We used acoustic telemetry and environmental monitoring to elucidate preferred microhabitats of juvenile steelhead trout (Oncorhynchus mykiss) in a Central California intermittent estuary (IE) during historic drought. We collected over half a million fish locations in the Pescadero IE (San Mateo County, CA) across 15 weeks during an extended sandbar-closed period which permitted quantification of fine scale habitat use and movement patterns. Tagged juvenile steelhead expressed strong site fidelity, especially at night when core habitat area - defined as the 50% probability of being present in an area - contracted by over one order of magnitude. The rate of movement was slow overall (~0.4 to 0.6 lengths·s−1) and remained at baseline levels at night (~40 mm∙s−1). The daytime rate of movement generally tracked solar radiation levels and appeared to be moderated by water temperatures. Spikes in the rate of movement occurred during crepuscular periods and the maximum hourly rate of movement (138 mm∙s−1) was observed during the early study period from 10:00 to 11:00 when water temperatures were physiologically optimal (17–18 °C). Water quality worsened upstream when water temperatures exceeded 18 °C and dissolved oxygen concentrations declined below 7.0 mg·L−1. Fish tag detections at stationary receivers in the upper estuary declined linearly with deteriorating water quality conditions. Qualitative analysis of juvenile steelhead habitat utilization indicated a strong preference for two microhabitat features in the estuary during the study; both were shallow (~1.5 m), wind-protected, and possessed cover and sandy substrates that occurred within the fresh or near fresh epilimnion where lagoon water quality was best and benthic prey was likely most abundant. Upstream movement occurred in late fall for over half of the tagged cohort, which likely enhances population resiliency by allowing these fish to escape lethal water quality conditions coincident with the transition from closed to open estuary in late fall. Climate projections for California’s Central Coast predict an increase in extreme dry events and the information presented here can help natural resource managers prepare for the future, such as the critical need to promote development of a sufficiently oxygenated epilimnion during extended sandbar-closed ecosystem states.

Methods by data set

 

Telemetry data – Data sets 1-4

Here we use acoustic telemetry to elucidate preferred microhabitats of juvenile steelhead trout (Oncorhynchus mykiss) in a Central California intermittent estuary (IE) during historic drought. We collected over half a million fish locations in the Pescadero IE (San Mateo County, CA) across 15 weeks during an extended sandbar-closed period which permitted quantification of fine scale habitat use and movement patterns, including via a VEMCO Positioning System array (VPS positions, data set 1), mobile tracking surveys (active acoustic telemetry, data set 2), and two stationary receivers deployed at the upper extent of the estuary (passive acoustic telemetry, data set 3). Data set 4 includes the geographic locations of all the moored VPS equipment (receivers and synchronization transmitters) used in this study.

1_ALL VPS POSITIONS_DATA.csv

The VEMCO Positioning System (VPS) was comprised of 12 strategically-placed omnidirectional acoustic receivers (VEMCO VR2W-180 kHz) with overlapping ranges capable of triangulating fine-scale fish positions according to preliminary range testing. Eight receiver time synchronization transmitters (VEMCO V6-180 kHz; nominal code transmission delay: 500-700 s range) were strategically deployed at stations with or without VPS receivers. Synchronization transmitters are needed by the VPS to improve positioning accuracy by correcting for clock drift between stationary receivers. Due to unexpected station movements, the VPS software was used to determine the calculate receivers and synchronization transmitter locations based on the observed arrival time differences between signals at the receivers. Determinations of the geographic latitude and longitude coordinates of fish positions from VPS receiver detections were post-processed and provided by VEMCO (Bedford, Nova Scotia).

2_ALL MOBILE POSITIONS_Fig 4a_DATA.csv

To supplement the information from the VPS array, fish positions throughout the lower, middle, and upper estuary were determined by mobile tracking surveys conducted during the afternoon hours on October 1, November 7 and 21, and December 14 in 2013 throughout all navigable waters using a kayak-mounted acoustic receiver (VEMCO VR100) and omnidirectional hydrophone (VEMCO VH165). During the September 25 (both pre-noon and post-noon hours) and November 21 (afternoon hours only) fish surveys, lagoon water temperatures, salinity, pH, and DO were measured every 4 s using a compact water quality sonde (YSI 600XLM, YSI Inc.) that was slowly bobbed up and down throughout the water column in front of a foot pedal-powered kayak. Geographic coordinates were recorded during water quality cruises using a handheld GPS device (Garmin GPSMAP 78, Garmin Ltd., Olathe, KS).

3_ALL ST13 AND ST14 DETECTIONS_DATA.csv

Two stationary receivers were positioned upstream of the VPS in the Pescadero (station 13) and Butano (station 14) creek arms of the estuary (Fig. 1). Detections from these receivers allowed us to determine presence of acoustically tagged fish outside of our main array in the upper estuary, but did not allow us to triangulate positions. Rather, we used data from these two stationary receivers to infer upstream movement.

4_STATION LOCATIONS_Fig 1_DATA.csv

Locations (latitude and longitude) of the receivers and synchronization transmitters used in this study.

 

Environmental data – data sets 5-11

Water depth, temperature, salinity, pH, DO, and light were measured throughout the study area, including at fixed water depths at multiple locations and at multiple water depths at fixed locations in order to investigate potential water quality effects on fish microhabitat utilization.

All geographic data are presented using the WGS84 datum for coordinates and all times are UTC-8 hours. Fixed environmental sensor data were automatically logged at 15 min intervals except those obtained from the station 08 sonde cluster (30 min pulse rate). Some data gaps exist because of instrument unavailability, technical difficulties, or sensor biofouling.

5_SONDE_MULT DEPTHS_FIXED LOC_Fig 3_DATA.csv

Water quality sondes (Hydrolab MS5, OTT Hydromet-Hach^® Co., Loveland, CO) were also deployed throughout the water column at 0.60, 1.60, 2.10, and 2.35 m depths in the middle of the VPS zone at station 08.

6_CTD_FIG S1-1_DATA.csv

The conductivity-temperature-depth (CTD) sensor clusters (XR-420 CTD, RBR Ltd., Ottawa, Ontario) were secured to weighted moorings and positioned approximately 0.25 m above the bottom of the estuary throughout the VPS array (stations 01, 02, 06, 09, 11, and 12). A CTD was also deployed 0.25 m below the water surface in the middle estuary at station 06.

7_SONDE_MOBILE_Fig S1-2_DATA.csv

During the September 25, 2013 (both pre-noon and post-noon hours) and November 21, 2013 (afternoon hours only) fish surveys, lagoon water temperatures, salinity, pH, and DO were measured every 4 s using a compact water quality sonde (YSI 600XLM, YSI Inc.) that was slowly bobbed up and down throughout the water column in front of a foot pedal-powered kayak. Geographic coordinates were recorded during water quality cruises using a handheld GPS device (Garmin GPSMAP 78, Garmin Ltd., Olathe, KS).

8_WSE_FIG S1-3a _DATA.csv

Periodic measurements of a land-surveyed stage gauge attached to the CA Hwy-1 bridge in the lower estuary were used as reference points to convert CTD depth data to water surface elevations (WSEs). Lagoon WSE data were converted to meters using the NAVD88 vertical datum (GEOID 2009 model).

9_LUX_FIG S1-3b_Table S1-1_DATA.csv

Solar radiation [and temperature, see below] sensors (HOBO^® Pendant Temperature/Light Data Loggers, Onset Computer Corp., Bourne, MA) were deployed aerially in the upper estuary (37.260807°N, 122.407951°W) and within the VPS and non-VPS zones of the stationary array at water depths of 0.75 m (stations 02, 03, 06, 08, 12, 13), 1.25 m (stations 02, 06, 08, 12, 13, 14), 1.50 m (st01), and 1.75 m (stations 08, 12).

10_SONDE_FIXED DEPTH_MULT LOC_FIG S1-4_DATA.csv

Temperature, salinity, pH, and DO concentrations were measured by multiparameter water quality sondes (YSI 6600, YSI Inc., Yellow Springs, OH) moored to stations in the lower (st02) and upper (stations 13, 14) estuary at 1.25 m depth.

11_TEMP_FIG S1-5_DATA.csv

Temperature [and solar radiation, see above] sensors (HOBO^® Pendant Temperature/Light Data Loggers, Onset Computer Corp., Bourne, MA) were deployed aerially in the upper estuary (37.260807°N, 122.407951°W) and within the VPS and non-VPS zones of the stationary array at water depths of 0.75 m (stations 02, 03, 06, 08, 12, 13), 1.25 m (stations 02, 06, 08, 12, 13, 14), 1.50 m (st01), and 1.75 m (stations 08, 12).

Additional temperature sensors (HOBO^® Pendant Temperature Data Loggers, Onset Computer Corp., Bourne, MA) were deployed within the VPS and non-VPS zones of the stationary array at water depths of 0.25 m (stations 01, 02, 03, 05, 07, 08, 09, 10, 13, 14), 0.75 m (stations 04, 05, 10, 11), 1.25 m (stations 04, 05, 09, 10, 11), and 1.75 m (stations 08, 12) (Fig. 1).

 

 

Rate of Movement data (data set 12)

12_ROM_FIGS 6_8e-h_DATA.csv

Methods: The Tracking Analyst extension in ArcGIS 10.5® was used to determine distances from successively ordered fish positions for individual fish to calculate distance traveled per unit time or the “rate of movement” (ROM). All ROM analyses were restricted to instances when the time interval between successive position measurements was less than or equal to the maximum fish tag delay (90 s) to minimize error due to deviations from straight path movements.

 

We include usage notes within "readme" files for each data set.