Tanner, Richelle L: Community function under Phragmites invasion in Suisun Marsh CA [dataset bundled publication]. PANGAEA, https://doi.pangaea.de/10.1594/PANGAEA.987847 (dataset in review)

Three sites in Suisun Marsh were selected for their relative spread of P.australis, walking accessibility, and tidal restoration status to be monitored in 2020-2021 (Fig. 1). Since each site had different hydrogeomorphic features, sampling methods were altered slighted between them. Tule Red (38.128880, -121.980554) was restored in 2019 as the first tidal restoration project in Suisun Marsh; thus, we focused more of our efforts on ecological monitoring within this wetland immediately post-restoration. Hill Slough (38.232834, -122.020285) was officially restored to tidal action in 2022; however, pre-restoration levee breaches created a wetland with partial tidal flow during the sampling period. Blacklock (38.183957, -121.889321) was restored in 2006 through an accidental levee breach and required kayaking for full accessibility due to high rates of sediment loss and widening channels. Blacklock also had P. australis ongoing control administered by the Department of Water Resources (methods: mowing followed by glyphosate and imazapyr herbicide treatment), so this study additionally monitored the effects of P. australis control on community function at one site. All sampling and observations of plant, invertebrate, and avian communities were conducted along a series of transects. Observations were made every month between November 2020 and December 2021. These transects were designed to start at a secondary or tertiary channel edge and proceed 50m directly perpendicular onto the marsh plain. Tule Red had three pairs of P. australis/native transects (n=6), Hill Slough had two pairs (n=4), and Blacklock followed a slightly different design detailed below, due to hydrogeomorphic differences. Avian communities were surveyed using a trained aural method, noting the presence of bird calls within ~20m of the transect tape (in perpendicular width) and their corresponding vegetation stand for 50m. Researchers trained on local California birds using the Cornell Lab All About Birds guide with audio files (https://www.allaboutbirds.org/guide/) and completed multiple field training sessions before collecting data. To account for disturbance, one researcher would walk slightly ahead to listen and the other would note their observations on a clipboard indicating the meter number at which they were heard. Data were noted using 4-letter alpha codes that are standard for bird species identification (see www.birdpop.org). Often the bird(s) were visually spotted during this survey, which provided confirmation of recording accuracy. Additionally in the first 20m, quadrats were used every 5m to obtain a subsampling of the transect for plant and invertebrate biodiversity and community characteristics (completed at 0m, 5m, 10m, 15m, 20m). This was accomplished using a 1m2 quadrat placed over the vegetation and a 0.25m2 sub-quadrat placed at each corner of the 1m2 quadrat (n=4 biological replicates per meter sampled). The following plant measurements were recorded: dominant species present and its shoot density, average shoot height, average shoot circumference, life stage [growing, flowering (presence of flowers), senescing, dead (no green on stalk but standing), and litter]. We also recorded if other plant species were present within the sub-quadrat. To evaluate the invertebrate community within these same quadrats, we collected benthic, pelagic, and terrestrial samples (completed at 0m, 5m, 10m, 20m). Benthic mud cores (14.5cm deep and 6cm in diameter) were collected using a PVC pipe and stored into a plastic Ziploc bag. If water was present in the quadrat, a sample was collected using a large turkey baster (~60g). Terrestrial vegetation samples along with their invertebrate inhabitants were collected at random to fill an 8oz container. All invertebrates were collected under California Scientific Collecting Permit S-201970002-20281-001. At Tule Red and Hill Slough, the paired transect sampling design was possible due to the availability and accessibility of vast swaths of marsh plain. At Blacklock, this transect design was modified to account for high inundation of the wetland, resulting in little marsh plain available for surveying. Instead, we established general plot areas, at which three plant and invertebrate quadrat measurements were taken instead of sampling along the transect. As stated in site selection, Blacklock was also unique in the presence of P. australis control treatment areas (mowing and herbicide), which were ~10m x 10m plots of fully cleared mudflat within P. australis stands. These were included in the paired plot areas, such that there were three groups of three plot areas that each had three replicate quadrats (n=9 each of treated P. australis, extant P. australis, and native canopy quadrats across the site). Avian communities at Blacklock were still surveyed on 50m transects, but this was done along channel edges from a kayak. Invertebrate sample processing, identification, and quantification followed a standardized US Geological Survey protocol with a quality assurance/quality control (QA/QC) step (Moulton II et al. 2000). All invertebrate samples were transported to the UC Davis Center for Aquaculture and Aquatic Biology within two hours of collection in coolers. Benthic samples were weighed, rinsed with deionized water to remove sediment, and filtered using a 0.5mm sieve. Retained invertebrates and vegetation were preserved in a rose bengal-dyed 70% ethanol solution. Pelagic water samples were weighed and rinsed with deionized water using a 0.125mm sieve, then also preserved in a rose bengal-dyed 70% ethanol solution. Terrestrial invertebrate samples were identified at time of processing (within seven days of field collection) and individuals were preserved in a 70% ethanol solution. Records noted where invertebrates were found on vegetation (stem, leaf, flower, root, seed etc.). To control for slight differences in sample size capture accuracy, counts per sample were normalized to the weight of the original sample. Invertebrates were identified to morphospecies level, which has shown accurately estimates species number in other studies (Oliver and Beattie 1996). Pelagic invertebrate samples were sorted under a dissecting microscope to the lowest taxonomic unit and counted for abundance. 50% of each benthic invertebrate collection (8 oz sample) was used as a representative sample to reduce processing time, which was determined using a portioned tray and a random number generator to select sample material for processing. The selection of 50% for accurate representation of benthic samples was determined using the below quality assurance/quality control process. Due to the length of this process for the quantity of samples collected, only pelagic and terrestrial samples were quantified and identified for the full monthly dataset. Benthic samples were quantified and identified on a quarterly basis for the dataset (January, March, June, September, December 2021). For the QA/QC process, a sample set (n=74) of benthic collections were used in a quality assurance/quality control report to determine if an initial random 25% of the sorted sample was representative of the full sample. Sample sorting was increased from 25% to 50% due to high variance in invertebrate count. Additionally, we performed a QA analysis of 14% of each individual sorter, per the recommendations of the original protocol and to account for our engagement of a large team of undergraduate student sorters in this process. If an error rate of >14% is found, all samples sorted by that individual were re-sorted by an expert. Our QA/QC analysis also concluded that all pelagic samples were to be sorted twice.