Vegetation community mapping of Estero Santa Cruz by Jeffrey Frisch Jr

Vegetation Community Mapping of Estero Santa Cruz

Elisa Elizondo Jeff Frish Kaitlin Greenfield Kumara MacLeod Brian Stultz January 2014

Map 1. Estero Santa Cruz and surrounding area with the Ramsar boundary (Google Maps)

Introduction Estuaries are unique ecosystems dependent on tidal flows and characterized by high saline substrates. They are one of the most productive ecosystems on the planet, supporting a high diversity of animal species, including waterbird species (Reigner 2001). Estero Santa Cruz (see Map 1), situated off the Gulf of California in the Central Gulf Coast subdivision of the Sonoran Desert, is a very important migratory bird corridor (Fleischner and Gates 2009). Estero Santa Cruz is home to 162 species of birds, 60 of which are high priority for conservation (Fleishman 2013). Due to the results of monitoring efforts this estero has been designated as both an Important Bird Area (IBA) and a Ramsar Wetland of International Importance (Ramsar site). An overview of Estero Santa Cruz with the Ramsar boundary is shown in Map 1.

Most monitoring has been conducted in the northern 30% of the estero (Fleishman 2013). Bird monitoring research has not been conducted in the majority of the estero, including large areas where there are lagoons and mangrove channels. Mapping vegetation communities in Estero Santa Cruz will help researchers understand the vegetation communities of the entire estero. The vegetation community map will help inform future studies in conservation, especially of the spatial use of the estero by high priority species.

Site Description Estero Santa Cruz is located 4 km south of Bahia Kino, Sonora, Mexico (Reigner 2001). The estuary is considered a negative estuary due to arid conditions in which evaporation exceeds precipitation. This is because freshwater from the Rio Sonora no longer flows into the estuary due to overuse upstream. Therefore, salinity is higher at the head of the estuary than at the mouth (Reigner 2001). Additionally the southeast section of Estero Santa Cruz has been made into shrimp farms, with a channel dredged out on either side to allow estuarine water to flow in and out. Despite this, the area is still very productive. Surrounding the estuary is a variety of plant communities often defined by tidal fluctuation (Fleishman 2013). During summer, tides are higher, inundating more land than in winter months (Fleishman 2014).

Materials & Methods Preliminary Entitation A World View-2 multispectral satellite image was obtained by Prescott College to facilitate the delineation of spatial characteristics of Estero Santa Cruz. The image is a 4 band multispectral image acquired on 07 June 2013. Spectral bands include red, green, blue, and near- infrared. Initial entitation and sample distribution was based on two entities, tidal and dry land. These entities were determined by Abram Fleishman through visual interpretation of the satellite imagery. Using these two entities, ten plots were chosen randomly in each for a total of twenty plots in the northern part of the estuary. The second entitation was performed using GIS technology (ArcGIS v.10.2.1), based on measurements of light reflectivity from land and vegetation in satellite imagery of Estero Santa Cruz. An unsupervised classification of the imagery was performed to generate a sampling stratification to inform determination of floristic community composition in the field (see Appendix A). An initial calculation was completed using a formula to create a Normalized Difference Vegetation Index (NDVI) value that was calculated using near-infrared (NIR) and red light spectrums. An Isocluster Unsupervised Classification was then created with inputs of the NDVI, green, blue, red, and NIR spectral bands in various combinations. Four maps were generated in ArcGIS to represent different classifications of satellite imagery through different combinations of spectral bands. The four Isocluster Unsupervised Classifications were made up of the following inputs: Unsupervised Classification #

# of classes

NDVI

Blue spectrum

Green spectrum

Red spectrum

NIR spectrum

The imagery created in the GIS software resulted in preliminary entities that show both vegetation communities and non-vegetative entities. These entities were distinguished by variability in refraction captured by the satellite. Ultimately, it was decided that the unsupervised classification 3 best fit the project’s objectives. It was selected for its ability to show distinctions between vegetation, soils, and simplicity as it lumped together places thought to be the same entity. The other three maps showed more detail giving a more mottled look and making it more difficult to find associations within known communities such as the mangroves. Using unsupervised classification 3, the stratified random sampling method (Mueller-Dombois and Ellenberg 1974) was used to place additional points within different entities presumed to represent different vegetation communities. These points became the sites of further relevé sampling to further build associations while mapping and field observations in the Estero Santa Cruz (See Appendix A). To define parameters for data collection, a data dictionary was developed in the GPS Pathfinder office 2.90 which was then transferred into the Trimble Juno 3 (GPS) unit. The data dictionary included the initial entities, date, initials of data collectors, and GPS file name for each point. The randomly sampled points were uploaded into the GPS.

Field Relevé Sampling The Terrasync software in the GPS unit was used to navigate to the points chosen during the preliminary entitation phase. Once a group of researchers arrived at each point, a GPS relevé point was collected for three minutes while a pin flag was placed marking the southwest corner of the northeast plot, which was also the northeast corner of the southwest plot.

The meter tape was laid out ten meters in each of the cardinal directions from the pin flag using a compass to take a bearing for each. To complete the 100m² plots, a pin flag was then placed in each of the far corners to complete a10m by 10m quadrat for both the southwest and the northwest plots. Two members of the group then used the clinometer to determine slope and aspect of each plot. At each point the relevé method (Mueller-Dombois and Ellenberg 1974) was used to define the vegetation community to be sampled and assessed. For each of the 100m2 plots, a species list was made according to Felger’s (2002) nomenclature, and unknown plants were identified according to his dichotomous key of plants of Northwestern Mexico. The Braun-Blanquet Cover-Abundance Scale (Mueller-Dombois and Ellenberg 1974) was used to estimate relative species cover for each species present within the plot. The scale is as follows:

Braun-Blanquet Cover-Abundance Scale Scale

Cover

1-5%

5-25%

25-50%

50-75%

75-100%

Scale

Cover

abundant but small in cover area

rare with little cover

Mangrove Plotless Sampling In addition to using the relevé method to measure cover-abundance, a team of students were sent into the mangrove at the south end of the Estero Santa Cruz to collect data using a plotless method. The objective of this sampling was to take preliminary data on mangrove density, height, and cover uniformity (or non-uniformity) to assess the data’s value for future research of bird habitat according to mangrove structure. This method was chosen to simplify accessibility to points located along the estuary’s channels, as mangroves are too dense to use a plot method accurately. Points were marked using a GPS unit on opposite banks of the channel every 100 meters. At each point measurements and data were taken for height of mangrove vegetation using a tool marked with distances, uniformity of height in three classes, density/cover using a 3 class scale based on passability, and species found within a visible radius from the center point.

Data Processing and Analysis During both 2008 and 2014 classes, 88 plots were conducted in the field to sample vegetation. Once sampling was completed, data from releve plots were organized in Microsoft Excel and then transferred into TWINSPAN (two way indicator species analysis) statistical software. This software groups possible vegetation communities based on multivariate analysis of species in each plot using the cover-abundance data from the relevés. Because of erroneous data from the 2008 data, including many unknown species, we decided to rerun the software with just the data from 2014. A much cleaner and more relevant set of six floristic communities emerged that were named based on Felger and Moser’s (1991) and Felger and Wilder’s (2012) vegetation classifications of the flora in the Central Gulf Coast subdivision of the Sonoran Desert. Each plot was assigned to a certain community. However, we found that a few of the plots had to be reassigned to other vegetation classifications more representative of their species composition. This was based on crossreferencing a Microsoft Excel plot-by-plot list of statistical classifications with a plot-by-plot list of known classifications ground truthed in the field. 2008 data included very detailed notes on environmental variables and characteristics which were more useful in combination with a list of species present and rated according to relative cover. 2014 data tended to have much fewer unknown species, but lacked detailed notes about site characteristics. Due to inconsistency in species documentation used in TWINSPAN, these notes were very helpful in reconstructing a picture of the vegetation community at each site sampled in 2008. The output of TWINSPAN was used to

characterize areas on the map not sampled in 2014. Each plot was cross referenced with 2014 data, which was further cross referenced with the known vegetation community type. Three classifications not based on vegetation but substrate type were created independently and assigned to relevés that lacked vegetation: mudflat, salt flat, and microbial mat.

Digitization of Vegetation Communities Once all plots were assigned to a vegetation community or non-vegetated entity, they were entered in to Microsoft Excel and transferred into an ArcMap attribute table. Several locations that had appeared especially mottled but recognizable had to be digitized using the classified image. These plots were also assigned values and added to the initial classification. The resulting classifications showed a very accurate community map. After the final classification, all plots were assigned a classification based on vegetation and non-vegetation communities previously defined and in accordance to Felger.

Results Description of Vegetation Communities and Non-Vegetation Classifications Six distinct vegetation communities were classified. To maintain consistency, they were named in accordance with their corresponding association identified by the January 2012 Field Methods of Plant Ecology vegetation mapping group (Attebury et. al 2012) who mapped Estero Santa Rosa using Felger and Moser’s (1991) and Felger and Wilder’s (2012) descriptions. For communities that do not correspond to those found in Estero Santa Rosa, Felger and Moser or Felger and Wilder were the sole reference. A few are listed in parenthesis according to names assigned during the statistical analysis phase where these differ from the official vegetation community title. Each of the classifications are followed by the names of species which dominate by cover (according to the Braun-Blanquet cover and abundance scale and statistical analysis in TWINSPAN). Refer to Appendix B for a complete list of species identified in Estero Santa Cruz. Unknown species were not included inthis list. Beach Dunes (Felger and Wilder 2012)

Fore Dune Scrub (Halophytic Dune) (Attebury et. al 2012) – Abronia maritima, Frankenia palmeri, Atriplex barclayana, and Distichlis palmeri. This community is typically found closest to the sea, situated right behind the beach. Specific dominant species vary around the estero, but halophytic succulents

(Allenrolfea occidentalis, and sub-shrubs are dominant in cover and abundance. Also present and secondarily dominant are salt grasses and desert shrubs such as Jatropha cinerea, Lycium spp. The substrate is sandy and very loose. Other species may be Euphorbia leucophylla, Dalea sp., Palafoxia arida, and Atriplex canescens.

Back Dune Scrub (Desert Dune) (Attebury et. al 2012) â&#x20AC;&#x201C; Jatropha cinerea and Bursera microphylla, and Croton californicus. Desert shrubs dominate in cover and abundance, while halophytic species have a secondarily dominant presence. The substrate is fairly loose sand, but as a whole the dune is more stabilized than the fore dune scrub. On the sand spit and around the mouth of the estero it is right behind the fore dune scrub (See Map 1). Cylindropuntia fulgida, Frankenia palmeri, Encelia sp., Astragalus sp. and Lycium fremontii may also be present. Littoral Scrub (Felger and Moser 1991)

Salt Scrub (Halophytic Flat) â&#x20AC;&#x201C; Allenrolfea occidentalis, Salicornia bigelovii, Frankenia palmeri. Salt scrub almost exclusively consists of halophytic succulents. Batis maritima, Monanthochloe littoralis are also present along the edge of salt scrub as a transition zone between salt scrub and mangrove forest habitat. Other species that may be present sparingly are Atriplex barclayana, Sesuvium portulacastrum, Avicennia germinans, and Distichlis palmeri.

Mangrove (Mangrove Scrub and Mangrove Forest)- Avicennia germinans, Rhizophora mangle, Batis maritima The community is different depending on the part of the estuary. Mangrove Scrub tends to be a thin band of mangrove on the edge of extensive mudflats which receive daily tidal variation. In Mangrove Scrub A. germinans is present mixed with R. mangle with vegetation characterizing salt scrub present beneath the canopy of the mangrove and immediately surrounding it. Mangrove Forest tends to be a more extensive continuous canopy surrounding estuarine channels.

Desert Scrub (Felger and Moser 1991)

Mixed Desertscrub and Coast Scrub combination (Desert Hills and Hillocs) - Fouquieria splendens, Cylindropuntia fulgida, Lycium fremontii, Frankenia palmeri are present on stabilized substrate often further from the coast except where the slope is very high, then it may be present near the coast. Sometimes the substrate is microbiotic encrusted. Columnar cacti are also present.

Mesquite Scrub (Bosquecito) - Prosopis glandulosa and Pennisetum ciliare. This community is present inland at the base of a slope of mixed desert scrub and at the edge of salt scrub. It is not always present in these areas. Mesquite scrub has denser cover than mixed desertscrub. Also present are Lycium fremontii. Lycium brevipes,, Frankenia palmeri, Atriplex canescens, Atriplex barclayana, Atriplex polycarpa, Cylindropuntia fulgida.

Non-Vegetation Classifications

Salt Flat - The substrate is dry sandy and salt-encrusted, estuarine soil.

Mud Flat - The substrate is cracked muddy sand present closer to the estuary than the salt flat. These zones are periodically inundated by tidal flow.

Microbial Mat - The substrate is covered with a cracked, spongy, and muddy cyanobacterial mat. This is present in one location in the entire estero, situated in a low-lying depression between the foredune and the mangrove. Disturbed Area - These are areas of heavy human influence. The salt plant and shrimp farming in the east side of the estuary are the best example of this.

Discussion of Vegetation Communities and Future Considerations The vegetation community map (see Appendix D), generated through entitation, site sampling, statistical analysis, and interpretation of vegetation associations, will be used as a component in mapping and describing critical habitat for priority waterbird species. The sites with a slope of zero degrees and undefined aspect tend to indicate that there was a tidal influence on the site. To determine habitat classes for mapping priority waterbird habitat, tidal influence and substrate cover will also need to be evaluated in each of the vegetation classifications. This was not done quantitatively at each site, as the primary focus of this project was to determine vegetation cover for mapping vegetation communities. With enough relevĂŠs placed throughout the mixed desertscrub, it may be possible to sub-divide this community into at least three different sub-communities: 1. Cactus scrub community of columnar cacti and teddy bear-cholla, 2. Drought-deciduous shrub community with F. splendens, J. cinerea, and F. palmeri. and 3. Coast scrub community. Due to a lack of sufficient sampling across the mixed desert scrub area, all of these potential communities had to be lumped into one. We found invasive Pennisetum ciliare in the Mesquite Scrub vegetation community. This is possibly because it requires summer moisture (Chambers and Hawkins 2002) which can be retained in xeroriparian microclimates under the canopy of the Mesquite Scrub. P. ciliare should be controlled to prevent introduction of fire into desert plant

communities which are not adapted for fire disturbance, as well as to prevent dense stands which would not allow native species establishment. The entire ecosystem could be altered should this be allowed to spread (Chambers and Hawkins 2002). Statistical evaluation would have benefited from a more accurate plant list. The plant list of Estero Santa Cruz, used to input data for statistical evaluation, is not exhaustive. There are three reasons for this. First, many plants listed in the 2008 data, and a few in 2014 data were either identified to the genus level or were completely unknown. Second, data has been collected during the winter, when it may be impossible to identify a species using the dichotomous key. Third, plants may not have been included due to a lack of enough relevĂŠs in areas, which may turn out to become sub-communities. A group of researchers should return in the spring when flowers and fruits are available for identification of species that are unknown or only identified to the genus level. Statistical evaluation would have also benefited from inclusion of soil texture and slope, as these factors tended to differentiate between types of halophytic and desertscrub communities. This is important information pertaining to characteristics of actual vegetation communities represented in Estero Santa Cruz. It would have also benefited from consistency in documentation of 2008 and 2014 data. TWINSPAN clearly identified salt scrub and mangrove vegetation for both 2008 and 2014 data. It did not clearly differentiate between back dune scrub, which includes desert plants and some halophytic plants, and desert/coast scrub, which includes similar vegetation, but lacks halophytic vegetation. The exception is F. palmeri, a non-preferential halophyte, which appears to be almost anywhere except with other halophytic vegetation found in the salt scrub classification. Presence of biotic soil crust is a confirming factor of desert and coast scrub. This is not something that could be statistically evaluated as it is not always present is this community where this vegetation type is found closer to the estuary. The substrate characteristics identified through natural history observation were sandy dunes, comprised of a mix of halophytic and desert plants, sandy hillocks comprised of desert vegetation and often stabilized by microbial crust, and salt-encrusted sandy tidal flats. The latter would either be comprised of halophytic vegetation or characterized as salt or mud flats if the flats were free of vegetation. A unique substrate free of vegetation was the microbial mat made up of muddy sand and mats of cyanobacteria. While not statistically evaluated, data on the presence of microbial crust as well as slope and aspect data could be used to determine the tidal influence of each plot. It is possible that microbial crust needs time to develop, and this process could be interfered with in the presence of seasonal inundation of estuarine tidal water. More research would be needed to understand the presence of the microbial crust. Ground truthing will be necessary to evaluate the accuracy of the statistical analysis. More relevĂŠs may be performed as necessary to further refine the map. The map of vegetation communities will serve to aid further research of waterbird habitat and conservation of the Estero Santa Cruz.

Literature Cited Attebery, Joshua, Dillion Metcalfe, Eleanore Nelson, Vincent Weber, Lisa Zander. 2012. Vegetation Mapping of Estero Santa Rosa and Associated Uplands. Prescott College Kino Bay Center for Cultural and Ecological Studies. Unpublished. Bahia de Kino, Sonora. Chambers, Nina and Trica Oshant Hawkins.2002. Invasive Plants of the Sonoran Desert. Sonoran Institute and Environmental Education Exchange. Tuscon, Arizona. Felger, Richard Stephen. 2000. Flora of the Gran Desierto and Rio Colorado of Northwestern Mexico. University of Arizona Press: Tuscon, Arizona. Felger, Richard Stephen and Mary Beck Moser. 1991. People of the Desert and Sea: Ethnobotany of the Seru Indians. University of Arizona Press: Tuscon, AZ. Fleishman, Abram B. 2013. Creation of a habitat map and mapping Critical Habitat for priority waterbird species in Estero Santa Cruz, Sonora, Mexico. Prescott College Kino Bay Center for Cultural and Ecological Studies. Unpublished. Bahia de Kino, Sonora Fleishman, Abram B. January 21, 2014. field class boat ride to Estero Santa Cruz, personal communication. Fleishner, Thomas Lowe, and H.R. Gates. 2009. Shorebird Use of Estero Santa Cruz, Sonora, Mexico: Abundance, Diversity, and Conservation Implications. Waterbirds 32:36-43. Mueller-Dombois D., and Heinz Ellenburg. 1974. Aims and Methods of Vegetation Ecology. The Blackburn Press: Caldwell, New Jersey. Reigner, Mark. 2001. The Mangrove Community of the Kino Bay Region. In Prescott College Course Reader for the Kino Bay Region. Prescott College Publications. Prescott, Arizona.

Appendix A: Preliminary Entitation and Stratified Random Sampling of RelevĂŠ Points

Appendix B: Plants of Estero Santa Cruz, Sonora, Mexico Family

Species

Acanthaceae

Avicennia germinans

Aizoaceae

Mesembryanthemum sp. * Sesuvium portulacastrum

Amaranthaceae

Fore Dune

Back Dune

Salt Scrub x

Mangrove

x X

Allenrolfea occidentalis

Atriplex barclayana

Atriplex canescens

Salicornia bigelovii Suaeda nigra Asteraceae

Cryptantha sp.

Burseraceae

Bursera hindsiana

Cactaceae

Bursera microphylla Cylindropuntia fulgida

Celastraceae Euphorbiaceae

X x

x X

x X X

Lophocereus schottii

Mammillaria sp.

Pachycereus pringlei

Stenocereus thurberi

Maytenus phyllanthoides Croton californicus

x x

Euphorbia sp.

Jatropha cinerea

x x

Parkinsonia microphylla

X X

Prosopis glandulosa Fouquieriaceae Frankeniaceae Krameriaceae

Frankenia palmeri Krameria sp.

Malvaceae

Melochia tomentosa

x X

Olneya tesota

Psorothamnus (Dalea) sp. Fouquieria splendens

Acacia sp. Astragalus sp. Errazurizia megacarpa

Jatropha cuneata Fabaceae

Batis maritima

Boraginaceae

Ericamerica nauseosa (Chrysothamnus nauseosus) Isocoma sp Palafoxia arida Bataceae

X X

Baccharis sarothroides Encelia sp.

x X x

Mesquite

Atriplex polycarpa

Mixed Desert

X x x X

X X

X x

X X x

Sphaeralcea sp.

Nyctaginaceae

Abronia maritima

Poaceae

Distichlis sp. Monanthochloe littoralis

X x

x X

X X

Pennisetum ciliare *

Rhizophoraceae

Rhizophora mangle

Sapindaceae

Cardiospermum corindum

Solanaceae

Lycium andersonii Lycium brevipes

x X

Lycium fremontii

Zygophyllaceae

x x

Larrea tridentata

X X

* designated invasive species X designates more common species (Braun-Blanquet number more than 1 and in more than 1 releve) x designates species less common or found in a transition between two communities

Appendix C: TWINSPAN Generated Vegetation Community Groups

Appendix D: Map of Vegetation Communities of Estero Santa Cruz