Sampling event dataset for ecological monitoring of riparian restoration effort in Colorado foothills

Abstract Background The foothills and shortgrass prairie ecosystems of Colorado, United States, have undergone substantial and sustained anthropogenic habitat change over the past two centuries. Riparian systems have been dramatically altered by agriculture, hydrological engineering, urbanisation and the introduction of non-native invasive species. In 2016, Denver Botanic Gardens began a restoration effort of Deer Creek which seeks to modify the hydrology of the creek by mimicking the effects of beaver dams with artificial structures. The site, owned by the US Army Core of Engineers and managed by Denver Botanic Gardens, had been the subject of previous botanical surveys. With the initiation of the restoration project, permanent transects were established along the stream and are sampled for ground vegetation richness and abundance, canopy cover, soil and stream conditions and aquatic macroinvertebrate community makeup on an annual basis. To provide a means for tracking any post-intervention changes in the riparian ecosystem, this resource reports all recorded occurrences and measurements, along with methodologies and motivations from past and current surveys in the form of a sampling event dataset. New information The current project and past surveys document 382 plant taxa and 157 aquatic macroinvertebrate taxa. A total of 16304 occurrences and 7422 measurements are included in the resource. Occurrence and measurement data taken from transects provide a means to measure species abundance, ground cover and other biotic and abiotic characteristics relevant to assessing the effects of hydrological restoration on riparian plant communities.


Introduction
Riparian corridors and waterways in the American West have been drastically altered though agricultural disturbance, hydrological engineering, exotic species introductions, urbanisation and historical exploitation of the North American beaver, Castor canadensis (Poff et al. 2011, Naiman et al. 1988. Within this arid region, amid a complex matrix of fragmented habitat and land use change, waterways are crucial resources for ecosystem services and biodiversity refugia (Palmer et al. 2013, Seavy et al. 2009, Sweeney et al. 2004).
In 2016, Denver Botanic Gardens initiated long-term ecological restoration of Deer Creek in southern Jefferson County, Colorado, United States. A section of Deer Creek runs from west to east through a Jefferson County Open Space property and Denver Botanic Gardens Chatfield Farms property. The creek and its surrounding area had been subjected to human disturbance such as channelling, livestock grazing, hay production and urbanisation, dating back as far as the mid-19 century (Colorado Encyclopedia 2016). Such disturbances have contributed to an overwhelming dominance of non-native plant species in the understorey of the riparian area along Deer Creek, as well as the presence of non-native tree species within the overstorey. The hydrology of the creek was modified, resulting in increased flow energy, run-off volume and intensity and deepened, undercut channels. The restoration project saw the installation of small channel structures that function like beaver dams to facilitate over-bank flows to move water from the stream channel and distribute it across the floodplain. We hypothesise that these techniques will restore the hydrological conditions suitable for the regeneration of native riparian plant species through active and passive measures.
To track progress, we established permanent transects to monitor the ground vegetation community, canopy cover, stream conditions, water quality and aquatic macroinvertebrate diversity. Presented as a sampling event dataset, using the Darwin Core standard and relevant extensions, we provide records for all data, samples and specimens pertaining to th the restoration project's progress, as well as specimen data from previous surveys in the area of interest (Levy et al. 2020).

General description
Purpose: Sampling transect data were recorded to monitor any changes in ground vegetation, canopy cover, water quality and aquatic invertebrate community over the course of an ongoing restoration effort of the hydrological conditions of the stream. Herbarium specimens were collected in previous and the current surveys to document plant species richness in the areas described in this dataset and are provided here for additional context.  Sampling description: All sites were sampled once per year, during the growing season when most vegetation was mature enough to make proper species identifications.

Project description
For the first two years of monitoring (2016-2017), twelve 25-m transects were installed to measure ground and canopy cover. For ground cover, every 0.25 m was sampled via the point intercept method. Ground vegetation species were recorded as top canopy (1st hit) or lower canopy (2nd hits) and presented here as occurrences, based on human observation. In 2016 and 2017, the ground surface type was recorded only when no vegetation was present, but beginning in 2018, ground surface type was recorded every 0.25 m. Ground surface type is provided in the extendedMeasurementOrFact extension within this resource. When no vegetation was present at a point along the transect, we provide this information in the form of an occurrence record with the status "absent" and indicate the type of ground cover in the occurrenceRemarks. For canopy cover, every 0.5 m was sampled. Canopy species observed through a GRS densiometer were recorded and are provided here as occurrences, based on human observation. Any plant species observed within 1 m of either side of the transect, that were not recorded as part of the point intercept sampling, were also recorded as observation occurrences. Voucher specimens of plants were taken when identification to species was not confident or possible in the field. Sections of stream, directly adjacent to the vegetation transects, were sampled for stream conditions and water quality measurements, including stream velocity, stream depth, stream width, bank height, bank to thalweg distance, streambed substrate at thalweg, water surface to bankful distance, wetted channel width, estimated percent of pools, estimated percent of runs, estimated percent of riffles, estimated percent of undercut bank, water nitrogen levels, E. coli content, dissolved oxygen, water temperature, electrical conductivity, pH, coliform levels, total dissolved solids and visual condition of water in stream. Water samples were sent to a contractor for measurements. Aquatic macroinvertebrate communities were also sampled within the stream and sent to a contractor for sorting and identification.
In 2018, six additional transects were added upstream of the temporarily installed dam-like structures. Several additional measurements were also recorded along the vegetation transects: soil moisture percentage was measured every 1.0 m, canopy cover percentage was measured with a spherical densiometer every 0.5 m and ground surface type, regardless of the presence of vegetation, was recorded every 0.25 m. These measurements are provided within the extendedMesurementOrFact extension of this resource.
Voucher specimens from previous botanic surveys, aimed at documenting species richness of the area, are also included in this resource as occurrences, based on preserved specimens. The property on the eastern portion of the stream reach is managed by Denver Botanic Gardens and, consequently, has been an area of thorough botanical survey. Specimen occurrence data from these varied botanical surveys is provided here to document the historical existence and/or location of plant species in the area, as this passive long-term restoration effort may rely on seedbanks and the movement or expansion of existing local populations. Methods used in previous surveys were not as well documented, but are similiar to those in Alba and Islam (2019)  Quality control: Raw data from sampling transects were checked upon transcription into digital format. Once data were submitted into a relational database, a random sample of records was produced and checked against the raw data. During ecological surveys, herbarium voucher specimens were collected when species identification could not be confidently determined in the field.
Pull out the 25 m tape in between two rebar posts. The line should be taut and as close to the ground as possible.

2.
Take photograph at origin of transect. Stand behind the post, face the endpoint and take the picture with the post in the photo. 3.
Begin at the "0" end of the line, move at 0.25 m intervals towards the end. 4.
At origin (0 m), midpoint (12.5 m) and end (25 m), measure distance from transect to bank and bank height. 5.
The starting point will be 0.25 m. Always stand on the same side (away from the stream) of the line. 6.
Drop a pin flag to the ground from a standard height of 1 m next to the stream side of the tape. The pin should be vertical. The pin should be dropped from the same height every time. Do not guide the pin to the ground, let it fall freely.

7.
Once the pin flag is on the ground, record every species it intercepts. The first species it hits (the highest one/furthest from the ground) is the "Top canopy". If no leaf, stem or plant base is intercepted, record "NONE" in the "Top canopy" column. Record all additional species intercepted by the pin in the "Lower Canopy Layers" column. Record them in order from closest to the top canopy to furthest (highest to lowest). Record each species only once, even if it is intercepted multiple times. If species cannot be identified at the current stage, flag the plant and record location on "Unidentified Species" datasheet and "Unidentified Species" section of the vegetation datasheet. Return later to identify or collect voucher specimen of same species from outside the transect. 8.
Record the ground surface the pin flag rests on. Options are litter, bare soil, rock (> 5 mm diameter), standing dead vegetation, water, downed woody debris (logs/large branches), road/trail (paved or gravel trail).
Measuring soil moisture (Hufft et al. 2019a) 1. Beginning at the "0" end of the transect, measure the soil moisture on the right side of the tape at 1 m intervals, starting at 1 m.

2.
At each point, insert the soil moisture meter at the right side of the transect 20 cm deep into the soil. 3.
Record the percent volumetric soil moisture that appears on the screen. If the soil is too hard or rocky to fully insert the moisture meter, record that the measurement was unable to be taken.
Measuring tree canopy cover (Hufft et al. 2019a) 1. Beginning at the "0" end of the transect and starting at the 0.5 m mark, measure the tree canopy cover every 0.5 m. Stand on the side of the tape furthest from the creek facing the end point of the transect.
Hold the densiometer out so that the bubble in the corner is in the centre of its circle, indicating that the instrument is level.

4.
Hold the densiometer about 30-46 cm away from you and low enough so you can see all 24 squares in the window.

5.
Imagine 4 dots at each corner of each of the 24 squares. Count the number of dots in which a tree is visible. 6.
Additionally, record species of every tree that appears in the densiometer window.
After measuring for percent cover, use the metre stick as a guide to search the belt transect area for any species that were not recorded while measuring percent cover.

2.
Record additional species identified that are rooted within the 25 m × 2 m belt. Collect a voucher specimen, if unable to identify in the field. Take water samples at the thalweg origin or, if stream is too deep for wading, at the deepest point possible. Make sure to collect probe data and water samples at the same place and record this location on the datasheet. 8.
Samples are TIME SENSITIVE. Samples must be dropped off within 8 hours of sampling. No sample drop-offs on Fridays.
Stream Measurements (Hufft et al. 2019b) 1. Start at thalweg adjacent to vegetation transect origin. If thalweg is too deep to wade, take measurement at the deepest point possible and record this point on datasheet.

2.
For each probe, make sure to not submerge probes past the point where the storage caps seal and swish the probe in water to remove air bubbles and allow reading to stabilise before recording. 3.
Using the appropriate probes, collect the following data and record on data sheet: If water is too deep at the thalweg to wade in, take measurements at the deepest point possible adjacent to the origin and record location on datasheet. This is especially important for stream reaches with dams. (Hufft et al. 2019b) 1.

Aquatic Macroinvertebrate Collection
Since the water is moving when we sample, we use the kicknetting method.

2.
Start at thalweg at 20 m mark downstream from origin. Start downstream and move upstream towards origin (See Fig. 1) 3.
Conduct kicknetting for 1 minute every 5 m, for five sampling bouts moving upstream.

4.
Five sampling bouts should be conducted for each transect.
• However, samples should be 5 m apart, so if large parts of the stream are dry, only take as many samples as the stream allows.

5.
At each sampling bout, • Disturb area 1 m2 upstream of net, using heel or toe to dislodge the upper layer of cobble/gravel and scrape underlying bed.

•
Pick up larger substrate and rub by hand to remove attached organisms.

•
If the water is slow moving, use your hands or feet to push what has been kicked up into the net.

•
Exclude specimens clinging to the outside of nets. 6.
Place contents of net into the mesh bucket.
• Rinse outside of net to move sediment and specimens inside the net to one corner.
• Flip net inside out in bucket and rinse down outside of net with more water to wash all contents into bucket.

•
To avoid contamination of the sample, do not pour water into the side of the net with the specimens. Only pour water on the outside of the net.

•
Continue adding contents of net into mesh bucket for the length of the transect. 7.
Scoop specimens into 1 litre plastic rectangular Nalgene sampling jar by hand. It may be necessary to place the mesh bucket in the stream and swirl to get specimens to one side.
• Release any fish, amphibians, reptiles or crayfish back into stream, but record their presence on the data sheet. 8.
Fill jar with no more than 50% of sample material from the stream. Use more than one jar per sample, if necessary.
• Add ethanol to the bottles to create a 50:50 sample to ethanol ratio.

•
In 2018, we used an average of 2-3 bottles per sample site (max 5 at TSP and dammed sites) and roughly 2.5 x 750 ml of ethanol per day. 9.
Pick out and scrape off larger rocks in the bucket to remove any macroinvertebrates clinging to them. Smaller gravel can be added to bottle. 10.
Properly label each bottle using a marker that is not alcohol-soluble. Check naming conventions file to make sure samples are labelled consistently from year to year. 11.
Follow the instructions below for proper storage and sample drop-off for identification. 12.
Backwash the net with stream water before collecting samples from the next site. Section of Deer Creek that was monitored, including transect and channel structure locations in Colorado, United States.

Geographic coverage
Description: Data were collected from 18 sites along Deer Creek (Fig. 2)
Notes: Three botanical survey efforts were undertaken prior to implementation of restoration effort and ecological monitoring. locationID An identifier for the set of location information (data associated with dcterms:Location). May be a global unique identifier or an identifier specific to the dataset.

country
The name of the country or major administrative unit in which the Location occurs. stateProvince The name of the next smaller administrative region than country (state, province, canton, department, region etc.) in which the Location occurs.
county The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department etc.) in which the Location occurs. locality The specific description of the place. Less specific geographic information can be provided in other geographic terms (higherGeography, continent, country, stateProvince, county, municipality, waterBody, island, islandGroup). This term may contain information modified from the original to correct perceived errors or standardise the description. geodeticDatum The ellipsoid, geodetic datum or spatial reference system (SRS), upon which the geographic coordinates given in decimalLatitude and decimalLongitude are based.
coordinateUncertaintyInMeters The horizontal distance (in metres) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the kingdom The full scientific name of the kingdom in which the taxon is classified. phylum The full scientific name of the phylum or division in which the taxon is classified. class The full scientific name of the class in which the taxon is classified. order The full scientific name of the order in which the taxon is classified. family The full scientific name of the family in which the taxon is classified. genus The full scientific name of the genus in which the taxon is classified. specificEpithet The name of the first or species epithet of the scientificName. infraspecificEpithet The name of the lowest or terminal infraspecific epithet of the scientificName, excluding any rank designation. taxonRank The taxonomic rank of the most specific name in the scientificName.

Data set name: multimedia.txt
Character set: UTF-8

Author contributions
R.L. prepared the dataset, wrote the metadata description and wrote the manuscript. M.P. collected and transcribed much of the data, provided consultation for the metadata description and manuscript and contributed to the methodology. R.H. designed and directed the study.