DOI: 10.5061/dryad.3j9kd51xc
title: Elkhorn Slough National Estuarine Research Reserve: Bank erosion and rapid mudflat biomonitoring

description: Scientists from the Elkhorn Slough National Estuarine Research Reserve and
 the Monterey Bay National Marine Sanctuary conducted surveys in Elkhorn
 Slough, California, USA every other year from 2001-2023 to assess bank
 erosion, mudflat erosion, and to conduct rapid biomonitoring surveys of
 the mudflats.  There are thus three components associated with
 this dataset: Bank Erosion: The purpose of this monitoring program was to
 track erosion rates of banks along the main Elkhorn Slough channel and at
 various sites on the Reserve, as a component of overall habitat change
 analysis (bathymetry data, remote sensing of marshes and tidal creeks)
 shedding light on tidal scour.  Erosion rates can be correlated
 to other measured variables, such as cliff height or crab hole density.
 Mudflat Erosion: The purpose of this monitoring program was to track
 erosion or deposition rates in intertidal mudflats at sites throughout the
 estuary. Rapid Mudflat Biomonitoring: One purpose of this program was to
 detect new invasions, potentially early enough to attempt eradication, and
 to track changes in distribution and abundance of a set of conspicuous
 existing invaders.  We also were interested in detecting major
 changes in bivalve populations or other native ecological dominants.
description: <strong>Bank Erosion Monitoring</strong>
 At each station, there was an upstream and downstream PVC stake
 10 m apart, parallel to the shore.  We ran a transect tape perpendicular
 measured the distance from the stake to the bank edge and to the
 vegetation edge (the most seaward live plant in transect).  While the
 primary interest was bank erosion, at stations with low or multiple
 cliffs, it wasn’t always clear which to use as the bank edge, so the
 measurement to vegetation edge is more repeatable. When there was no clear
 bank edge at all, we used distance to vegetation edge as the distance to
 bank edge measurement. As necessary we moved stakes backwards from edge to
 prevent their loss, and add this amount to datasheet to adjust
 calculations.  We averaged the data from the two stakes per site (useful
 because if one stake is missing, we still had a measurement for that
 site).  From these data we calculated annualized bank erosion rates for
 different Slough regions. We also assessed a series of other parameters,
 hole density, bank height and undercut.   In 2013, we
 added shorter stakes 1 m (or closer on very narrow banks, specified on
 datasheet if different than 1 m) behind original tall PVC to allow us to
 have a repeatable angle for bank measurements, and to make it more likely
 that at least one of the stakes would still be present two years later, so
 we wouldn’t lose the time series as we’d done previously if a stake was
 missing. From 2013 forward, we conducted all measurements from the most
 landward shorter stake (so distance from PVC to shorter stake, usually 100
 cm, was subtracted from all measurements from 2013 forward to make them
 equivalent to earlier ones). Because of some evolution
 of methods over time, and because of missing data from some years and
 stakes, the raw data for this monitoring is complicated and not
 user-friendly.  We have archived the raw data (“D erosion raw”) in an
 Excel file for completeness, but strongly recommend that users used the
 curated data (the CSV) for statistical analyses. The curated dataset uses
 the average value of the two stakes per station (providing a more
 consistent time series because in many early years we had missing stakes
 and lost time series), and omits stations with artificial banks and sites
 with muted tidal exchange.  It also omits the plant type and cover
 measurements taken in early monitoring years, which proved to be
 unreliable due to variation in placement of the quadrats.
 <strong>Mudflat erosion</strong>
 After 2013, we also added a new element, mudflat
 erosion/deposition, evaluated by measuring how many cm of a short PVC
 stake were emergent above the mudflat surface, and quantifying changes in
 this over time.  The short PVC stakes placed at +1.5 ft above MLLW in the
 intertidal, in the transect line from each bank stake. 
 <strong>Rapid Mudflat
 Biomonitoring</strong> We carried out the
 monitoring at all the bank erosion stations (mudflats).  In the 10 m long
 rectangle in between the bank stakes and the mudflat stakes (located at
 +1.5 ft above MLLW), we assessed the mudflat. While the search area was
 always 10 m long (parallel to shore), it varied in width depending on
 slope, yielding a search area typically 10-100 square meters.  Before 2013
 we estimated search area; after 2013 it was marked by the low PVC stakes
 placed at +1.5 ft above MLLW and was measured; it remained the same from
 then on. At each station, we searched for a targeted list of conspicuous
 epifaunal organisms, mostly invaders but also some key natives.
 Distinctive burrow openings were included (gapers, ghost shrimp).  Each
 was given an abundance value (0-4, see Section 8 for scoring).  If other
 organisms (greater than about 2 cm in size) were also abundant (scores
 3-4), we identified them to whatever level we could. Relative abundance
 was calculated as a function of available habitat, separately for
 organisms on mudflat (most of area) vs. organisms on hard substrates (a
 tiny percentage of the search area).  E.g., we assessed what percentage of
 the only two rocks present at the site had barnacles, rather than what
 percentage of the mudflat had barnacles.  Over time, we
 added new taxa that we hadn’t previously searched for, such as Ulva and
 the holes of crabs.  For such species, their abundance in early years is
 listed as NA rather than zero, and should be treated differently than
 zeros.  For a time series of any particular species, one should look only
 at those years in which the species was assessed (has numerical data, not
 NAs). The field datasheets with exact definitions used
 and field instructions are archived as tabs on the Excel database for this
 monitoring dataset (“M field erosion datasheet”, “M field bio datasheet”,
 “M field instructions”).
 <strong>Sites</strong> Monitoring
 occurred at about 20 stations each year. Those along the main channel were
 established by Chris Malzone in the 1990s, and numbering is his.  New
 stations were added on ESNERR in 2001.  At each station, there was an
 upstream and downstream stake, 10 m apart on the bank.  These were often
 lost in early years (eroded away), which meant rate of change in distance
 from stake to edge could not be calculated.  Later, a second stake 1 m
 back from first was added, making it easier to replace one of the stakes
 if lost.  Mudflat stakes were added in 2013 to delineate the biomonitoring
 search area and to monitor mudflat erosion.   Over
 time, some stations were dropped.  This applied to various ones on eroding
 levees, which had eroded so badly that there was no space left for
 measuring bank erosion.   Stations are described and
 coordinates provided in the “M Station Info” tab of the Excel
 database. <em>Bank Erosion
 Monitoring</em> The curated CSV includes only
 those stations on natural banks with full tidal exchange.  Stations on
 artificial banks were dropped because levees entirely eroded away, because
 measurements were unreliable (very variable from year to year in
 unrealistic ways), and because the main focus of this monitoring is on
 loss of natural salt marsh banks.  Stations with muted tidal exchange were
 dropped for the latter two reasons.  Sites with low
 cliffs (indicated in column in data) can optionally be omitted from
 analysis of bank erosion rates, since these sites have less reliable
 measurements (they usually have multiple low banks so there is some choice
 as to which to measure to) and since bank erosion studies typically focus
 on higher banks. <em>Mudflat
 erosion</em> The curated CSV includes all
 stations except 2 (no stakes installed) and stations on the Reserve that
 were not monitored for long after stakes were installed (61,
 80-81).   <em>Mudflat
 Biomonitoring</em> The curated CSV includes all
 stations. <strong>Data collection
 period</strong> Bank erosion monitoring occurred
 from 2001-2023, mudflat erosion monitoring from 2015-2023, and rapid
 mudflat biomonitoring from 2005-2023. Monitoring was typically conducted
 on two Fall season low tides, in odd years, though a few even were done
 early on (2002 and 2004).  On one day, walk-in stations were assessed by
 three teams working separately; on the other day, boat-based stations were
 jointly assessed by one large team. Survey dates and
 team members are listed on the “M survey dates teams” metadata tab in the
 Excel database. <strong>Explanation of
 variables</strong> The field datasheets with
 exact definitions used and field instructions are archived as tabs on the
 Excel database for this monitoring dataset (“M field erosion datasheet”,
 “M field bio datasheet”, “M field instructions”). Only a brief overview is
 provided below because detailed metadata are provided in these tabs. All
 clean datasets include the region, subregion, area and subarea using
 standard placenames designated for all Elkhorn Slough datasets to allow
 for cross referencings. <em>Bank Erosion
 Monitoring</em> The core data collected are
 distance from marker to bank and vegetation edge, which are converted into
 annualized rates of change averaged between the two stakes per station in
 the clean dataset for analyses. Annualized rates are much more reliable
 and user-friendly than raw distances, because these changed as stakes were
 replaced and because monitoring intervals varied. Note that the annualized
 rate of change covers the two-year period preceding each survey year
 (e.g., the annualized rate listed for 2023 describes what happened from
 Fall 2021-Fall 2023); this is important to consider if correlating rates
 to environmental variables such as ENSO index (which should thus also be
 averaged for the same two year period). Supplemental data collected
 include cliff height, undercut, distance between vegetation and bank edge,
 and large and small hole in a 0.25 m-2 quadrat.  All measurements are in
 cm (or for rates, cm/year).   Key variables 
 Annualized_Change_Distance_To_Bank_Edge: if
 negative, erosion rate; if positive, would be progradation;
 cm/year 
 Annualized_Change_Distance_Veg_Edge: if negative, landward marsh
 retreat; if positive, seaward expansion; cm/year 
 Annualized_Change_Bank_To_Veg_Edge: change in distance
 between bank edge and vegetation edge; negative numbers mean distance is
 getting smaller; positive means distance is getting larger (vegetation
 retreat); cm/year 
 <em>Mudflat Erosion Monitoring</em>
 Erosion/deposition rates were calculated by comparing how much of
 each marker PVC in mudflat was protruding in consecutive measurement years
 and converting this to annualized rates of change, averaged across the two
 stakes per station. Measurements are in cm/year. Key 
 variable: 
 Annualized_Change_Sediment_At_Mudflat_Stake: if negative, erosion
 rate; if positive, deposition rate; cm/year 
 <em>Rapid Mudflat
 Biomonitoring</em> The data consist of a relative
 abundance estimate for live species. 0=absent
 1=trace presence: present on &lt;1% of available
 substrate 2=rare: on 1-10% of available
 substrate 3= abundant: on 10-50% available substrate
   4= very abundant: on &gt;50% available
 substrate For dead bivalves, the abundance is a count
 of valves (individual shells – so a complete clam shell would have a value
 of 2, while a single half-shell would have a value of 1).
description: # Elkhorn Slough National Estuarine Research Reserve: Bank erosion and
 Rapid Mudflat Biomonitoring Dataset DOI:
 [10.5061/dryad.3j9kd51xc](10.5061/dryad.3j9kd51xc) ## Description of the
 data and file structure Bank Erosion: The purpose of this monitoring
 program was to track erosion rates of banks along the main Elkhorn Slough
 channel and at various sites on the Reserve, as a component of overall
 habitat change analysis (bathymetry data, remote sensing of marshes and
 tidal creeks), shedding light on tidal scour.  Erosion rates can be
 correlated to other measured variables, such as cliff height or crab hole
 density. Mudflat Erosion: The purpose of this monitoring program was to
 track erosion or deposition rates in intertidal mudflats at sites
 throughout the estuary. Rapid Mudflat Biomonitoring: One purpose of this
 program was to detect new invasions, potentially early enough to attempt
 eradication, and to track changes in the distribution and abundance of a
 set of conspicuous existing invaders.  We were also interested in
 detecting major changes in bivalve populations or other native ecological
 dominants. The missing data are represented as NA. ### Files and variables
 #### File: ESNERR_Bank_Erosion.csv **Description:** dataset on bank
 erosion at Elkhorn Slough, from measurement of distance to bank edge and
 associated variables at permanent markers, and calculating the rate of
 change since the last measurement ##### Variables * Station: location
 where data were collected; latitude and longitude provided the the Station
 Info tab of the Excel file uploaded as Supplementary Material * Region:
 Upper vs. Lower portion of Elkhorn Slough * Subregion: finer
 categorization of region used by ESNERR; see the KMZ file uploaded
 separately * Area:  finer categorization of subregion used by ESNERR, see
 the KMZ file uploaded separately. * Subarea: finer categorization of
 subregion used by ESNERR, see the KMZ file uploaded separately. *
 Geographic_Category: combined region and area name used for ESNERR
 analyses * Cliff_Height_Category: low &lt;20 cm, med 20-60 cm, high&gt;60
 cm * Year: monitoring year * Distance_Bank_To_Veg_Edge: distance (in cm)
 between bank edge and most seaward live marsh plant tissue in the transect
 * Cliff_Height: bank height in cm * Undercut: deepest undercut in the bank
 in cm * Small_Hole_Density: number of holes between 2 mm and 1 cm in size
 in a 0.25 m2 quadrat (mostly small crab and isopod Spheroma holes) *
 Large_Hole_Density: number of holes between &gt;1 cm in size in 0.25 m2
 quadrat (mostly grapsid crab holes) * Total_Hole_Density: sum of small and
 large holes as above * Annualized_Change_Distance_To_Bank_Edge: change
 (cm/year) in distance from permanent marker to bank edge since last
 measurement; negative numbers represent erosion, positive numbers
 represent progradation  * Annualized_Change_Distance_To_Veg_Edge: change
 (cm/year) in distance from permanent marker to most seaward marsh plant
 tissue in transect since last measurement; negative numbers represent
 landward marsh retreat, positive numbers represent seaward expansion of
 marsh * Annualized_Change_Bank_To_Veg_Edge: change (cm/year) in distance
 between bank edge and most seaward marsh plant tissue in transect since
 last measurement; negative numbers represent a decrease in distance,
 positive numbers represent an increase (vegetation retreating farther from
 the edge) #### File: ESNERR_Mudflat_Erosion.csv **Description:** dataset
 on mudflat erosion at Elkhorn Slough, from measuring how much of the
 permanent marker protrudes above the mudflat, and calculating the rate of
 change since the last measurement ##### Variables * Station: location
 where data were collected; latitude and longitude provided the the Station
 Info tab of the Excel file uploaded as Supplementary Material * Region:
 Upper vs. Lower portion of Elkhorn Slough * Subregion: finer
 categorization of region used by ESNERR; see the KMZ file uploaded
 separately * Area:  finer categorization of subregion used by ESNERR, see
 the KMZ file uploaded separately. * Subarea: finer categorization of
 subregion used by ESNERR, see the KMZ file uploaded separately. *
 Geographic_Category: combined region and area name used for ESNERR
 analyses * Year: monitoring year *
 Annualized_Change_Sediment_At_Mudflat_Stake: sediment deposition (positive
 numbers) or erosion (negative numbers) in cm/year since last measurement
 #### File: ESNERR_Mudflat_Biomonitoring.csv **Description:** dataset on
 mudflat biomonitoring at Elkhorn Slough, from rapid search of species
 &gt;2 cm in size on a 10 m stretch of mudflat in front of the bank erosion
 monitoring station; cover class abundance estimate is made separately on
 hard vs. soft substrate, plus count of shells found in the area is
 provided. ##### Variables * Year: monitoring year * Species: species
 encountered * Taxon: larger taxonomic group * Native status: native or
 non-native - Observation type: either a cover class estimate on available
 mudflat area, a cover class estimate on available hard substrate, or a
 count of shells NOTE:  Station numbers are listed as columns, and then
 categorized at the bottom of the file, in the format needed for analysis
 in Primer, which is the software used by ESNERR for analyses of these
 data.  For observation type "Shells", a raw count of shells is
 provided.  For observation types "Attached to hard substrate" or
 "On mudflat", a cover class estimate is provided. | 0=absent  |
 3= abundant: on 10-50% available substrate | |
 :------------------------------------------------------ |
 :-------------------------------------------- | | 1=trace presence:
 present on &lt;1% of available substrate | 4= very abundant: on &gt;50%
 available substrate | | 2=rare: on 1-10% of available substrate |   | *
 Station: location where data were collected; latitude and longitude
 provided the the Station Info tab of the Excel file uploaded as
 Supplementary Material * Region: Upper vs. Lower portion of Elkhorn Slough
 * Subregion: finer categorization of region used by ESNERR; see the KMZ
 file uploaded separately * Area:  finer categorization of subregion used
 by ESNERR, see the KMZ file uploaded separately. * Subarea: finer
 categorization of subregion used by ESNERR, see the KMZ file uploaded
 separately. #### File: Elkhorn_Slough_Names_Oct2024.kmz
 **Description:** This is a Google Earth file showing how the Elkhorn
 Slough National Estuarine Research Reserve subdivides the estuary into
 regions and areas that are included as columns in the dataset #### **The
 supplemental files uploaded to Zenodo are:** **File:
 Bank-Erosion-Mudflat-Monitoring-Metadata-2024-11-30.pdf**
 **Description:** this is the complete metadata file generated according to
 a template used by the Elkhorn Slough National Estuarine Research Reserve
 **File: Bank-Erosion-Mudflat-Monitoring-2024-11-30.xlsx**
 **Description:** this is an Excel file used by the Elkhorn Slough National
 Estuarine Research Reserve for this monitoring program.  It includes
 station locations (lat & long), team members involved in different
 surveys, field datasheets and definitions used, raw data, and summary data
 tables.  This is the source data used to generate the preceding CSVs,
 which are the clean/simple/curated forms of the data which will be useful
 to most people. ## Code/software Three CSV files were uploaded with the
 cleanest, simplest version of the data.  No special software is required
 to open them.  One file, "ESNERR Mudflat Biomonitoring," is
 structured in a format compatible with the software Primer, with samples
 as columns and information about the samples at the bottom. We have also
 uploaded a PDF metadata file and an Excel file that has station
 information, datasheets, summary tables, and the raw data that generated
 the CSVs. We uploaded a KMZ file that shows the regions and areas referred
 to in the CSV files; this can be opened using Google Earth.