Nearshore
Harbour Salt marsh
Channel
3
Chance
Harbour Salt marsh
Channel
Nearshore
Salt marsh
Channel
12
Fyke net
12
Fyke net
Seine
11
Fyke net
11
Fyke net
32
10min
2
2
1*
2-4
2
2
10min
3
2
1-2*
2
1*
3-4
3
2
10min
2-4
Nekton
3
2
1*
1-2*
Nekton
Seine
Nearshore
Saints
Rest
Marsh
2
Data collection
Nekton/sentinel
Nekton
Nekton
Nekton/sentinel
Appendix D: Species list
Table 4: Species list of fish caught within and around Musquash MPA.
Class/Family
Species name
Common name
References
Ammodytidae
Ammodytes americanus
American sand lance
Arens 2007
Ammodytidae
Ammodytes sp.
sand lance
Ipsen 2013
Anguilidae
Anguilla rostrata
American eel
Ipsen 2013, Arens 2007, Gratto 1986
Atherinopsidae
Menidia menidia
Atlantic silverside
Ipsen 2013, Arens 2007, Gratto 1986
Clupeidae
Clupea harengus
Atlantic herring
Ipsen 2013, Arens 2007, Gratto 1986
Clupeidae
Alosa aestivalis
blueback herring
Arens 2007, Groto 1986
Clupeidae
Alosa pseudoharengus
alewife
Ipsen 2013, Arens 2007, Gratto 1986
Clupeidae
Alosa sapidissima
shad
Groto 1986
Cottidae
Myoxocephalus scorpius
shorthorn sculpin
Ipsen 2013, Arens 2007, Gratto 1986, Stevens
1997
Cottidae
Myoxocephalus aenaeus
grubby
Arens 2007
Cottidae
Myoxocephalus
octodecemspinosus
longhorn sculpin
Arens 2007
Cottidae
Cyclopteridae
Hemitripterus americanus
Cyclopterus lumpus
sea raven
lumpfish
Ipsen 2013, Arens 2007, Gratto 1986
Ipsen 2013, Arens 2007, Gratto 1986
Fundulidae
Fundulus heteroclitus
mummichog
Ipsen 2013, Gratto 1986, Stevens 1997
Fundulidae
Fundulus diaphanus
banded killifish
Gratto 1986
Gadidae
Microgadus tomcod
Altantic tomcod
Ipsen 2013, Arens 2007, Gratto 1986
Gadidae
Gadus morhua
Atlantic cod
Ipsen 2013, Arens 2007
Gadidae
Urophycis tenuis
white hake
Ipsen 2013, Arens 2007
Gadidae
Gadidae
Pollachius virens
Urophycis chuss
pollock
squirrel hake
Ipsen 2013, Arens 2007, Gratto 1986, Stevens
1997
Gratto 1986
Gasterosteidae
Apeltes quadracus
fourspine stickleback
Arens 2007
Gasterosteidae
Pungitius pungitius
ninespine stickleback
Ipsen 2013, Gratto 1986
Gasterosteidae
Gasterosteus aculeatus
Stevens 1997
Ipsen 2013, Arens 2007, Gratto 1986,
Gasterosteidae
Gasterosteus wheatlandi
threespine stickleback
blackspotted
stickleback
Osmeridae
Osmerus mordax
rainbow smelt
Ipsen 2013, Arens 2007, Gratto 1986
Pholidae
Pholis gunnellus
rock gunnel
Ipsen 2013, Arens 2007, Gratto 1986
Pleuronectidae
Limanda ferruginea
yellowtail flounder
Gratto 1986
Pleuronectidae
Pseudopleuronectes
americanus
winter flounder
Ipsen 2013, Arens 2007, Gratto 1986
Pleuronectidae
Liopsetta putnami
smooth flounder
Ipsen 2013, Gratto 1986
Salmonidae
Salvelinus fontinalis
brook trout
Gratto 1986
Scophthlmus
Scophthalmus aquosus
windowpane flounder
Arens 2007
Zoarcidae
Zoarces americanus
ocean pout
Gratto 1986
33
Ipsen 2013, Arens 2007
Appendix E: Nekton Sampling Sheet Template
Sampling Team:
Date:
Site Name:
Latitude:
Longitude:
Time:
Tidal height:
Gear:
Photographs taken:
Weather:
Comments:
Environmental parameters
Temperature ( ):
pH:
Salinity (PPT):
DO (mg/L):
Turbidity:
Species collected
Gear
Tow
Species
Length mm
(FL)
Sample preserved
Sentinel species
and labeled?
collected?
34
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