Quantifying Efficacy of Submersed Aquatic Vegetation Management

in the Sacramento-San Joaquin Delta

Micheal Finnell

Geography 342

Fall 2016

INTRODUCTION

The purpose of this study was to use consumer-grade hydroacoustics to map submersed aquatic vegetation (SAV) and

quantify percent change in biovolume during a herbicide treatment program in the Sacramento-San Joaquin River Delta

(hereby referred to as the Delta). The raw sonar files were processed using an online GIS algorithm, and the derived data

was downloaded and imported to an ArcGIS model. The model generated pre- and post-herbicide map products and

quantified the temporal/treatment change in SAV biovolume. An accuracy assessment was conducted using geo-tagged

photographs to reference areas of high SAV biovolume and compare with sonar-derived maps. The metrics produced by

this study will be used to guide future SAV management decisions in the Delta.

BACKGROUND

Submersed aquatic vegetation (SAV) is a term used to describe vascular plants that grow completely underwater except

for the flowering parts in some aquatic angiosperms. The Delta is host to many species of SAV, both native and invasive

(pers. obs.). The most dominant SAV in the Delta is Egeria densa, the Brazilian waterweed. E. densa is an invasive

macrophyte from Brazil that has been established in the Delta for approximately 30 years (CDBW 2001). This fast

growing weed clogs waterways and can create problems for boat navigation. Studies have also shown that this weed is

actually changing the structure of the Delta ecosystem by reducing both water flow and turbidity and creating habitat

that supports other invasive species (Santos et al. 2011).

Since 2001, the Department of Parks and Recreation Division of Boating and Waterways (DBW) has been designated the

state lead agency in controlling invasive aquatic plants in the Delta (Harbors & Navigation Code 64 & 64.5). Currently,

DBW is using a combination of hydroacoustic mapping, field surveys, and an herbicide treatment plan to monitor and

control E. densa and other invasive species such as curlyleaf pondweed (Potamogeton crispus), coontail (Ceratophyllum

demersum), and watermilfoil (Myriophyllum spicatum).

The sonar equipment used by DBW are consumer echo sounders and the data processed by a cloud-based algorithm

called Biobase (www.cibiobase.com). Biobase produces data on depth, SAV presence/absence, SAV height, bottom

hardness, and biovolume (Winfield et al. 2015). The Lowrance / Biobase combination has a distinct advantage over other

sonar systems for mapping aquatic vegetation with lower hardware and analysis costs as well as quicker processing

times (Radomski and Holbrook 2015). In addition, Biobase outputs are adjusted to Mean Lower Low Tide for consistency

across all measurements; an important feature when mapping tidal-influenced systems like the Delta. The service

provided by Biobase offers vegetation point data, kriged vegetation grids, default maps and tabular data that can be

viewed online or downloaded to the subscription holder. However, the default biovolume maps are portable network

graphic images which are not GIS-friendly and can only be assessed qualitatively. By acquiring the processed data

directly, I will be able to use ArcGIS to create SAV map products, quantify change in percent biovolume at treatment

sites, and provide a metric of treatment efficacy for the 2016 season.

METHODS

Study Sites and Survey Procedures

Hydroacoustic surveys were conducted in the legal Delta area (California Central Valley; UTM 627133.242E,

4216458.982N; 2424.5 surface acres). Twenty six sites were selected for treatment and mapping based on confirmation

of visual surveys for high densities of E. densa and other invasive SAV (Fig. 1). As per the herbicide treatment schedule,

all sites were scheduled for pre-treatment and post-treatment hydroacoustic surveys. Surveys were completed by

various DBW Aquatic Invasive Species Unit (AIS) staff using unit research vessels. The Delta is comprised and connected

by sloughs, riverine areas, and large shallow waterbodies such as Frank’s Tract. Large areas were gridded to ~ 30 meter

intervals for survey transects. In smaller slough and marina areas, transects followed the contours of the shoreline and

internal structure (ie. boat docks, tule islands) and ranged between 10 and 30 meters in width. Transects were

performed in water depths ranging from 1 to 7 meters as SAV are shallow-water plants not typically found deeper than 7

meters.

Data Collection and Biobase Processing

Acoustic and GPS data were obtained using Lowrance™ HighDefinition System (HDS®) consumer echosounders

(www.lowrance.com) connected to 200-Khz 200 tranducers mounted on the boat sterns. Settings for the echosounders

followed those recommended by Biobase (2013). The Lowrance unit’s internal global positioning system (GPS) was

differentially corrected using a wide-area augmented system (WAAS). The unit was set to collect 15 acoustic pings s -1 and

GPS coordinates collected every 1 ms-1. The acoustic and GPS signals were logged to a secure digital (SD) card in sl2 and

slg format.

Upon completion of a survey, the sonar data was uploaded to Biobase. The Biobase algorithm computed a plant height

and water depth for every ping, averaged the 15 pings, and assigned the mean value to the appropriate GPS coordinate.

These computed values are a proportion termed biovolume (plant height/water depth). The Biobase algorithm

interpolated these points to a raster grid by a process called kriging. The original vegetation point data and the raster

grids were downloaded from Biobase as text files in csv format.

Figure 1. Proposed Egeria densa treatment and hydroacoustic mapping sites for the 2016 season.

Egeria Tool and Map Products

The Egeria tool was created using ModelBuilder in ArcGIS 10.4.1 (ESRI 2011). The Egeria tool simultaneously uses pre-

and post-treatment raster grid text files as inputs. The tool projected the points into the NAD 1983 UTM Zone 10

Projected Coordinate System, preserved the outline shape of the point grid within the site boundary as a polygon, and

used the Spline with Barrier tool to create pre- and post-treatment raster grids. A raster calculator was used to

normalize the data for values above 1 and below zero. It is surmised that the tidal adjustment to the outputs variably

produced slightly inaccurate values at some points due to the distance of the nearest tide monitoring station. A

subsequent raster calculator subtracts the post-treatment raster values from the pre-treatment raster values and a

change raster is produced. Biovolume values that were present in one raster but not the other due to surveying

discrepancies were assigned NoData in the change raster. The mean values from each of these raster products were

multiplied by 100 to produce mean percent biovolume for treatment rasters and mean percent change for the change

raster. Map products were created from these Egeria tool outputs. In addition, a one-sided t-test was conducted on the

resulting data for overall percent mean change with 95% confidence intervals.

Accuracy Assessment

Due to time constraints, a simple accuracy assessment was instituted using a Panasonic Lumix TS4 12.1MP Waterproof

Digital Camera. Twenty-two geo-tagged photographs were taken of SAV ‘at or near’ the water surface (> 80%

biovolume) during the post-treatment hydroacoustic mapping effort at Franks Tract. The Python script tool, Geo-tagged

Photos to Points, was used to create a shapefile of the points and were overlaid on the final Franks Tract map for a

qualitative assessment of our biovolume data.

Results

Seventeen of the twenty-six E. densa treatment sites were mapped for pre- and post-treatment. A preliminary total of

~1053 surface acres were analyzed with the Egeria tool (Fig. 2). Four sites are still scheduled for post-treatment

hydroacoustic surveys and two sites were dropped from the treatment schedule. Franks Tract (Sites 173, 174, 175) had

no pre-treatment survey but was mapped for post-treatment. Owl Harbor (Site 20) had the greatest reduction in

biovolume with a mean of -29.25%, while Brannan Island (Site 22) had the greatest increase in biovolume with a mean of

38.43% (Fig. 2) Piper Slough (Site 107) was treated and mapped during two different periods: Phase I and Phase II. Piper

Slough Phase I had an increase in biovolume of 18.86%. Piper Slough Phase II had a decrease in biovolume of -17.33%.

Estimated mean changes for each of the 17 sites are shown in Table 1 and Figure 5. The overall mean for the 17 sites

was -7.65 + 8.44 percent biovolume reduction (t-test, t = -1.9209, df = 16, p = 0.07275).

The qualitative accuracy assessment results are shown in Fig 4. The geotagged photograph points correspond with areas

of high biovolume (>80%) on the Franks Tract post-treatment map.

Conclusion

The overall mean biovolume change between pre- and post-treatment mapping for all 17 sites analyzed in this study

seemed exceptionally low (~-8.0 %), as noted by many of our staff. However, this quantitative metric sets a baseline for

future comparisons and will provide data we can use to guide next seasons treatments. Four sites still remain to be

analyzed which could potentially change this statistic and remains to be determined. Examining these results from a

different perspective, 15 of 17 sites (~88 %) showed improvement and removing the two outliers, Brannan Island and

Piper Slough Phase I, the overall mean decreases further to ~-12 %. The Brannan Island site was definitely an exception

to the rule with almost a 40% increase in biovolume. Given proximity to the main river channel, tidal influence is strong

and most likely diluted the herbicide rendering the treatment ineffective. Like Brannon, Owl Harbor post-treatment

showed an increase of biovolume at the mouth of the slough near the main channel, however the site extends well

beyond the main channel and hydrologic flow probably decreases with distance in dead-end sloughs. Given these

assumptions, acquisition of a hydrological model for the Delta would be beneficial in further examination of the

variables affecting treatment efficacy.

The Egeria tool proved to be an effective intermediary between exported data from Biobase and the final map products,

automating and reducing the processing time. The limitation to the tool is raster cells from both pre- and post-treatment

rasters must overlap to provide a change value other , which is no fault of the tool but leads to the consideration of

Figure 2. The Egeria tool constructed in ArcGIS ModelBuilder 10.4.1. The tool processes text files downloaded from Biobase and computes mean change between pre- and post-treatment hydroacoustic surveys.

standardizing the hydroacoustic surveys to assure that both pre- and post- treatment sites are follow the same mapping

regime.

Considering future applications, hyperspectral imagery has been used for the past decade to map aquatic vegetation in

the Delta (Mulitsch and Ustin 2003, Santos et al. 2009). I believe our quantitative hydroacoustic data and map products

will prove useful for comparing with hyperspectral data, and validating the comparisons with field surveys to determine

the appropriate strategy to use with each technology.

Figure 3. Output from Egeria tool for sites 20 and 22, Owl Harbor and Brannan Island. Note that Brannan had a mean increase in biovolume possibly due to proximity to main river channel with high tidal influence. Similar trend observed in increased biovolume near the mouth of the main river channel for Owl Harbor.

Figure 4. Geo-tagged photos were taken in areas where SAV was visible at or just below water surface and correspond with high biovolume (>80%) presented in this raster grid of post-treatment Franks Tract.

Sources of Materials

Table 1. Site names, numbers, and mean percent change in biovolume. Data derived from change detection raster.

Figure 5. Site comparison ordered by percent biovolume change.

ESRI 2011. ArcGIS Desktop: Release 10.4.1 Redlands, CA: Environmental Systems Research Institute.

Lowrance high-definition system consumer echosounder, Lowrance,

12000 E. Skelly Dr., Tulsa, OK 74128. www.lowrance.com

Navico BioBase, Navico Inc., 2800 Hamline Ave. N #223, Roseville, MN 55113. www.cibiobase.com

Literature Cited

CALIFORNIA DEPARTMENT OF BOATING AND WATERWAYS. (2001). Environmental Impact Report for the Egeria densa

Control Program. CDBW, Sacramento, California.

Mulitsch, M., & Ustin, S. L. (2003). Mapping invasive plant species in the Sacramento-San Joaquin Delta region using

hyperspectral imagery. Report to the California.

Radomski, P. A. U. L., & Holbrook, B. V. (2015). A comparison of two hydroacoustic methods for estimating submerged

macrophyte distribution and abundance: a cautionary note. Journal of Aquatic Plant Management.

Santos, M. J., Anderson, L. W., & Ustin, S. L. (2011). Effects of invasive species on plant communities: an example using

submersed aquatic plants at the regional scale. Biological Invasions, 13(2), 443-457.

Santos, M. J., Khanna, S., Hestir, E. L., Andrew, M. E., Rajapakse, S. S., Greenberg, J. A., ... & Ustin, S. L. (2009). Use of

hyperspectral remote sensing to evaluate efficacy of aquatic plant management. Invasive Plant Science and

Management, 2(3), 216-229.

https://www.researchgate.net/profile/Maria_Santos20/publication/

232695806_Use_of_Hyperspectral_Remote_Sensing_to_Evaluate_Efficacy_of_Aquatic_Plant_Management/links/

02bfe512730ce3b715000000.pdf