Senior Thesis-FINAL

The Health Status of Disturbed and Undisturbed Non-‐Saline Estuaries: A CRAM-‐based assessment

By, Eria E. Garnica

Senior Thesis

Dr. Jeffery A. Foran

May 14, 2014

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Table of Contents Page Title Page 1

Abstract 3

Introduction

Objective 3

Approach 5

Significance 6

Methods 7

CRAM Field Book description 9

Buffer and Landscape 9

Hydrology 10

Physical Structure 11

Biotic Structure 12

Results 13

CRAM Scores 13

Graphs, Tables, Maps, Figures 19

Discussion 30

References 34

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Abstract

This senior project analyzes and compares two perennial, non-‐saline

estuaries in California by using the California Rapid Assessment Method for Wetland

(CRAM) to signify the differences between undisturbed and disturbed estuaries.

The California Rapid Assessment Method, is used to rapidly assess wetland

ecological features for water purification and influencing wildlife habitat. These

four attribute are used to comparatively analyze the variation between disturbed

and undisturbed estuarine wetlands. CRAM is a useful reference tool to evaluate

quick results for the health status of California Wetlands.

Introduction Objective

Estuaries are valuable, complex ecosystems that filter contaminants,

pollutants, solids, wastes, pesticides, and other urban runoff. They also stabilize

shorelines from erosion, decrease the effects of coastal storms, and increase aquatic,

terrestrial biodiversity. Estuaries are significant because they create habitats for

fish and wildlife, including threatened or endangered species listed. Currently,

perennial non-‐saline estuaries in California suffer from sea level rise, salt-‐water

intrusion, and other human impacts. Most signs of human disturbance degrade

wetlands services and functions, particularly fish and wildlife habitats (Parker et al

2011). Today, scientists have acknowledged a 91% loss of California wetlands, and

only 44,456 acres of estuaries remain (CA State of Wetlands Report 2010). As a

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result, the state has made wetlands restoration a priority in California. The

California Wetlands Conservation Policy (executive order W-‐59-‐93) explains the

course of action for restoring, monitoring, and protecting California wetlands under

state agencies, public and private partnerships, and the federal government (Snow

2010).

Disturbed and undisturbed wetlands are both affected by sea level rise increasing

salt-‐water intrusion into the freshwater and brackish marshes. Salt-‐water intrusion

could shift the wetland composition by decreasing freshwater plant species to salt

tolerant plant species. Recent studies state and increase in sea level rise results a

shift in the salinity gradient, and a dramatic decrease in San Francisco Bay-‐Delta’s

tidal marsh biodiversity (such as, Sarcocornia pacifica, Spartina foliosa, and Distichlis

spicata), (Mall 1969). Also, the increase in carbon dioxide will affect soil carbon

storage, soil nutrient cycling, plant respiration, rates of decomposition, mycorrhizal

symbionts, and herbivory (Parker et al 2011). These freshwater estuarine values

(wetland composition structure) take part in the water purification cycle (wetland

function). The ecological processes include chemical, physical, and biological

processes that all take part in the water purification cycle (Kadlec 1996). In

addition to the water purification cycle, system components include plants, soils,

detritus, bacteria, protozoa, water levels, depth, temperature, dissolved oxygen, and

pH (Sherwood et al 1995).

This project will analyze and compare two restored CA freshwater

estuaries (Rush Ranch Estuary and Arroyo Burro Estuary) and their health status by

using the California Rapid Assessment Methods (CRAM) along with quantitative

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data for correlation. Non-‐saline estuaries are I hypothesize that there are significant

differences between the performance standards of disturbed and undisturbed, non-‐

saline estuaries located in California. CRAM is a cost-‐effective way to rapidly assess

the health status of California wetlands. CRAM, uses a grading rubric with a series of

four scores that indicate the total score for the wetland health status. This method

assists scientists and researchers in understanding what actions need to be

addressed to improve wetland restoration.

The California Rapid Assessment Methods for wetlands consists of three-‐

tiered assessment levels from the California Wetlands. The three-‐tiered assessment

levels correlate one another by showing a more in-‐depth contextual understanding

of the overall estuarine wetland condition (Solek, Stein, and Sutula 2011). Level One,

Landscape Assessment, consists of using remote sensing data and field surveys in an

inventory database that is created by the California State Resources Agency. Level

two, Rapid Assessment, includes assessing wetland conditions by using field

diagnostics and existing data. Level three, Intensive Site Assessment, consists of data

that validates the CRAM results along with exemplifying the condition. Receiving

validation on the CRAM results for the study sites is a very important analytical step

to assess the estuarine wetland health status.

Approach

There are four different attributes that this project will focus on to score the

perennial, non-‐saline estuaries: buffer and landscape, hydrology, physical structure,

and biotic structure. Attribute 1: Buffer and Landscape includes A: an evaluation of

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the landscape context, B: Assessment Area and buffer width, C: buffer condition.

Attribute 2: Hydrology includes A: water source, B: hydroperiod, C: hydrologic

connectivity. Attribute 3: Physical Structure consists of A: structural patch richness,

B: topographic complexity. Attribute 4: Biotic Structure A: number of plant layers.

B: number of co-‐dominant plant species, C: invasive plant species, D: horizontal

interspersion, E: vertical biotic structure.

I will compare disturbed and undisturbed perennial, non-‐saline estuaries in

California. By evaluating the CRAM scores for each freshwater estuarine marsh, I

will be able to distinguish the differences between disturbed and undisturbed

estuaries. I predict natural estuaries will have a higher CRAM scores because they

have fewer environmental impacts disrupting the wildlife habitat.

Significance

The results from this project may be used to support better restoration and

mitigation planning in the future. The Society for Ecological Restoration (SER) states,

“Ecological restoration is the process of renewing and maintaining ecosystem health

(SER Board of Directors, 1995).” Ultimately, this method can be a cost-‐effective way

to rapidly assess the health status of California wetlands.

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Methods

I chose two perennial non-‐saline estuaries as my samples from the E-‐CRAM

state database, one high quality and one low quality score. I evaluated their health

status by using CRAM; The California Rapid Assessment Method for Wetlands,

perennial Estuarine Wetlands Field book, version 6.1. The scores will be in numeric

form this includes, 12/12, 9/12, 6/12, or 3/12. The two non-‐saline estuaries were

chosen because of their documented CRAM scores that are based on high and low

quality scores, and they are available on Eco-‐Atlas’s website. The documented

CRAM scores clarify problem areas of the non-‐saline estuaries. The problem areas

allow scientists to analyze their significant environmental impacts, disturbance

levels, and artificial inputs. This project focuses on comparing the differences

between disturbed and undisturbed estuaries by using CRAM to distinguish the

variation in their health status. Undisturbed and disturbed wetlands are

comparatively analyzed from their ecological processes, system components,

topographic complexity features, and what they are mainly intended for.

Undisturbed wetlands are the perfect reference wetlands that are used to compare

the function too since they have not experienced moderate to high levels of

degradation (net loss in abotic factors).

I conducted this California Rapid Assessment Methods with a professional

Senior Wetland Ecologist/Botanist, Mr. Russell Huddleston. Mr. Huddleston is a

trained professional in the California Rapid Assessment Methods for Wetlands and

he helped me with assessing and receiving accurate data. The line transects

extended 250 meters north, south, west, and east in the Assessment Area and Buffer

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(figure 1). All line transects extended the 250 meters without any interruptions by

unnatural inputs or disturbances.

Two sites that were chosen for this project are: Rush Ranch Estuary and

Arroyo Burro Estuary. Rush Ranch Estuary is located Southern Solano County, CA,

latitude 38.211529 and -‐122.029459 longitude. Rush Ranch Estuary occurs in the

upper western portions of the Suisun Slough (Vasey et al 2012). This tidal marsh is

located within the San Francisco Bay. The Arroyo Burro Estuary is located in the

Santa Barbara Region near Mesa Creek, latitude 34.40473°N, and longitude -‐

119.73982°W. Down below in map1 shows the locations of the two wetlands used

for this senior project.

Figure 1. Two CA freshwater estuarine wetlands

(Google Earth)

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Perennial Estuarine Wetlands: Field Book ver. 6.1

I. CRAM Field Book:

The CRAM field book includes four attribute sections that make up the

grading rubric and total numeric scores. The CRAM scoring sheet for perennial

estuarine wetlands is located after the four attribute terms. Each attribute score can

provide significant information about effects or environmental impacts. If the score

is low, one can analyze the reasoning behind the low score, and influences that could

result in environmental impacts, artificial inputs, or newly restored plant species.

By using the CRAM field book, scientists can rapidly assess individual wetlands and

rate their health status.

II. Buffer and Landscape:

The buffer and landscape attribute section consists of four parts, this aquatic

area abundance; buffer sub-‐metric A: percent of Assessment Area with Buffer;

buffer sub-‐metric B: average buffer width; and last buffer sub-‐metric C: buffer

condition. All these sections under the Buffer and Landscape attribute section are

significant towards calculating the final attribute score.

The aquatic area abundance is a spatial region that has aquatic corridors (e.g.

rivers, streams, and channels) in the landscape. Line transects are scored from the

number of times aquatic corridors are crossed by line transects.

The buffer sub-‐metric A: percent of AA with buffer is the buffer joining the

Assessment Area (AA). The buffer is 5 meters wide and extends along the perimeter

of AA. The buffer percent is how long the line transects could extend without

interruption. The wetland buffer is not continuous with buffer breaks: golf courses,

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commercial developments, fences, intensive agriculture, parking lots, railroads,

residential areas, sound walls, sports fields, urbanized parks, pedestrian side walks

and trails (very active), bike and foot trails (not very active), horse trails, natural

upland habitats, wild-‐land parks, land and pastures, railroads (only 2 trains a day),

swales and ditches, and vegetated levees.

The sub-‐metric B: average buffer width, consists of required measurements

for the buffer width. For example, if the buffer width is 5 meters or less then it

cannot be considered a buffer width. In addition, open water is not included in the

buffer width calculations.

The sub-‐metric C: buffer condition, includes the disturbance levels along with

plant species. The three categories of plant species include California natives, non-‐

natives, or invasive plant species in the buffer. The disturbance levels are rated by

soil compactions, level of human disturbance, and the presence or absence of a

buffer.

III. Hydrology:

The hydrology attribute section consists of three sections that make up the

total hydrology score, such as water source, hydro-‐period, and hydrologic

connectivity.

Water source is the extent, duration, and frequency of hydrologic regimes in

the Assessment Area. Undisturbed estuaries are recharged naturally by

precipitation, tidal inflows, and watershed runoff. Disturbed estuaries are

recharged by water pumps, and the hydrologic dynamics are controlled by storm

drains, weirs, dams, and grade control structures.

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The hydro-‐period discuses the frequency and duration period of water

saturation and inundation. The water levels in undisturbed estuaries vary through

out the year because of the four seasons. However, disturbed estuaries may be

affected by tide gates, culverts, open channels, water pumps, rip-‐rap, and bridges.

The hydrologic connectivity describes the water flow of the estuary. The

water flow includes inflows and out flows of the wetland. The restrictions on the

hydrologic connectivity consist of levees, dikes, and road grades..

IV. Physical Structure:

The physical structure consists of two sources that make up the total physical

structure score. The two sources are structural patch richness and topographic

complexity.

The structural patch richness includes the following characteristics:

abundant wrack or organic debris in channel or on floodplain, animal mounds and

burrows, bank slumps or undercut banks in channels, debris jams, filamentous

macro-‐algae and algal mats, large woody debris, non-‐vegetated flats, pools on

floodplains, plant hummocks or sediment mounds, point bars and in-‐channel bars,

pools or depressions in channels, secondary channels, shellfish beds, soil cracks,

standing snags, and submerged vegetation.

Topographic complexity describes how complex the estuary is. The

topographic complexity characteristics consist of micro and macro topographic

relief, elevation gradients, and how the tidal channels are formed. The topograghic

complexity is a way to see potential for restoration work.

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V. Biotic Structure:

The biotic structure consists of five different parts that make up the total

score for the attribute section. The five parts are, plant community sub-‐metric A:

number of plant layers, plant community sub-‐metric B: number of Co-‐dominant

species, plant community sub-‐metric C: percent invasion, horizontal interspersion,

and vertical biotic structure.

Under the plant community sub-‐metric A, includes the number of plant

layers present in the Assessment Area. The number of plant layers must consist of

at least 5% cover to be considered a plant layer. If the Assessment Area (AA) holds

less then 5% plant layers, has no plant layers, or has artificial inputs, it will receive a

“D” score. The artificial inputs that could cause a “D” score are rip-‐rap, concrete, or

newly transplanted plants.

Sub-‐metric B: number of Co-‐dominant species is the percent cover of a plant

species that only constitutes 10% in the AA. In section sub-‐metric C: percent

invasion is for invasive plant organisms in plant layers.

The last two features in the grading rubric are horizontal interspersion and

vertical biotic structure. The horizontal interspersion is an overview of the AA

including vegetation layers. The vertical biotic structure is an interspersion and

complexity of plant layers.

The results will consist of the “scoring sheet: perennial estuarine wetlands”

for the two non-‐saline estuaries (Rush Ranch and Arroyo Burro). Each attribute

section is a component of a functional assessment that estimates the whole

landscape context of the wetland. The results will include numeric scores that will

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focus on problem areas. The scores will give relevance toward explaining the health

status and performance standards for each estuarine wetland. The health status

will determine the difference between these two perennial freshwater marshlands.

By using the scores as a guide, one can refer to the environmental effects and

artificial inputs that could alter the wetland composition and its function. For

example, a low score under the hydrology section can indicate unnatural inputs or

human disturbance. In addition, the problem areas will be supported by

quantitative data to correlate the California Rapid Assessment Method scores.

Results

The results show a distinct difference in two attributes, hydrology and biotic

structure while the other two attributes did not show enough variation (Graph 1).

The graphical approach was used to show variation between the two estuaries and

their attributes (Graph 1) furthermore the two estuaries were compared with

California non-‐saline estuaries by their total CRAM scores (Graph 2). The results

also included information on the biodiversity that occurs at Rush Ranch (Table 3),

and newly restored plant species that were transplanted in the Arroyo Burro

Estuary streambed (Table 4).

CRAM Scores

The scoring for Rush Ranch estuary has two different scores that consist of

documented scores from Eco-‐Atlas and my own scores that I conducted with Mr.

Huddleston a trained professional in the California Rapid Assessment Methods for

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Wetlands (CRAM field book 2013). The scores for Arroyo Burro Estuary are

documents from the Eco-‐Atlas. However there is a lack of information in regards to

specific locations of the Assessment Area (AA) and Buffer during the CRAM. With

out a map showing the location of the AA and Buffer it would be difficult to spot the

problem areas.

Buffer and Landscape Context

Attribute Aquatic Area Abundance: Rush Ranch Estuary scored a “12/12”

while Arroyo Burro Estuary scored a “9/12” (Table 1). Not enough variation

between the two study sites for this attribute. Rush Ranch has rich aquatic

corridors (Figure 2 and 3). However, Arroyo Burro Estuary had a higher score than

predicted because it is surrounded by urbanization and lacks aquatic corridors

(Figure 4). There is no documented maps showing the Assessment Area or Buffer,

and trying to indicate if the line transects crossed aquatic corridors is an issue.

Attribute Percent of Assessment Area with Buffer: Rush Ranch Estuary

received “12/12” while Arroyo Burro Estuary received “9/12” (Table 1). There is no

variation between the two estuaries.

Attribute Average Buffer Width: Rush Ranch Estuary scored a “12/12”

compared to Arroyo Burro “9/12” (Table 1). The results showed no variation

between the two study sites.

Attribute Buffer Condition: Rush Ranch Estuary resulted a “12/12” while

Arroyo Burro Estuary scored a “9/12” (Table). There was not enough difference

between the two estuaries. Results have shown that this attribute along with the

other physical structure attributes, show no importance of the buffer condition,

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percent, width, or aquatic abundance areas. Since, an undisturbed wetland can have

no difference in buffer scores compared to a highly disturbed wetland. Results,

specifies the dependence on mapping the buffer and assessment area location in the

study site.

Hydrology

Attribute Hydrologic Connectivity: Rush Ranch Estuary received a “12/12”

compared to Arroyo Burro Estuary “6/12” because of unnatural inputs (such as

levees, dikes, and road grades) that count for 50-‐90% of the wetland in the

Assessment Area (Graph 1 and table 1). The results demonstrated a difference

between the two estuaries in the hydrologic connectivity. The changes that were

made to restore the Arroyo Burro Estuary’s streambed included an open new

channel, slope, levees, vegetation, dikes, and removal of a 300ft. concrete culver that

all contribute into lowering the hydrology score (URS 2014). While Rush Ranch

Estuary has several secondary and primary tidal channels resulting in a rich aquatic

corridors (Figure 2 and 3).

Attribute Hydro-‐Period: Rush Ranch Estuary scored a “12/12” while Arroyo

Burro Estuary received an “12/12.” There is no difference between the two study

sites in this attribute section. The hydro-‐period score for Arroyo Burro Estuary was

higher than predicted however, this shows great streambed restoration planning.

The first year of monitoring the Arroyo Burro Estuary, have shown a 57% of

abundance in California native plant cover, and a 80% survival rate for newly

restored plants species (native and non-‐native plant species) (Kisner 2007). Since

there was an increase in relative abundance it results in a high score for the hydro-‐

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period attribute. Changes in channel morphology, drainage network density, and

the relative abundance of plants could raise the hydro-‐period attribute score (CRAM

dictionary 2013).

Attribute Water Source: Rush Ranch scored a “12/12” while Arroyo Burro

scored a “6/12”. These scores specify a difference between the two estuarine

wetlands. Arroyo Burro Estuary consists of urban runoff, direct irrigation, storm

drains, and regulated water releases controlled by a large reservoir within 2km

upstream of the Assessment Area (CRAM field book 2013). Recent studies have

shown fecal coliform concentrations in the Arroyo Burro watershed, Vs =4/17E-‐6

for the average settling velocity of fine grain sediments, sediment resuspension rate

Rt= 0 kg/m2s summer versus 5.49E-‐4 kg/m2s winter, and total suspended solids

concentration TSS= 0.3 kg/m3s summer and 1.5 kg/m3s winter (Steets et al 2003).

The Arroyo Burro Estuary is under the “Water Quality Limited segments in the

Clean Water Act Section 303-‐(d) List” and Arroyo Burro was reported in 1999 as

4E6 and 8E6 MPN/m3 while the “California’s Single Sample Standard for fecal

coliforms in recreational water regions should not exceed 4E6 MPN/m3 ”(Sercu et al

2008). Other studies sampled the pH and dissolved oxygen levels of Arroyo Burro

Estuary: pH= 8.2 drain, 7.9 creek, 8.0 lagoon, and 8.2 surf zone; dissolved oxygen=

8.4 surf zone, 13.4 lagoon, 8.8 drain, and 7.8 creek (Sercu at al 2008). Rush Ranch

however has no signs of human disturbance or water pollution that occurs in the

estuary.

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Physical Structure

Attribute Structural Patch Richness: Rush Ranch Estuary resulted in a “ 3/12”

while Arroyo Burro received a “9/12” (Table 1). Rush Ranch Estuary resulted in a

lower score compared to Arroyo Burro Estuary this indicates only two or less

structural patch richness features that occurred in this study site. However, the

score I received was “6/12” for Rush Ranch Estuary indicating four out of sixteen

structural patch richness features, and we found organic debris in the channel, bank

slumps, depressions in channels, and secondary channels (Table 1 and figure 2).

These scores could result from the choosing of the Assessment Area and Buffer

locations because the wetland composition could vary through out the study site.

Attribute Topographic Complexity: Rush Ranch resulted a “9/12” while

Arroyo Burro Estuary scored a “6/12” (Table 1). There was no difference between

the two study sites. Arroyo Burro Estuary resulting in a low score signifies lack of a

tidal channels and soil cracks furthermore this particular estuary had the tidal

channel restored because of drainage and sediment filling issues. Arroyo Burro

Estuary has a large reservoir that builds up sediment along with regulating water

releases this could impact fecal coliform loadings. However, tidal flushing and

storm-‐water could raise the fecal coliform contamination levels (Steets et al 2003).

Biotic Structure

Attribute Plant Number of Plant Layers: Rush Ranch Estuary received a

“12/12” while Arroyo Burro Estuary scored a “9/12” (Table 1). This attribute did

not show enough variation between the two study sites.

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Attribute Number of Co-‐Dominant Species: Rush Ranch Estuary scored a

“12/12” while Arroyo Burro Estuary scored a “9/12” (Table 1). These results did

not show much difference between the two freshwater estuarine wetlands.

Attribute Percent Invasion: Rush Ranch Estuary scored a “12/12” while

Arroyo Burro Estuary did not have a documented percent invasion CRAM score in

the Eco-‐Atlas or show signs of invasive plant species in the Year One Annual

Monitoring Report (Kisner 2007). Rush Ranch Estuary has been comparatively

analyzed by topographic data that correlated estuarine plant species and their

distributions. The topographic data concludes, the habitat of Rush Ranch is

considerable, but will have continuous exotic plant species invading the ecosystem

(Andrew et al. 2009).

Attribute Horizontal Interspersion: Rush Ranch scored a “12/12” while

Arroyo Burro Estuary received a “3/12” (Table 1). The results show a difference

between the two study sites (Table1 and graph 1). A vegetation study was

conducted on Rush Ranch Estuary with species richness by calculating their relative

abundance: subplot= 5.2±0.2, plot=12.4±0.6, plot_all= 15.9±0.7, site=39, and

site_all= 44 (table 5) (Vasey et al 2013). The results showed no obvious signs of

human disturbance, no shifts in wetland composition, rich plant biodiversity, no

invasive plant species, and rich vegetation patterns. Rush Ranch Estuary is a very

rich ecosystem with rich biodiversity in plant species, such as Cirsium hydrophillum,

Schoenoplectus acutus, Typha latifolia, Typha domingensis, Typha angustifolia,

Schoenoplectus californicus (Vasey et al 2012). The low score for Arroyo Burro

Estuary indicates the Assessment Area supporting less than 5%, no plant layers, or

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signs of concrete, rip rap, or newly restored vegetation. The One Year Annual

Report for the Arroyo Burro Estuary Restoration Project consisted of 57% of

California native plant cover and 11% non-‐native plant cover (Table 4 and 5),

(Kisner 2007). Furthermore, Arroyo Burro Estuary also consists of rip rap that was

installed along the newly constructed tidal channel (URS 2013).

Attribute Vertical Biotic Structure: Rush Ranch Estuary scored a “12/12”

while Arroyo Burro Estuary scored a “3/12” because the Assessment Area is

deficient in living vegetative canopy. The results showed a difference between the

two study sites indicating lack of dense canopy and shelter for wildlife in Arroyo

Burro Estuaries habitat (Table 1 and graph 1). Recent studies have shown with

quantitative data on Arroyo Burro Estuary, 31 non-‐native plant species and 84

California native plant species that occurred along the line transects (Table 5),

(Kisner 2007). This study concludes the relative abundance: an average of 57% of

average plant cover, 36% of average bare ground cover, 80% survival rate for the

first year of newly restored plants (Kisner 2007).

Table 1. CRAM Scoring Sheet: Perennial Estuarine Wetlands

Attributes Rush Ranch (I conducted these scores)

Rush Ranch (Documented scores)

Arroyo Burro (Documented scores)

Aquatic Area Abundance

6 12 9

Percent of AA* with Buffer

12 12 12

Average Buffer Width

12 12 9

Buffer Condition 9 12 9

Water Source 12 12 6

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Hydro-‐period 12 12 12

Hydrologic Connectivity

9 12 6

Structural Patch Richness

6 3 9

Topographic Complexity

9 9 6

Horizontal Interspersion

12 12 3

Vertical Biotic Structure

12 12 3

Number of Plant Layers

12 12 9

Number of Co-‐dominant Species

12 12 9

Percent of Invasive species

12 9 IN.

*Assessment Area

Table 2. The total attribute scores and total CRAM score for each estuary.

Attributes Rush Ranch (I conducted these scores)

Rush Ranch (Documented scores)

Arroyo Burro (Documented scores)

Buffer and Landscape

68% 100% 79%

Hydrology 92% 100% 67%

Physical Structure

63% 50% 63%

Biotic Structure 100% 92% 44%

Total CRAM* score

81% 86% 63%

* California Rapid Assessment Methods for Wetlands

Table 3. Biodiversity at Rush Ranch Species Common Name Species Latin Name Salt Marsh Harvest Mouse

Reithrodontomys raviventris

Suisun Ornate Sorex ornatus sinuosus Delta Smelt Hypomesus transpacificus

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Sacramento Splittail Pogonichthys macrolepidotus

Giant Garter Snake

Thamnophis gigas

California Clapper Rail Rallus longirostris obsoletus

California Black Rail Laterallus jamaicensis Suisun Song Sparrow Melospiza melodia

maxillaris American White Pelican Pelecanus erythrorhynchos Waterfowl (Vasey et al 2012)

Table 4. Transplanted California native plant species in Arroyo Burro Estuary.

Species common name Species Latin name

California Boxelder Acer negundo var californicum White alder Alnus rhombifolia rhombifolia Yerba mansa Anemopsis Californica Mugwort Artemisia douglasiana Marsh baccharis Baccharis douglasii Plummer’s Baccharis Baccharis plummerae Mule fat Baccharis salicifolia Creek dogweed Cormus sericea Saltgrass Distichlis spicata Common spikerush Eleocharis macrostachya Seacliff buckwheat Eriogonum parviflorum Western goldenrod Euthamia occidentalis Everlasting Gnaphalium canesceus Toyon Heteromeles arbutifolia Coast goldenbush Isocoma menziesii Basket rush Juncus textilis Giant rye grass Leymus condensatus Coascliff aster Malacothrix saxatilis Western sycamore Platanus reacemosa Black cottonwood Populus balsamifera subsp trichocarpa Hollyleaf Cherry Pruns ilicifolia Coast Live Oak Quercus agrifolia Lemonade sumac Rhus integrifolia Fuchsia flowered gooseberry Ribes speciosum California Blackberry Rubus ursinus Arroyo Willow Salix lasiolepis Purple sage Salvia leucophylla

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Black sage Salvia Mellifera Alkali bulrush Scirpus maritimus (Kisner 2007)

Table 5. Quantitative Data for Rush Ranch Estuary.

Site CC PM CI RR BI SMS

Subplot 2.5±0.1 2.8±0.1 2.3±0.1 5.2±0.2 4.7±0.2 5.4±0.2

Plot 5.2±0.5 5.8±0.5 4.8±0.6 12.4±0.6 10.4±0.6 10.8±0.8

Plot_All 6.2±0.4 7.1±0.7 6.2±0.7 15.9±0.7 13.2±0.8 13.4±1.1

Site 10 14 21 39 48 44

Site_All 10 17 23 44 55 56

(Vasey et al 2012)

CC=China Camp

PM= Petaluma Marsh

CI=Coon Island

RR=Rush Ranch

BI= Browns Island

SMS= Sand Mound Slough

Table 6. Non-‐native plant species on line transects at Arroyo Burro Estuary.

Scientific Name

Common Name

A B C D E F G H I J K L

Agrostis virdis Water bent grass

*

Anagallis arvensis

Scarlet pimpernel

*

Brassica nigra Black mustard

*

Chamaesyce maculata

Spotted Spurge

* *

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Chenopodium spp.

Goosefoot * * * *

Conium maculatum

Poison Hemlock

*

Convolvulus arevensis

Bind weed * *

Cyperus involucratus

Umbrella plant

*

Foeniculum vulgare

Sweet fennel

*

Junglans regia English walnut

*

Malva parviflora

Cheeseweed * *

Malva polymorpha

Bur clover *

Nicotiana glauca

Tree tobacco

* * * *

Oxalis pes-‐caprae

Bermuda buttercup

*

Plantago major Broadleaf plantain

* * *

Polypogon monspeliensis

Rabbitsfoot grass

* *

Raphanus sativa

Radish *

Rumex spp. Dock *

Vicia sativa Vetch *

Total 0 1 6 1 0 0 6 8 2 2 1 4

(Kisner 2007)

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Graph 1. The bar graph for the 4 attribute scores on each estuary.

0

20

40

60

80

100

120

Buffer & Landscape

Hydrology Physcial Structure

Biotic Structure

Num

eric Scores

4 Attribute Scores

The 2 non-‐saline estuaries

Rush Ranch (documented)

Rush Ranch (I conducted)

Arroyo Burro (document)

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Graph 2. Percent CRAM Score of all non-‐saline estuaries throughout California.

Table 7. Total CRAM scores for CA non-‐saline estuaries.

Location Name of Estuary Total CRAM Score San Francisco Suisun City Rush Ranch 86% San Francisco Browns Island 85% San Francisco Napa Pond 2 84% San Francisco Montezuma Bridge 80% San Francisco Pacific Atlantic Terminal 76% San Francisco Mackavoy Marsh 74% San Francisco Suisun City 72% San Francisco Browns Island

Oversample 71%

San Francisco Port Chicago Pier 2 72% San Francisco Pond 2A Over Sample 71% San Francisco Grey Goose 70% San Francisco Coyote Creek Lagoon 70%

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

Total CRAM Score (%

)

Individual Non-‐saline Estuaries

Total CRAM Scores CA Non-‐saline Estuaries

Rush Ranch

Arroyo Burro

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San Francisco Coyote Creek 69% Central CA Tembladero Lower Marsh 66% Southern CA Arroyo Burro Estuary 63%

Figure 2. Rush Ranch Estuary

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Figure 3. The line transects in Rush Ranch Estuary.

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Map 3. Arroyo Burro Estuary

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Figure 1. Arroyo Burro Estuary and Mesa Creek, before restoration

(USFWS Photos)

Figure 2. Arroyo Burro Estuary and Mesa Creek, after restoration.

(USFWS Photos)

30

Conclusion

Discussion

I am accepting my hypothesis for this senior thesis because I have supportive

evidence to distinguish the difference between disturbed and undisturbed non-‐

saline estuaries in California. I established discernible differences between Rush

Ranch Estuary (undisturbed wetland) and Arroyo Burro Estuary (disturbed

wetland), by using the Level II California Rapid Assessment Methods for Estuaries to

comparatively analyze the CRAM scores. Furthermore, undisturbed versus

disturbed wetlands are comparatively analyzed by their ecological processes,

system components, topographic complexity features, and their intended purpose.

The results show Rush Ranch Estuary having the highest score 86% and

being well above average 75%, versus Arroyo Burro Estuary having the lowest score

63% (Graph 1 and table 7). This graphical approach visually demonstrates

variation between the two study sites among other California non-‐saline estuaries,

and their differences include hydrology and biotic structure. There was no

difference between the buffer and landscape context, and physical structure.

However in this case disturbed compared to undisturbed wetlands are different in

the landscape context.

Rush Ranch Estuary functions as a high quality, undisturbed non-‐saline

estuary while Arroyo Burro Estuary functions as a low quality, highly disturbed non-‐

saline estuary this type of low quality function is known as wetland treatment

system (Kadlec 1996). Disturbed and undisturbed wetlands are very different in the

landscape context because Arroyo Burro Estuary has no room for marsh migration.

31

Since there is lack of undisturbed areas and the affect by human fecal pollutants

contaminating the storm drains (Sercu et al 2008). While undisturbed areas

dominate Rush Ranch Estuary and are used for marsh migration.

An undisturbed wetland such as Rush Ranch Estuary provides a high quality

wildlife habitat for the Salt Marsh Harvest Mouse Reithrodontomys raviventris,

Suisun Song Sparrow Melospiza melodia maxillaries, and Waterfowl (Table 3). In

addition, Rush Ranch Marsh is also the ecological niche for endemic species of San

Francisco, such as Lathyrus jepsonii and Cirsium hydrophilum var., 200 organisms, 47

plant species, 15 mammals, and 230 birds (Parker et al 2011), (Andrew et al. 2009).

Rush Ranch is the largest remaining tidal wetland located in the Suisun Bay with

rare and valuable ecological features, such as up-‐land transition habitats making

this estuarine wetland a National Research Reserve under the San Francisco Bay

National Estuarine Research Reserve (Vasey et al 2012). Rush Ranch is a great

example of an undisturbed freshwater marsh since it is anticipated for conserving

and protecting threatened or endangered tidal marsh species (Table 3), (Whitcraft

et al 2011). Species listed under the State or Federal Endangered Species Act fall

under the legal jurisdiction of the ESA, and any damage to critical habitat or species

is prohibited.

The notion of the rapid assessment tactics discusses the environmental

impacts, such as degradation, bank erosion, and poor water quality. These

environmental impacts are results from human caused alterations toward wetlands.

Therefore, Arroyo Burro Estuary functions as a treatment wetland to improve the

water quality from bacteria loading and subsequent beach closures that increase

32

pollution levels caused by urbanization (Aguinaga et al 2004). Arroyo Burro

Estuary is under the “Water Quality Limited segments in the Clean Water Act

Section 303-‐(d) List”, for example the California’s single sample standard for fecal

coliform in a recreational waters should not exceed 4E6 MPN/m3 and in February

1999 the Arroyo Lagoon resulted in a 4E6 and 8E6 MPN/m3 (Sercu et al 2008),

(Steets et al 2003). The stressors that were found to affect the Arroyo Burro

Estuary was the urbanization runoff, urban residential, industrial and commercial,

active recreation, excessive human visitation, discharges of urban runoff,

contaminated storm drain, rip rap, engineered channel, nutrient impaired, bacteria

and pathogens impaired (CRAM field book 2013).

These two different non-‐saline estuaries differ in a few ways that include

function, wetland composition, and wetland condition. An assumption of the

California Rapid Assessment Method for Wetlands indicates any sign of human

disturbance is as a negative environmental impact on the estuary and will lower the

CRAM score. High CRAM scores indicate that the wetland is in excellent condition

compared to other wetlands in that class, and they may provide a reference for

wetland restoration or conservation.

The California Rapid Assessment Methods for Wetlands is not accurate for

determining the performance standards, health status for individual wetlands, or

should be used for a statistical approach. Since the Assessment Area and Buffer

could both be mapped in a biased location within the study site of Arroyo Burro

Estuary. Arroyo Burro Estuary received a higher CRAM scores even though it lacks

in water quality, hydrologic connectivity, aquatic abundance, buffer width, buffer

33

condition, buffer percent. CRAM is a way to rapidly compare and contrast the

wetland condition, stressors, and condition of the wetland.

34

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Documents

Senior Thesis-FINAL