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Assessment of the Abundance of Submersed Aquatic Vegetation (SAV) Communities in the Chesapeake Bay and its Use in SAV Management

Assessment of the Abundance of Submersed Aquatic Vegetation (SAV) Communities in the Chesapeake Bay and its Use in SAV Management

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K.A. Moore et al.

10.1 Introduction

Throughout many littoral regions of the Chesapeake Bay and its tributaries both direct observation and other evidence have indicated that broad declines of seagrasses

and other submersed aquatic vegetation (SAV) have occurred since the 1930s, with

precipitous declines beginning in the 1970s (Orth and Moore 1983a). These declines have been thought to be principally the result of increasing inputs of nutrients and sediments into the estuarine waters from the watershed and directly from

the atmosphere (Kemp et al. 1983, Twilley et al. 1985, Kemp et al. 2005). These

contribute to reduced light availability for plant photosynthesis by increasing water

column turbidity and periphyton fouling of the aquatic plant leaves (Neckles et al.

1993, Moore et al. 1996, 1997). Recent losses of SAV have not just been observed

in the Chesapeake Bay, but broad-scale declines attributed to human influences

have been documented in populations worldwide (Orth et al. 2006a, Ralph et al.


SAV is a highly valuable bay resource whose presence serves as an important indicator of local water quality conditions (Dennison et al. 1993, Batiuk et al. 2000).

Throughout most of the Chesapeake Bay SAV are currently found growing at water depths of 2 m mean low water (MLW) or less. Even in these shallow depths

high levels of nutrient and suspended sediments can decrease SAV growth and survival; and because SAV beds are non-motile, their presence or absence can serve as

an integrating measure of variable water quality conditions in local areas (Moore

et al. 1996, Kemp et al. 2005, Rybicki and Landwehr 2007). Research indicates that

the growth, survival and depth limits of SAV can be directly related to water column light levels (Duarte 1991, Dennison et al. 1993, Nielsen et al. 2002). Water

quality requirements for SAV growth are particularly crucial as barometers of the

health of the Chesapeake Bay littoral environment and because of the direct relationships between SAV and water quality (Kemp et al. 2005), trends in the distribution

and abundance of Chesapeake Bay SAV over time are very useful in understanding

trends in water quality and bay restoration in general (Batiuk et al. 2000, Kemp et al.


Because of the value of SAV in the Chesapeake Bay ecosystem and their apparent large scale declines, a SAV mapping program was instituted in the late

1970s to assess the status of the resource. Archived black and white photography available from agencies such as the U.S. Geological Survey, U.S. Department

of Agriculture Soil Conservation Service, National Oceanic and Atmospheric Administration and the Virginia and Maryland Departments of Highways was used

to develop a historical composite picture of a few selected areas dating back to

the 1930s (Orth and Moore 1983b). This provided the initial evidence that the

low abundances first observed in 1960s and continuing into the early 1970s in

all sections of the bay were likely unprecedented in recent bay history (Orth and

Moore 1983a). The intensity of the decline was greatest in upper bay and western tributaries, suggesting a direct link with watershed processes and watershed



Assessment of Chesapeake Bay SAV Communities and its Use in Management


10.2 The Aerial Photographic Mapping Process

The comprehensive aerial photographic mapping inventory of SAV in the Chesapeake Bay began in 1978 and has been conducted on an annual basis since 1984,

by the SAV Mapping Laboratory at the Virginia Institute of Marine Science (VIMS,

Gloucester Point, VA). The mapping project has been funded by a variety of state

and federal partners with the support of the Chesapeake Executive Council consisting of the Governors of Virginia, Maryland, Pennsylvania, the Mayor of the District

of Columbia and the United States Environmental Protection Agency (USEPA) Administrator. In the initial years, high resolution black and white, aerial photographs

were taken using 9.5 in. square negative Aerographic type 2405 or Aerochrome MS

type 2448 film at scales of 1:12,000 –1:24,000. Prints of these photographs were analyzed directly with analog interpretation techniques based on photo-interpretation

by a seagrass biologist (Orth and Moore 1983b). The bed outlines were then transferred directly to mylar, 7.5 min series, 1:24,000 scale, United States Geodetic

Survey (USGS) topographic quadrangles for area determinations and perimeter digitization. In addition to the boundaries of the SAV beds, estimates of percent cover

for each bed were visually classified into four categories using a standard scale

(Fig. 10.1) to estimate cover of the vegetation. A black and white film type was and

continues to be used for the delineations despite the potential advantages of normalcolor imagery for seagrass mapping (Pasqualini et al. 2001), due principally to the

finer grain, smaller storage requirements for scanned images, and lower cost. Currently Aviphot Pan 80 black and white film is used to obtain the images flown at

12,000 ft, yielding 1:24,000 scale photographs.

Guidelines for acquisition of aerial photography used in this monitoring program

were initially developed to address tidal stage, seasonal plant development, sun angle, atmospheric transparency, water turbidity, wind, sensor operation and sufficient

land features for geographic orientation (Orth and Moore 1983b) and these continued to be used to the present (Orth et al. 2006b). For example, for SAV in the

Chesapeake Bay: photography must be acquired at low tide, ±0–1.5 ft, as predicted

by the National Ocean Survey tables; imagery must be acquired when growth stages

ensure maximum delineation of SAV, and when SAV species phenologic state overlap is greatest; photography must be acquired when surface reflection from sun glint

does not cover more that 30% of frame; sun angle is between 20◦ and 40◦ to minimize water surface glitter; there is at least 60% line overlap and 20% side lap;

photography must be acquired during periods of no or low haze and/or clouds below the aircraft as well as no more than scattered or thin broken clouds, or thin

overcast above the aircraft to ensure maximum SAV to bottom contrast; turbidity

must be low enough that when viewed from the aircraft the SAV can be seen by the

observer; there should be little or no wind, with offshore winds preferred to onshore

winds when slight wind conditions cannot be avoided; photography must be acquired in the vertical mode with less that 5◦ tilt; scale, altitude, film and focal length

combination must permit resolution and identification of one square meter area of

SAV at the surface; each flight line must include sufficient identifiable land area to


K.A. Moore et al.

Fig. 10.1 Categories used for estimating density of SAV from aerial photography. Rows of squares

with black and white patterns represent three different arrangements of vegetated cover for a given

percentage. <10% = Category 1; 10–40% = Category 2; 40–70% = Category 3; 70–100% =

Category 4. (Reproduced from Moore et al. 2000, by permission)

assure accurate location of grass beds. These guidelines have become a standard for

mapping SAV (Dobson et al. 1995). Adherence to the guidelines assures acquisition

of photography under as optimal conditions as possible for detection of SAV, thus

ensuring accurate photo interpretation. Deviation from any of these guidelines requires prior approval by VIMS staff. Quality assurance and calibration procedures

are consistently followed. The altimeter is calibrated annually by the Federal Aviation Administration and the aerial camera is calibrated by USGS.

Camera settings are currently selected by automatic exposure control. Flights

are scheduled within a sun angle window of 20◦ – 40◦ to minimize sun glint in the


Assessment of Chesapeake Bay SAV Communities and its Use in Management


frame. In addition, the camera is equipped with a computer controlled intervalometer that establishes 60% line overlap and 20% sidelap providing duplicate coverage

for areas obscured by glint. An automatic bubble level holds the camera to within

one-degree tilt. The scale, altitude, film, and focal length combination is coordinated

so that SAV patches of one square meter can be resolved. Ground-level wind speed

is monitored with realtime data available on the web. Under normal operating conditions, flights are usually conducted under wind speeds less than 10 mph. Above

this speed, wind-generated waves stir bottom sediments, which can easily obscure

SAV beds in less than one hour. During the flight the pilot evaluates water clarity

conditions. During optimum flight conditions where the turbidity is sufficiently low

to permit complete delineation of the SAV beds, the shoals are clearly visible and

the pilot is usually able to distinguish bottom features such as SAV or algae.

Excessively turbid conditions generally preclude photography and the determination of optimum cloud cover level is based on pilot experience. Records of pilot

observation are kept in a flight notebook. Cloud cover below 12,000 ft is limited to

5% of the area covered by the camera frame, but a thin haze layer above 12,000 ft

is acceptable. Experience with the Chesapeake Bay has shown that optimal atmospheric conditions generally occur two to three days following passage of a cold

front, when winds have shifted from north-northwest to south and have moderated

to less than 10 mph. Within the guidelines for prioritizing and executing the photography, the flights are planned to coincide with these atmospheric conditions where

possible. A 9-inch by 9-inch, black-and-white contact print is produced for each

exposed frame and reviewed by a scientist/photointerpreter to determine if each

Fig. 10.2 A Typical aerial image used for mapping with arrows indicating several areas of dark

SAV signatures near the island


K.A. Moore et al.

flight line is suitable for SAV delineation. Each photograph is labeled with the date

of acquisition as well as the flight line number and frame number (Fig. 10.2). Film

and photographs are stored under appropriate environmental conditions to prevent


Currently the Chesapeake Bay SAV aerial photography (Orth et al. 2006b) consists of 173 flight lines, which cover approximately 3,800 flight line km (Fig. 10.3).

These flight lines are positioned to include all areas known to recently or historically support SAV, as well as other areas of appropriate depths of less than 2 m

mean low water (MLW) that have the potential for SAV growth. Typically, the flight

lines are similar from year to year so as to provide a consistent image base. Flight

lines are prioritized by sections and flights timed to occur during the peak growing

season of the SAV species known to occur in each section. Specific areas known to

have had significant SAV coverage are given a high priority. Higher salinity seagrass

dominated regions in the lower bay are generally flown during May through June.

Here, the dominant seagrass species, eelgrass (Zostera marina), reaches maximum

biomass during this late spring-early summer period (Moore et al. 2000). Mid-bay

Fig. 10.3 Chesapeake Bay and coastal bays annual aerial photography flight lines. Solid lines

indicate flightlines


Assessment of Chesapeake Bay SAV Communities and its Use in Management


and upper bay areas that are dominated by a mix of freshwater and oligohaline tolerant species which reach peak biomass in the late summer (Moore et al. 2000) are

flown later.

10.3 Orthorectification and Mosaic Production

Scanned aerial photography negatives are georectified and orthographically corrected to produce a seamless series of aerial mosaics following standard operating

procedures. Leica LPS image processing software (Leica Geosystems GIS & Mapping, LLC. Atlanta, Ga. 2005) is used to orthographically correct the individual

flight lines using a bundle block solution. Camera lens calibration data is matched

to the image location of fiducial points to define the interior camera model. Control

points from USGS DOQQ images provide the exterior control, which is enhanced

by a large number of image-matching tie points produced automatically by the software. The exterior and interior models are combined with a 30-m resolution digital

elevation model (DEM) from the USGS National Elevation Dataset (NED) to produce an orthophoto for each aerial photograph.

The orthophotographs that cover each USGS 7.5 min quadrangle area are adjusted to approximately uniform brightness and contrast and are mosaicked together

using the ERDAS Imagine mosaic tool to produce a one-meter resolution quad-sized


10.4 Photo-Interpretation and Bed Delineation

The SAV beds are interpreted on-screen from the orthophoto mosaics using commercial GIS software and a custom tool, which includes editing palettes, that was

developed to facilitate the process. The identification and delineation of SAV beds

by photo interpretation utilizes all available information including: knowledge of

aquatic grass signatures on film, distribution of SAV from aerial photography,

ground survey information, and aerial site surveys. In addition to delineating SAV

bed boundaries, an estimate of SAV density within each bed is made by visually

comparing each bed to an enlarged crown density scale (Fig. 10.1) similar to those

developed for estimating forest tree crown cover from aerial photography (Paine

1981). Bed density is categorized into one of four classes based on a subjective

comparison with the density scale. These are: 1, very sparse (<10% coverage); 2,

sparse (10–40%); 3, moderate (40–70%); or 4, dense (70–100%). Substantial sections of larger beds that differ in density are delineated separately. Either the entire

bed or sections within the bed are assigned a bed density number (1–4) corresponding to the above density classes. Additionally, each distinct SAV unit (bed or bed

section) is assigned an identifying one or two letter designation unique to its map.

Coupled with the appropriate SAV map number and year of photography, these one

or two letter designations uniquely identify each SAV bed in the database.


K.A. Moore et al.

Interpreting the outer, deeper edges of the SAV beds can be problematic especially in turbid systems. Mount (2003) has determined that the detection depth of

SAV bed boundaries is approximately 60% of the in situ water transparency secchi

depth. Typically, SAV in the Chesapeake Bay are found growing below mean sea

level to depths equal to 100% of the local secchi depth (Dennison et al. 1993), which

in the Chesapeake Bay commonly ranges from 0.5 m to 2.0 m. Given tidal ranges

throughout the bay of approximately 0.5–1.0 m, aerial photography taken around the

low tidal stage is usually sufficient to identify the deeper bed boundaries (Fig. 10.4).

Local constraints such as wind generated turbidity or phytoplankton blooms can obscure the evidence of SAV in some areas; however, most SAV boundaries can be

mapped with precision. Other constraints such as weather patterns, including summer

atmospheric haze and restricted fly zones, typically provide a number of challenges

for the acquisition of imagery suitable for mapping SAV. Timely and direct communication between the aerial photography contractor and the SAV mapping program

scientist is critical in directing the aerial photography missions to the most appropriate flight lines for the local conditions. Strict adherence to mission constraints

as well as pilot and other mission personnel experience and knowledge of the SAV

natural resource also are extremely important in the acquisition of useful imagery.

Fig. 10.4 SAV beds on aerial black and white photograph showing photointerpreted bed boundaries and individual bed numeric density category (1–4) classifications

10.5 Ground Survey Sampling

Ground survey information is collected annually by a variety of partners including

researchers, state and federal management agency personnel, and trained individuals

including private citizens and non-profit groups. The data are submitted in a variety


Assessment of Chesapeake Bay SAV Communities and its Use in Management


of formats including direct correspondence, transfer of GIS data files, and an interactive website. These reports of species presence and abundance and location

are reviewed by scientific personnel at VIMS, tabulated and entered into a SAV

geographic information system database. Based on eleven years of ground survey

information from 1985 to 1996 Moore et al. (2000) were able to identify four distinct species associations (ZOSTERA, RUPPIA, POTAMOGETON, FRESHWATER MIXED) that were distributed throughout the Bay and its tidal tributaries

principally by decreasing salinity regimes (Table 10.1).

Evaluation of the how well the photo-interpreted density classification (Fig. 10.1)

represents actual SAV coverage has been investigated using transects consisting

of point-intercept sampling by divers made across a range of SAV beds of different densities and species at 35 locations throughout the Bay system (Moore

et al. 2000). These ground survey cover measurements were then compared to the

photo-interpreted density class zones comprising each sampling area (Fig. 10.5).

This relationship indicates that the photo-interpreted density class zones provide

good measures of SAV abundance with a slight under estimate of SAV abundance

by photo-interpretation in lower density areas, and over estimate in higher density areas. No effects of community type or depth of SAV growth on the relationship between measured ground cover and density class assignment could be

determined. Therefore, the photo-interpreted density classification is applicable

throughout the Bay system. Ground survey field measurements of SAV bottom cover

Table 10.1 Chesapeake Bay SAV Communities. Species occurrence in community exceeds 10%

of species observations. Reprinted with permission from Moore et al. 2000

ZOSTERA Community

Zostera marina∗

Ruppia maritima

RUPPIA Community

Ruppia maritima∗

Potamogeton perfoliatus

Potamogeton pectinatus

Zannichellia palustris


Potamogeton perfoliatus∗

Potamogeton pectinatus∗

Elodea canadensis

Potamogeton crispus


Myriophyllum spicatum∗

Hydrilla verticillata∗

Vallisneria americana∗

Ceratophyllum demersum

Heteranthera dubia

Najas minor

Elodea canadensis

Najas guadalupensis

Potamogeton crispus

Najas gracillima

Potamogeton pusillus

∗ Dominant



K.A. Moore et al.

Fig. 10.5 Comparison of SAV aerial density classifications to ground survey measurements.

(Reproduced from Moore et al. 2000 by permission)

have previously been demonstrated to provide very good estimates of SAV density

and biomass (r2 > 0.86; Orth and Moore 1988), and therefore the combination of

ground survey information, aerial photography and density classification has been

used to quantify both current as well as historical SAV community biomass throughout the growing season of multiple years (Moore et al. 2000).

10.6 Mapping Historical SAV Beds

To develop reasonable SAV restoration targets and to formulate the strategies for

achieving these targets, it is necessary to first identify the potential for SAV restoration. Some shallow areas that may meet SAV water quality requirements are subject to high currents and wave activity or contain sediments that are very high in

organic content and may not have a high potential for SAV growth (Koch 2001).

Identification of those areas with previous evidence of SAV growth is an important

step in quantifying that potential. In addition, because of the direct relationships

between SAV and water quality, especially nutrient levels and water clarity, trends

in the distribution and abundance of SAV over time are also very useful in understanding trends in water quality. Initial reviews of photographic evidence from a

number of sites dating back to 1937 suggested that SAV, once abundant throughout the Chesapeake Bay system, had declined from historic levels (Orth and Moore

1984) and therefore water quality conditions may have similarly deteriorated (Orth

and Moore 1983b). Although the absence of SAV on historical aerial photographs


Assessment of Chesapeake Bay SAV Communities and its Use in Management


does not necessarily preclude SAV occurrence, SAV signatures are strong supporting evidence for the previous occurrence of SAV (Orth and Moore 1983b).

Photographic databases ranging from the 1930s through the early 1970s were

analyzed to develop a comprehensive evaluation of historical SAV abundances

throughout all littoral areas of the bay to serve as goals for SAV and water quality

restoration (Naylor 2002, Moore et al. 1999, 2001, 2003b, 2004). Key photographic

databases, including those of the Virginia and Maryland Departments of Transportation, local city and county photographic archives, National Oceanic and Atmospheric Administration (NOAA), United States Department of Agriculture (USDA),

United States Geological Survey (USGS), and the Virginia Institute of Marine Science (VIMS) archives as well as other published reports, were initially searched

by direct visits to local, state and federal repositories to view paper prints and color

transparencies for photography and other documentation relative to SAV ground survey information. Web-based USGS and NOAA databases were also searched online

using a web browser. Photographs that contained images of SAV were purchased

and then scanned, photo-interpreted and digitized. Photo-interpretation of the selected aerial photographs followed as closely as possible the methods currently used

to delineate SAV beds throughout the Chesapeake Bay in the annual aerial mapping

SAV surveys (e.g., Orth et al. 2006b).

Initial screening of photographic prints was accomplished by viewing under a

10X magnification viewer. Each print was searched for SAV signatures, and the

quality of the imagery for SAV delineation was estimated as “Good,” “Fair,” or

“Poor.” Those prints that showed some evidence of SAV signatures were scanned


image processing

at a resolution of 600 dpi and viewed using ERDAS Imagine


The aerial photography that was determined to have SAV signatures was processed using a heads-up, on-screen digitizing system. The system increases accuracy

by combining the series of images into a single geographically registered image

permitting the final SAV interpretation to be completed seamlessly in a single step

(Fig. 10.6). In addition, the images are available digitally and can be printed along

with the interpreted lines to show the precise character of the SAV beds.

The standard 9 inch × 9 inch, 1:24,000 scale black and white historical aerial

photographs, were scanned at a resolution of 600 dpi, forming pixels approximately

one meter in width. This was the minimum resolution required to accurately delineate SAV beds and resulted in files that were approximately 30 megabytes in

size. The scanned images were then transferred to a Windows 2000 workstation for


(ERDAS, Atlanta, Ga.). Horizontal conregistration using ERDAS Orthobase

trol was taken from USGS digital orthophoto quarter quads (DOQQ) and USGS

1:24,000 scale topographic quadrangles. USGS DEMs for the region were merged


and used for vertical control. The Orthobase software combined both sources of

control with a set of common “tag” points that were identified on pairs of photos

to generate a photogrammetric solution and orthorectify the images, producing a

single geographically corrected product that was used for interpretation. The total

RMS error for the solution varied among images from 2.6 m to 4.1 m with a mean

of 3.5 m.


K.A. Moore et al.

Fig. 10.6 Composited 1953 historical photographs of SAV along the northern shoreline of the York

River, Va. Lines indicate photo-interpreted SAV bed polygons

SAV bed outlines were traced directly from the combined image displayed on the

computer screen into a GIS polygon file. The image scale was held fixed at 1:12,000

and line segments for polygons characterizing the beds were set to be no shorter than

20 m to maintain consistency with previous historical SAV surveys. The interpreted

boundaries were drawn to include all visible SAV areas regardless of patchiness or

density (Fig. 10.6).

A variety of historical aerial photographic images were located and reviewed,

however the quality of the imagery for determination of SAV abundance ranged

from good to poor. As previously described, a number of criteria must be met for

acquisition of aerial photographs that are optimum for delineation of estuarine SAV

(e.g., Orth and Moore 1983b, Orth et al. 2006b). Most imagery used for historical SAV analyses was obtained for other purposes, usually land use or farming

analyses, and therefore, while criteria for atmospheric conditions were usually met

(e.g. sun elevation, atmospheric transparency, etc.), those important for SAV delineation (e.g., tidal stage, water transparency, plant growth stage) may not have been

met. In addition, while standard black and white, and color photographs are useful

for SAV delineation (Orth and Moore 1984) other film types such as infrared or

color infrared photography, which effectively delineates upland vegetation, are less

useful in delineating submerged vegetation because of the rapid absorption of the

infrared wavelengths of sunlight in water.

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