Data for: Direct and indirect ecosystem responses to vehicle compaction of soft sediments
Data files
Jan 02, 2026 version files 507.18 KB
-
BirdCamR.noblanks.csv
62.67 KB
-
infauna.csv
128.58 KB
-
Oyster_outplants2.GPS.csv
72.04 KB
-
PacificCultch.csv
6.79 KB
-
Penetrometer.csv
52.60 KB
-
README.md
22.49 KB
-
sediment.csv
83.35 KB
-
Shrimp.csv
52.30 KB
-
WP_multiplepass_shrimpcores.csv
26.37 KB
Abstract
In northeastern Pacific tidal flats, a native bioturbator, ghost shrimp Neotrypaea californiensis, engineers soft-sediment habitat and interacts antagonistically with bivalve shellfish. Vehicle compaction has been used in pest control of ghost shrimp, but this disturbance lacks quantitative evidence of its efficacy and environmental impacts. Through three large (~10 ha) experiments in Grays Harbor, Washington, USA, we tested the direct and indirect impacts of compaction by a tracked vehicle (MarshMaster) on ghost shrimp density, sediment conditions, and infauna. We also examined how oyster survival (cultch seeded with Pacific oysters, Magallana gigas) and waterbird usage of tidal flats responded post-compaction. In Experiment 1, compaction occurred on 13 Aug 2022 and 19 May 2023, and sampling occurred seasonally over three years, including immediately post-compaction. In Experiment 2, compaction occurred on 2 Aug 2023, and sampling occurred seasonally over one year. Due to minimal treatment effects at this site, a third experiment was set up on 0.16-ha beds that were compacted with 0, 1, 3, or 5 compaction passes on 24 Jul 2024 and followed for a year. Compaction pushed <20% of ghost shrimp to the surface, where they were vulnerable to predation and damage, yet did not significantly reduce subsurface densities within 1-2 days. Rather, declines in shrimp density and shifts to smaller size classes appeared at later sample timepoints and were more pronounced with more compaction passes. All compaction experiments resulted in firmer sediment for at least a year, even in the experiment where shrimp densities were unaffected by a single compaction pass. Where compaction briefly reduced shrimp densities below 50 m-2, sediment increased in mud and organic content and infauna increased in abundance, suggesting that these changes were mediated through reduced bioturbation rather than a direct impact of compaction. Similarly, multivariate responses of infauna appeared only in the experiments where compaction reduced shrimp densities. Habitat use by waterbirds was more influenced by tidal stage than by compaction; statistically, only dunlin (Calidris alpina) foraged more on compacted than on reference beds. Finally, although survival of outplanted oyster seed improved with compaction at one site, it remained too low (~34-40% yr-1) for viable farming.
Dataset DOI: 10.5061/dryad.fbg79cp8p
Description of the data and file structure
Intertidal flats of sandy soft-sediment dominated by ghost shrimp (Neotrypaea californiensis) in Grays Harbor, Washington (USA) were compacted with a tracked vehicle (MarshMaster MM 2LX, 1 pound per square inch ground pressure). Because the tracks of the MarshMaster have a gap between them, successive rounds overlapped so that all surface experienced ground pressure. In Experiment 1 (Damon Point), five 2-ha beds were established along an elevation contour of 0.2-0.6 m relative to mean lower low water (MLLW), and two beds (9 and 11) were compacted on 13 Aug 2022 and recompacted on 19 May 2023. In Experiment 2 (Westport Single), five 2-ha beds were established along an elevation contour of 0.4-0.5 m MLLW, and two beds (2 and 4) were compacted on 2 Aug 2023. In Experiment 3 (Westport Multiple), nine 0.16-ha beds were established along an elevation contour of 0.6 m MLLW; three were uncompacted (Reference) beds, and two each were compacted with 1x, 3x, and 5x passes of the MarshMaster. Six stations (subsamples) per bed were used to record responses on the 2-ha beds established in Experiment 1 and 2, and four stations per bed were used in Experiment 3. For each post-compaction sampling event, these subsamples were measured for: a) ghost shrimp density by coring (five times to 70 cm within a 1 m2 area, totaling 0.0625 m2); b) penetrability of the sediments based on depth of penetration of a standard metal rod; c) organic content of sediment by collecting a small core (5.4 cm depth, 30 ml), drying, and ashing at 500 C; d) mud content of sediment by dry-sieving the ashed sediment and determining the fraction that passed through a 63-micrometer screen; e) abundance and composition of invertebrate macro-infauna in cores (10 cm diameter, 10 cm depth) sieved to 500 micrometers. Additionally, at stations in Experiment 1 and 2, seeded cultch (small Pacific oysters, Magallana gigas, on a shell) were tethered on the ground and collected at intervals to determine oyster survival. Experiment 1 also was evaluated for bird use at low tide during spring migration (6 days in April 2023 and 7 days in April 2024) by photographs from remote cameras.
For all files, the "Notes" variable is entered as "none" when no notes were recorded. NA refers to data not available.
Files and variables
File: BirdCamR.csv
Description: Counts of birds by taxon within the field of view of a Go-Pro Hero3+ camera attached to a pole 1 m above the tidal flat, deployed before the water ebbed and retrieved as the water flooded. All cameras were deployed at a large experimental site 0.2-0.6 m above mean lower low water at Damon Point, Grays Harbor, Washington (Experiment 1).
Variables
- Date: Date when camera was deployed
- GPSN: WGS84 geoposition of camera in north latitude
- GPSW: WGS84 geoposition of camera, negative sign for west longitude
- Camera: Number identifying specific camera
- Bed : Number identifying the 2-ha Bed in which the camera was deployed. Beds 9 and 11 experienced vehicle compaction. Beds 8, 10, and 12 were reference beds.
- Stage: Tidal stage - Ebb was defined as the time at which the water’s edge passed the camera (when the frame appeared fully dry), and flood as the time at which it passed the bamboo stake 7 m from the camera (when the frame was fully flooded). Low water was defined as the timepoint halfway between the ebb and flood. The tidal stages were divided into six periods: 24-10 minutes before the ebb, 8 minutes before to 6 minutes after the ebb, 8-22 minutes after the ebb, 16 minutes around low water, 24-10 minutes before the flood, and 8 minutes before to 6 minutes after the flood.
- NumberImages: Number of photographs at 2-minute intervals used at that Stage
- DunlinNear: Number of Dunlin (Calidris alpina) closer than 7 m in the field of view
- DunlinFar: Number of Dunlin (Calidris alpina) farther than 7 m but not beyond 14 m
- DowitcherNear: Number of Dowitcher (Limnodromus spp.) closer than 7 m in the field of view
- DowitcherFar: Number of Dowitcher (Limnodromus spp.) farther than 7 m but not beyond 14 m
- GullNear: Number of Gulls (Larus spp.) closer than 7 m in the field of view
- GullFar: Number of Gulls (Larus spp.) farther than 7 m but not beyond 14 m
- CrowNear: Number of Crows (Corvus brachyrhychos) closer than 7 m in the field of view
- CrowFar: Number of Crows (Corvus brachyrhychos) farther than 7 m but not beyond 14 m
- UnidNear: Unidentifiable birds closer than 7 m in the field of view
- UnidFar: Unidentifiable birds farther than 7 m but not beyond 14 m
- Notes: Description of factors that could influence data collection
File: infauna.csv
Description: Counts of macroinfauna by taxon in cores (10 cm diameter, 10 cm depth) collected from Grays Harbor, Washington, in Experiment 1 (Damon Point, 0.2-0.6 m above mean lower low water), Experiment 2 (Westport, 0.4-0.5 m above mean lower low water), and Experiment 3 (Westport, 0.6 m above mean lower low water, identified as Westport Multiple). Treatments were applied at the scale of aquaculture beds, which were 2 ha in size in Experiment 1 and 2, but 0.16 ha in size in Experiment 3. Vehicle compaction occurred on Beds 9 and 11 at Damon Point, on Beds 2 and 4 at Westport, and in a gradient of compaction intensity (1x, 3x, 5x) at Westport Multiple. Infauna were collected on a 500-micron mesh sieve.
Variables
- Site: Experimental site
- SampleCode: Code denoting the Bed and position on the bed where the core was collected
- Bed: Code denoting the Bed
- DateSampled: Date used to designate one timepoint of sampling, which could span several consecutive days
- DateSampled_true: Actual date when core was collected
- DaysPostComp: Core collection date relative to the experimental setup when vehicle compaction occurred
- DateProcessed: Date when sample was sorted in the lab and infaunal taxa were identified and counted
- GPSN: WGS84 geoposition of core in north latitude
- GPSW: WGS84 geoposition of core, negative sign for west longitude
- Clinocardium_nuttallii: Species count (bivalve clam = cockle)
- Cryptomya_californica: Species count (bivalve clam)
- Macoma_spp: Count by genus (bivalve clam)
- Mya_arenaria: Species count (bivalve clam)
- Mytilus: Count by genus (bivalve mussel)
- Nutricola: Count by genus (bivalve clam)
- Nuttalia: Count by species (Nuttallia obscurata, bivalve clam)
- Ruditapes_philippinarum: Count by species (bivalve clam)
- Protothaca_staminea_(Leukoma): Count by species (bivalve clam)
- Tellina_modesta: Count by species (bivalve clam)
- Tellina_nuculoides: Count by species (bivalve clam)
- Allorchestes: Count by genus (amphipod)
- Ampithoie: Count by genus (Ampithoe, amphipod)
- Calanoida: Count by order (copepod, crustacean)
- Caprellidae: Count by family (amphipod)
- Cumacean: Count by order (Cumacea, crustacean)
- Crangon_fransiscorum: Count of Crangon franciscorum (shrimp, Decapod crustacean)
- Clausiidae: Count by family (copepod, crustacean)
- Eogammarus: Count by genus (amphipod)
- Eohaustorius_estuarius: Count by species (amphipod)
- Grandidierella: Count by genus (amphipod)
- Hemigrapsus_sp: Count by genus (crab, Decapod crustacean)
- Monocorophium_spp: Count by genus (amphipod)
- Neotrypaea_californiensis: Count by species (Thallassinid shrimp)
- Ostracoda: Count by class (crustacean)
- Paracorophium: Count by genus (amphipod)
- Pinnixa_spp.: Count by genus (crab, Decapod crustacean)
- Tanaidacea: Count by order (crustacean)
- Urothoe_spp.: Count by genus (amphipod)
- Capitellidae: Count by family (polychaete, annelid)
- Cirratulidae: Count by family (polychaete, annelid)
- Hesionidae: Count by family (polychaete, annelid)
- Hirudinea: Count by class (leeches, annelid)
- Glyceridae_Goniadidae: Count by families (polychaete, annelid)
- Magelonidae: Count by family (polychaete, annelid)
- Maldanidae: Count by family (polychaete, annelid)
- Nemertean: Count by phylum
- Nephtyidae: Count by family (polychaete, annelid)
- Nereididae: Count by family (polychaete, annelid)
- Oligochaete: Count by order (annelid)
- Opheliidae: Count by family (polychaete, annelid)
- Orbiniidae: Count by family (polychaete, annelid)
- Oweniidae: Count by family (polychaete, annelid)
- Paraonidae: Count by family (polychaete, annelid)
- Phoronidae: Count by phylum
- Phyllodocidae: Count by family (polychaete, annelid)
- Pilargidae: Count by family (polychaete, annelid)
- Polynoidae: Count by family (polychaete, annelid)
- Platyhelminthes: Count by phylum (flatworms)
- Sabellidae: Count by family (polychaete, annelid)
- Spionidae: Count by family (polychaete, annelid)
- Syllidae: Count by family (polychaete, annelid)
- Terebellidae: Count by family (polychaete, annelid)
- Barnacle: Count by subclass (Cirripedia, crustaceans)
- Cnidaria: Count by phylum
- Hydrozoa: Count by class (within Cnidaria)
- Nudibranch: Count by order (Nudibranchia, gastropod)
- Sea_urchin: Count by class (Echinoidea, echinoderm)
- Snail: Count by class (Gastropoda)
- Nematoda: Count by phylum
- Unknown_amphipoda: Count by class
- Unknown_bivalve: Count by class
- Unknown_polychaete: Count by class
- Decapod_zoea: Count by order
- Harpacticoida: Count by order
- Foraminifera: Count by phylum
- Chironomidae: Count by family (fly larvae)
- Cicadellidae: Count by family (leafhoppers)
- Chrysomelidae: Count by family (beetles)
- Hemiptera: Count by family (bugs)
- Hymenoptera: Count by family (wasps)
- Isotomidae: Count by family (springtails)
- Talitridae: Count by family (amphipod)
- Notes: Collection notes
- ID'd_by: Person doing identification
File: Penetrometer.csv
Description: Penetration depth into the sediment of a standard rod to determine sediment penetrability on intertidal flats in Grays Harbor, Washington, in Experiment 1 (Damon Point, 0.2-0.6 m above mean lower low water) and Experiment 2 (Westport, 0.4-0.5 m above mean lower low water). The penetrometer was a device consisting of a 159 cm tall metal rod with a movable 2.25 kg weight encircling an additional section of rod between two plates. For each subsample, the rod was placed vertically on the mudflat, the weight was dropped 3 times, and the distance measured from the plate to the sediment. The final measurement was subtracted from 159 to give the depth of penetration into the sediment in centimeters, a measure of bed softness.
Variables
- Site : Experimental site
- DateSampled_true: Actual date when penetrometer was used
- DateSampled: Date used to designate one timepoint of sampling, which could span several consecutive days
- DaysPostComp: Penetrometer use date relative to the experimental setup when vehicle compaction occurred
- Bed: Code denoting bed
- Sample: Code denoting the Bed and position on the bed where the penetrometer was used
- Treatment: Treatment applied to 2-ha bed, either Compacted by vehicle compaction, or Reference
- Elevation: For Westport Single only, refers to whether samples were well into the bioturbated area ("High") or at the lower edge near firmer sediment ("Low")
- GPSN: WGS84 geoposition of penetrometer sample in north latitude
- GPSW: WGS84 geoposition of penetrometer sample, negative sign for west longitude
- Penetr1: Rod height above the sediment after first drop of weight (cm)
- Penetr2: Rod height above the sediment after second drop of weight (cm)
- Penetr3: Rod height above the sediment after third drop of weight (cm)
- Notes: Observations that could affect penetrometer data
File: Oyster_outplants2.GPS.csv
Description: Counts of Pacific oysters (Magallana gigas) on cultch ("mother shell"). Cultch were tethered to posts inserted on tidal flats in Grays Harbor, Washington, at multiple stations on each bed in Experiment 1 (Damon Point, 0.2-0.6 m above mean lower low water) and Experiment 2 (Westport, 0.4-0.5 m above mean lower low water). Pre-outplant samples are from cultch having the same source as outplanted cultch, therefore representative of initial counts. When cultch were collected, each was counted for remaining live oysters (and in some cases for obvious dead oysters with open or missing top valves).
Variables
- DateSampled: Date when cultch was counted for oysters
- Site: Experimental site
- DaysPostComp: Number of days after vehicle compaction treatment
- Bed: Code denoting bed
- SampleCode: Code denoting the Bed and position on the bed where the cultch was tethered
- NGPS: WGS84 geoposition of tethered cultch in north latitude
- WGPS: WGS84 geoposition of tethered cultch, negative sign for west longitude
- Live: Count of live oysters
- Dead: Count of dead oysters
- Total_count: Count of live and dead oysters
- Live_shell_ht.mm: Dimension of live oyster shell in mm from hinge to lip
- Notes: Comments regarding cultch deployment or measurements
- Group: Separates three outplant experiments using different sets of cultch
File: PacificCultch.csv
Description: Counts of Pacific oysters (Magallana gigas) that were planted on 22 July 2023 by a commercial operator in a 1-acre (0.4 ha) area on a bed compacted by vehicle compaction on 12 and 13 August 2022 and on 13 May 2023. Quadrats were distributed along two transects separated by at least 20 m and running from NE to SW corner of the planted area. The planted area was within 46.9971 and 46.9977 degrees N, and within 124.1322 and 124.1329 degrees W (WGS84 datum).
Variables
- photo_id: Number assigned to this photograph by the camera used
- site: This commercial planting occurred only at Damon Point
- date: Date when photograph was taken
- area_m2: Area in the photograph used for counting (quadrat area)
- oyster_count: Count of visible apparently live oysters per quadrat, only counted once these were large enough on cultch to be seen in photographs
- cluster_count: Count of visible cultch or clusters per quadrat
- algae_presence: Proportional cover of green macroalgae
- holes: Count of surface holes in the sediment per quadrat
File: WP_multiplepass_shrimpcores.csv
Description: Samples collected from Grays Harbor, Washington, in Experiment 3 (Westport Multiple, 0.6 m above mean lower low water). Treatments were applied to plots that were 0.16 ha in size. Vehicle compaction occurred in a gradient of compaction intensity on 24 Jul 2024 by driving over the area with a MarshMaster MM2LX tracked vehicle. Treatments included 0 (reference), 1, 3, and 5 passes of vehicle compaction. The samples in this dataset are burrowing shrimp densities (Neotrypaea californiensis) in 70-cm deep cores and sediment penetrability measured with the same tool as described for the Penetrometer.csv dataset.
Variables
- Site: This dataset only includes one site, Westport Multiple
- Sample: Code denoting Plot and the placement on the Plot where the sample was collected
- Plot: Code denoting plot, which is a 40x40 m area of consistent treatment
- Treatment: reference (no compaction passes) or 1x, 3x, or 5x representing the number of passes with the tracked vehicle on 24 Jul 2024
- surface.or.core: "surface" if shrimp were counted in the top 2 cm of sediment in a 0.25 m2 quadrat within an hour of vehicle compaction; "core" if shrimp were counted in a 5-core sample, which entailed quintuplet cores within 1 m2, collected with a clam gun (stainless steel, 12.8 cm diameter and 36 cm length with 50-cm handle), inserted twice to reach the target depth of 70 cm
- quadrat.size.m: area of quadrat in m2
- DateSampled_true: Actual date of sampling
- DateSampled: Date used to designate one timepoint of sampling, which could span several consecutive days
- DaysPostComp: Number of days after vehicle compaction treatment
- GPSN: WGS84 geoposition of sample in north latitude
- GPSW: WGS84 geoposition of sample, negative sign for west longitude
- Holes: Count of surface holes per quadrat, including holes at least 5 mm in diameter
- Vegetation: % Cover or notes on seagrass or macroalgae
- L.Neo: Count of large Neotrypaea californiensis, carapace length >17.42 mm, per sample
- M.Neo: Count of medium Neotrypaea californiensis, carapace length 12.5-17.42 mm, per sample
- S.Neo: Count of small Neotrypaea californiensis, carapace length 8.29-12.49 mm, per sample
- XS.Neo: Count of extra-small Neotrypaea californiensis, carapace length 4-8.28 mm, per sample
- R.Neo: Count of recruit Neotrypaea californiensis, carapace length <4 mm, per sample
- Penetrometer1: Rod height above the sediment after first drop of weight (cm)
- Penetrometer2: Rod height above the sediment after second drop of weight (cm)
- Penetrometer3: Rod height above the sediment after third drop of weight (cm)
- Notes: Observations that could affect shrimp counts or penetrometer data
File: sediment.csv
Description: Sediment collected from Grays Harbor, Washington, in Experiment 1 (Damon Point, 0.2-0.6 m above mean lower low water), Experiment 2 (Westport, 0.4-0.5 m above mean lower low water), and Experiment 3 (Westport, 0.6 m above mean lower low water, identified as Multiple). Treatments were applied at the scale of aquaculture beds, which were 2 ha in size in Experiment 1 and 2, but 0.16 ha in size in Experiment 3. Vehicle compaction with a MarshMaster MM2LX occurred on Beds 9 and 11 at Damon Point, on Beds 2 and 4 at Westport, and in a gradient of compaction intensity (1x, 3x, 5x) at Westport Multiple. At east sample timepoint at each station, one sediment sample (30 mL) was collected with a syringe corer to a depth of 5.4 cm. Sediment was fully dried and then processed for organic content and the mineral sediment thereafter dry-sieved for particle size. Sediment was dried at 45°C for at least 72 hours, homogenized and weighed, held in a furnace at 500°C for 3 hours, and reweighed, to determine dry mass and organic content. Ashed sediment was dry-sieved through a sieve series (Wentworth scale, 63 micrometers to 2000 micrometers) on a sieve shaker (Ro-Tap, W.S. Tyler, Mentor, OH, USA). Sediment smaller than 63 micrometers was classed as “mud” (silt and clay).
Variables
- Site: Experimental site
- SampleCode: Code denoting Bed and the placement on the Bed where the sample was collected
- Bed: Code denoting Bed
- Treatment: Treatment applied to 2-ha bed, either Compacted by vehicle compaction, or Reference; for Multiple experiment applied to 0.16-ha plots, reference (no compaction passes) or 1x, 3x, or 5x representing the number of passes with the tracked vehicle
- DateSampled: Actual date of sampling
- DaysPostComp: Number of days after vehicle compaction treatment
- GPSN: WGS84 geoposition of sampling in north latitude
- GPSW: WGS84 geoposition of sample, negative sign for west longitude
- crucible.wt: weight (g) of empty crucible
- cruc.sed.wt: weight (g) of crucible with dry sediment
- cruc.ashed.wt: weight (g) of crucible with sediment that had been ashed at 500 C for 3 hr
- crucible.wt.2: weight (g) of empty crucible to be used with a second portion of sediment
- cruc.sed.wt.2: weight (g) of second crucible with a second portion of dry sediment
- cruc.ashed.wt.2: weight (g) of second crucible with a second portion of dry sediment after ashing at 500 C for 3 hr
- boat: weight (g) of weigh-boat, 0 if tared
- boat.2mm: weight (g) of ashed sediment caught on 2-mm sieve including any boat weight
- boat.1mm: weight (g) of ashed sediment caught on 1-mm sieve including any boat weight
- boat.05mm: weight (g) of ashed sediment caught on 0.5-mm sieve including any boat weight
- boat.025mm: weight (g) of ashed sediment caught on 0.25-mm sieve including any boat weight
- boat.0125mm: weight (g) of ashed sediment caught on 0.125-mm sieve including any boat weight
- boat.0063mm: weight (g) of ashed sediment caught on 0.063-mm sieve including any boat weight
- boat.fines: weight (g) of ashed sediment passing through 0.063-mm sieve including any boat weight
- Notes: Observations that could influence interpretation of sediment mass
- Exclude: "Y" if concerns about processing this sample mean it should be censored from analysis
File: Shrimp.csv
Description: Burrowing shrimp (Neotrypaea californiensis) samples from Grays Harbor, Washington, in Experiment 1 (Damon Point, 0.2-0.6 m above mean lower low water) and Experiment 2 (Westport, 0.4-0.5 m above mean lower low water). Treatments were applied at the scale of aquaculture beds (2 ha). Vehicle compaction with a MarshMaster MM2LX occurred on Beds 9 and 11 at Damon Point, and on Beds 2 and 4 at Westport. Shrimp were counted in 5-core samples, which entailed quintuplet cores within 1 m2, collected with a clam gun (stainless steel, 12.8 cm diameter and 36 cm length with 50-cm handle), inserted twice to reach the target depth of 70 cm.
Variables
- Site: Experimental site
- DateSampled: Date used to designate one timepoint of sampling, which could span several consecutive days
- DateSampled_true: Actual date of sampling
- DaysPostComp: Number of days after vehicle compaction treatment
- Bed: Code denoting Bed
- Bed.description: Code denoting Bed and the placement on the Bed where the sample was collected
- Treatment: Treatment applied to 2-ha bed, either Compacted by vehicle compaction, or Reference
- GPSN: WGS84 geoposition of sample in north latitude
- GPSW: WGS84 geoposition of sample, negative sign for west longitude
- holes.per.025.sq.m: Count of surface holes per quadrat, including holes at least 5 mm in diameter
- L.Neo: Count of large Neotrypaea californiensis, carapace length >17.42 mm, per sample
- M.Neo: Count of medium Neotrypaea californiensis, carapace length 12.5-17.42 mm, per sample
- S.Neo: Count of small Neotrypaea californiensis, carapace length 8.29-12.49 mm, per sample
- XS.Neo: Count of extra-small Neotrypaea californiensis, carapace length 4-8.28 mm, per sample
- R.Neo: Count of recruit Neotrypaea californiensis, carapace length <4 mm, per sample
- TotalShrimp: Sum of large, medium, small, and extra-small shrimp counts
- Shrimp_m2: Total shrimp scaled to count per square meter
- core_number: Number of cores per sample, usually 5 (quintuplet)
- Notes: Observations that could affect shrimp counts
Code/software
All data files are uploaded as comma-separated values.
